Expand v0.6.1 documentation suite

- Add COMPARISON.md for architecture and positioning analysis
- Add PERFORMANCE-TUNING.md for mutation engine optimization guidance
- Add TESTING.md documenting the 89-test security-focused test suite
- Document server, WASM, and shared crate test coverage
- Add operational guidance for tuning, validation, and verification
- Improve project maintainability and contributor onboarding

.gitignore

@@ -5,3 +5,5 @@ dist/
 *.log
 .env
 .idea/
+
+.antigravitycli/

Cargo.lock

@@ -245,7 +245,7 @@ dependencies = [
 
 [[package]]
 name = "chronoseal-server"
-version = "0.5.0"
+version = "0.6.0"
 dependencies = [
  "axum",
  "base64",
@@ -269,11 +269,12 @@ dependencies = [
  "tracing",
  "tracing-appender",
  "tracing-subscriber",
+ "valkey",
 ]
 
 [[package]]
 name = "chronoseal-wasm"
-version = "0.5.0"
+version = "0.6.0"
 dependencies = [
  "base64",
  "blake3",
@@ -285,6 +286,7 @@ dependencies = [
  "serde-wasm-bindgen",
  "serde_json",
  "shared",
+ "tracing",
  "wasm-bindgen",
 ]
 
@@ -1294,7 +1296,7 @@ dependencies = [
 
 [[package]]
 name = "shared"
-version = "0.5.0"
+version = "0.6.0"
 dependencies = [
  "base64",
  "blake3",
@@ -1303,6 +1305,7 @@ dependencies = [
  "rand 0.8.6",
  "serde",
  "serde_json",
+ "tracing",
 ]
 
 [[package]]
@@ -1749,6 +1752,15 @@ dependencies = [
  "wasm-bindgen",
 ]
 
+[[package]]
+name = "valkey"
+version = "0.0.0-alpha5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "591043068c3f8db7fc1dcf34852eb03994175d39045cf01ad036c099f3c4f888"
+dependencies = [
+ "tracing",
+]
+
 [[package]]
 name = "valuable"
 version = "0.1.1"

LICENSE-MIT

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2026 Sunil Purushottam Thakare
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

README.md

@@ -1,239 +1,748 @@
 # ChronoSeal
+
 <p align="center">
   <img src="logo/chronoseal.svg" width="220" alt="ChronoSeal Logo">
 </p>
 
-**Cryptographic anti-automation and browser attestation framework built with Rust, WASM, and behavioral continuity verification.**
+<p align="center">
+  <strong>Unix-native cryptographic attestation daemon for browser session continuity.</strong>
+</p>
 
-ChronoSeal makes it computationally expensive and operationally complex for AI scrapers, headless browsers, and automation tools to impersonate real users — while remaining completely invisible and frictionless to legitimate human visitors.
+<p align="center">
+  Privacy-first | Deterministic WASM parity | Silent rejection | Low overhead
+</p>
+
+<p align="center">
+  <a href="https://github.com/thakares/chronoseal-rs/blob/main/LICENSE">
+    <img src="https://img.shields.io/badge/license-MIT%20OR%20Apache--2.0-blue.svg" alt="License: MIT OR Apache-2.0">
+  </a>
+  <a href="https://github.com/thakares/chronoseal-rs">
+    <img src="https://img.shields.io/badge/rust-stable%20%E2%89%A5%201.87-orange.svg" alt="Rust stable >= 1.87">
+  </a>
+  <a href="https://github.com/thakares/chronoseal-rs/blob/main/docs/REFRACTORING-v0.6.0.md">
+    <img src="https://img.shields.io/badge/version-v0.6.0-green.svg" alt="v0.6.0">
+  </a>
+  <img src="https://img.shields.io/badge/wasm-rust--compiled-blueviolet.svg" alt="WASM">
+</p>
 
 ---
 
+ChronoSeal is a Linux-native cryptographic attestation service for browser session continuity and anti-automation defense. It runs as a small daemon, serves a browser WASM runtime, and validates signed heartbeat requests through deterministic server/client state progression.
+
+The core idea is simple: a real browser session should be able to keep advancing a private cryptographic state, a hash chain, and a deterministic synthetic gene mutation chain. Basic HTTP clients, stale replay attempts, and incomplete automation should fail without receiving a useful failure reason.
+
+ChronoSeal is a cost-raising attestation layer. It is not a CAPTCHA replacement, identity provider, fingerprinting product, or perfect bot blocker.
+
+## Contents
+
+- [Features](#features)
+- [How It Works](#how-it-works)
+- [Repository Layout](#repository-layout)
+- [Quick Start](#quick-start)
+- [Build From Source](#build-from-source)
+- [Run Locally](#run-locally)
+- [Install as a Service](#install-as-a-service)
+- [Docker](#docker)
+- [CLI Reference](#cli-reference)
+- [Configuration](#configuration)
+- [HTTP API](#http-api)
+- [Browser Integration](#browser-integration)
+- [Storage Backends](#storage-backends)
+- [Operations](#operations)
+- [Security Model](#security-model)
+- [Development](#development)
+- [Troubleshooting](#troubleshooting)
+- [Further Reading](#further-reading)
+- [License](#license)
+
+## Features
+
+- Native Unix daemon with `systemd` service support.
+- Axum-based HTTP service exposing `/init`, `/hb`, `/health`, `/metrics`, and `/stats`.
+- Rust/WASM browser runtime for key generation, signing, VM execution, and mutation preview.
+- Deterministic Synthetic Gene Mutation Engine shared by the server and WASM crates.
+- Ed25519 signatures over canonical heartbeat payloads.
+- Blake3 hash chain continuity across accepted heartbeats.
+- Silent rejection semantics: invalid heartbeats still return `{"status":"ok"}`.
+- Configurable behavioral trust checks for mouse movement, pauses, timing, and browser signals.
+- Runtime storage abstraction with `sqlite-in-memory`, `sqlite-in-disk`, and `valkey` modes.
+- CLI-first lifecycle, status, health, metrics, stats, config validation, key generation, and shell completions.
+- Privacy-oriented design based on ephemeral session state rather than long-term identity tracking.
+
 ## How It Works
 
-ChronoSeal establishes a continuous, cryptographically verifiable proof-of-presence for every browser session. It is inspired by the heartbeat model used in IoT firmware (ESP32-class devices): the client must keep emitting signed, chained attestations, or the session is silently invalidated.
+ChronoSeal creates a short-lived browser attestation session and advances it through signed heartbeats.
 
-```
-Browser                                    Server
-  │                                           │
-  │  WASM loads, generates Ed25519 keypair    │
-  │  Private key never leaves WASM memory     │
-  │                                           │
-  ├──── POST /init  { public_key } ──────────►│  Store session, salt, initial hash
-  │◄─── { session_id, salt, opcodes, H0 } ────┤
-  │                                           │
-  │  Every 12–25s (jittered):                 │
-  │  ┌─ Collect mouse entropy                 │
-  │  ├─ Execute VM opcodes → stack state      │
-  │  ├─ Compute H(n) = Blake3(H(n-1) ║ …)     │
-  │  └─ Sign payload with Ed25519             │
-  │                                           │
-  ├──── POST /hb  { session_id, sig, … } ────►│  Verify sig → chain → behavior → fingerprint
-  │◄─── { status, next_salt } ────────────────┤  Rotate salt, advance chain
-  │                                           │
-  │ On failure: server returns {"status":"ok"}│  Silent rejection — indistinguishable
+1. The browser loads the generated WASM package from `frontend/pkg`.
+2. The WASM runtime generates an Ed25519 keypair and returns the public key to JavaScript.
+3. The browser calls `POST /init` with the public key.
+4. The server creates a session and returns:
+   - `session_id`
+   - initial salt
+   - initial hash chain head
+   - VM opcode program
+   - gene size
+   - mutation step
+   - mutation order
+   - heartbeat timing bounds
+5. For each heartbeat, the browser:
+   - executes the VM opcode program
+   - collects entropy and browser signal data
+   - previews the next synthetic gene commitment in WASM
+   - signs the canonical heartbeat payload
+   - posts the request to `POST /hb`
+6. The server validates:
+   - session existence and expiration
+   - rate limit
+   - timestamp drift
+   - Ed25519 signature
+   - hash chain continuity
+   - behavioral trust checks
+   - mutation step
+   - gene commitment parity
+7. If the heartbeat is accepted, the server advances session state and returns the next salt and mutation order.
+8. If the heartbeat is rejected, the server returns only `{"status":"ok"}`.
+
+The silent failure model deliberately avoids exposing which validation failed.
+
+## Repository Layout
+
+```text
+.
+├── Cargo.toml                 # Rust workspace
+├── server/                    # chronoseal daemon and CLI
+├── shared/                    # shared protocol, gene model, mutation engine
+├── wasm/                      # WASM runtime crate
+├── frontend/                  # static browser integration files
+├── docs/                      # architecture, API, deployment, threat model
+├── scripts/                   # build, install, release, dev helpers
+├── chronoseal.service         # systemd unit
+├── Dockerfile                 # container image
+└── docker-compose.yml         # local container orchestration
 ```
 
----
+Workspace members:
 
-## Security Model
+- `chronoseal-server`: daemon binary crate. Binary name: `chronoseal`.
+- `shared`: common cryptographic and mutation logic used by server and WASM.
+- `chronoseal-wasm`: browser runtime compiled with `wasm-pack`.
 
-### What ChronoSeal protects against
+## Quick Start
 
-| Threat | Mechanism |
-|---|---|
-| Playwright / Puppeteer Stealth | Mouse entropy validation rejects synthetic or absent movement |
-| Replay attacks | Hash chain — each heartbeat references the previous hash; old payloads are invalid |
-| Signature forgery | Ed25519 private key generated inside WASM, never serialised or exposed to JS |
-| Clock manipulation | Server enforces ±30s timestamp window |
-| Credential sharing | Session is bound to a keypair generated fresh on every page load |
-| Flooding with fake sessions | Per-session rate limiting (5 req / 10s); stale entries evicted every 60s |
-| Passive analysis of traffic | Server always returns `{"status":"ok"}` — rejections are silent |
+For a full native install:
 
-### What ChronoSeal does not claim
-
-ChronoSeal is a cost-raising mechanism, not an impenetrable barrier. A sufficiently motivated adversary with a real browser, real input devices, and the patience to reverse the WASM can bypass it. The goal is to make scraping expensive and operationally complex enough to be impractical at scale.
-
----
-
-## Architecture
-
-```
-chronoseal-rs/
-├── shared/          Shared types, Blake3 hash-chain logic, constants
-├── server/          Axum HTTP server
-│   ├── routes/      /init and /hb handlers
-│   ├── session.rs   Session lifecycle: create, verify, advance chain
-│   ├── crypto.rs    Ed25519 signature verification (BTreeMap canonical JSON)
-│   ├── trust.rs     Behavioral signal validation (mouse speed, pauses)
-│   ├── fingerprint  Browser fingerprint sanity checks
-│   ├── vm.rs        Random opcode program generator
-│   ├── ratelimit.rs Token-bucket rate limiter with periodic eviction
-│   └── cleanup.rs   Background task: expire sessions + evict rate limiter
-├── wasm/            Rust → WASM client module
-│   ├── crypto.rs    Ed25519 keypair, signing, hash computation
-│   └── vm.rs        Stack machine executor (PUSH/ADD/SUB/MUL/XOR/AND/OR/ROT/NOT/HASH)
-└── frontend/        Vanilla JS glue
-    ├── heartbeat.js Session init, heartbeat scheduling, chain advancement
-    └── entropy.js   Mouse event collection
+```bash
+sudo bash scripts/install.sh
 ```
 
-### Stack Machine
+Check the daemon:
 
-The server generates a random program (8–16 opcodes) on session init. The client executes it on every heartbeat and includes the resulting stack state in the signed payload. This makes each heartbeat structurally unique without requiring any server round-trip.
-
-| Opcode | Mnemonic | Effect |
-|--------|----------|--------|
-| `0x00` | PUSH u32 | Push 4-byte little-endian literal |
-| `0x01` | ADD | Pop 2, push `a + b` (wrapping) |
-| `0x02` | SUB | Pop 2, push `a - b` (wrapping) |
-| `0x03` | MUL | Pop 2, push `a * b` (wrapping) |
-| `0x04` | XOR | Pop 2, push `a ^ b` |
-| `0x05` | AND | Pop 2, push `a & b` |
-| `0x06` | OR  | Pop 2, push `a \| b` |
-| `0x07` | ROT | Pop 2, push `a.rotate_left(b % 32)` |
-| `0x08` | NOT | Pop 1, push `!a` (unary) |
-| `0x09` | HASH | Blake3 of entire stack → single u32 |
-
-### Hash Chain
-
-```
-H(0) = Blake3( session_id ║ pub_key ║ salt₀ )
-
-H(n) = Blake3( saltₙ₋₁ ║ H(n-1) ║ timestamp ║ Blake3(entropy_json) ║ Blake3(stack_json) )
+```bash
+chronoseal status --format json
+chronoseal health
+chronoseal metrics
+sudo journalctl -u chronoseal -f
 ```
 
-Each heartbeat must present `H(n-1)` matching what the server stored. Forging a valid `H(n)` requires knowing the private key (for the signature), the salt (server-side only), and all prior state.
+For local development without installing:
 
-### Signature Canonical Form
-
-The client signs a JSON object with keys sorted alphabetically (matching `JSON.stringify(obj, Object.keys(obj).sort())`):
-
-```json
-{
-  "entropyData":  { "events": [ { "x": …, "y": …, "t": … } ] },
-  "fingerprint":  { "aspectRatio": "…", "devicePixelRatio": "…", "hardwareConcurrency": … },
-  "prevHash":     "hex…",
-  "sessionId":    "hex…",
-  "stackState":   { "stack": […], "ip": … },
-  "timestamp":    1234567890123
-}
+```bash
+bash scripts/build.sh
+cargo run -p chronoseal-server --bin chronoseal -- run \
+  --bind 127.0.0.1:3000 \
+  --frontend-dir frontend
 ```
 
-The server reconstructs this using `BTreeMap` (alphabetical key order) before calling `VerifyingKey::verify_strict`.
+Then open:
 
----
-
-## SQLite Schema
-
-```sql
-CREATE TABLE IF NOT EXISTS sessions (
-    session_id    TEXT     PRIMARY KEY,
-    public_key    BLOB     NOT NULL,
-    salt          BLOB     NOT NULL,
-    last_hash     BLOB     NOT NULL,
-    chain_length  INTEGER  NOT NULL DEFAULT 1,
-    created_at    INTEGER  NOT NULL,
-    last_seen     INTEGER  NOT NULL,
-    expires_at    INTEGER  NOT NULL
-);
+```text
+http://127.0.0.1:3000
 ```
 
-Sessions are stored in an in-memory SQLite database. All session state is lost on server restart by design — clients re-initialise transparently.
+## Build From Source
 
----
+### Requirements
 
-## Build
+| Tool | Minimum | Purpose |
+|---|---:|---|
+| Rust | 1.87 stable | Build server, shared crate, and tests |
+| wasm-pack | 0.13 | Build browser WASM package |
+| wasm32 target | current stable | WASM compilation target |
+| systemd | 248+ | Optional native service management |
+| Docker | 24.x | Optional container workflow |
+| Docker Compose | 2.x | Optional local orchestration |
 
-### Prerequisites
+Install the WASM target and `wasm-pack`:
 
-- Rust stable (≥ 1.87)
-- [`wasm-pack`](https://rustwasm.github.io/wasm-pack/installer/)
+```bash
+rustup target add wasm32-unknown-unknown
+cargo install wasm-pack
+```
 
-### WASM
+Build everything needed for the browser and server:
+
+```bash
+bash scripts/build.sh
+```
+
+That script:
+
+1. Builds `wasm/` with `wasm-pack build --target web --release`.
+2. Replaces `frontend/pkg` with the generated WASM package.
+3. Builds the `chronoseal` release binary.
+
+Manual build:
 
 ```bash
 wasm-pack build wasm --target web --release
+rm -rf frontend/pkg
 mv wasm/pkg frontend/pkg
+
+cargo build -p chronoseal-server --bin chronoseal --release
 ```
 
-### Server
+The binary is written to:
+
+```text
+target/release/chronoseal
+```
+
+## Run Locally
+
+Run the daemon directly from Cargo:
 
 ```bash
-cargo build -p server --release
+cargo run -p chronoseal-server --bin chronoseal -- run \
+  --bind 127.0.0.1:3000 \
+  --frontend-dir frontend
 ```
 
-### Dev (all-in-one)
+Probe it:
 
 ```bash
-bash scripts/dev.sh
+curl http://127.0.0.1:3000/health
+curl http://127.0.0.1:3000/stats
+curl http://127.0.0.1:3000/metrics
 ```
 
-The server serves the `frontend/` directory statically at `/` and the API at `/init` and `/hb`.
-
----
-
-## Deployment
-
-### Native + systemd
+Use the CLI wrappers:
 
 ```bash
-cargo build -p server --release
-sudo cp target/release/server /usr/local/bin/chronoseal
-sudo cp chronoseal.service /etc/systemd/system/
-sudo systemctl daemon-reload
-sudo systemctl enable --now chronoseal
+cargo run -p chronoseal-server --bin chronoseal -- status --bind 127.0.0.1:3000
+cargo run -p chronoseal-server --bin chronoseal -- health --bind 127.0.0.1:3000
+cargo run -p chronoseal-server --bin chronoseal -- stats --bind 127.0.0.1:3000 --format json
 ```
 
-### Docker
+## Install as a Service
+
+The installer builds the project, installs the binary, copies frontend assets, installs the `systemd` unit, and starts the service.
+
+```bash
+sudo bash scripts/install.sh
+```
+
+Installed paths:
+
+| Path | Purpose |
+|---|---|
+| `/usr/local/bin/chronoseal` | daemon and CLI binary |
+| `/opt/chronoseal/frontend` | static frontend assets copied by installer |
+| `/etc/systemd/system/chronoseal.service` | service unit |
+| `/run/chronoseal.pid` | default PID file |
+
+Service commands:
+
+```bash
+sudo systemctl status chronoseal
+sudo systemctl restart chronoseal
+sudo systemctl disable --now chronoseal
+sudo journalctl -u chronoseal -f
+```
+
+## Docker
+
+Build and run with Compose:
 
 ```bash
 docker compose up -d --build
 ```
 
-### Reverse Proxy
+The provided container exposes port `3000`.
 
-Place ChronoSeal behind nginx, Nginx Proxy Manager, or HAProxy. Enable:
-
-- TLS 1.3
-- HTTP/2
-- Aggressive upstream timeouts (the heartbeat interval is 12–25s)
-
----
-
-## Integration
-
-Drop two lines into any protected page:
-
-```html
-<script type="module" src="/pkg/antibot_wasm.js"></script>
-<script type="module" src="/main.js"></script>
+```bash
+curl http://127.0.0.1:3000/health
 ```
 
-`main.js` calls `initHeartbeat()` which handles WASM loading, session init, and schedules all subsequent heartbeats automatically. There is no visible UI, no CAPTCHA, no user interaction required.
+Important: the Dockerfile copies `frontend/` from the working tree. Build the WASM package into `frontend/pkg` before building the container if you need the browser runtime inside the image:
 
----
+```bash
+bash scripts/build.sh
+docker compose up -d --build
+```
+
+## CLI Reference
+
+Run:
+
+```bash
+chronoseal --help
+```
+
+Global options:
+
+| Option | Environment | Description |
+|---|---|---|
+| `--config <path>` | `CHRONOSEAL_CONFIG` | Explicit TOML config path |
+| `--format <text|json|yaml>` | - | Output format for machine-readable commands |
+| `--output <text|json|yaml>` | - | Alias for `--format` |
+| `--log <filter>` | `CHRONOSEAL_LOG` | Tracing filter, for example `info` or `chronoseal=debug` |
+
+Commands:
+
+| Command | Description |
+|---|---|
+| `chronoseal run` | Run the daemon |
+| `chronoseal status` | Check configured daemon reachability and PID state |
+| `chronoseal health` | Perform an HTTP health probe |
+| `chronoseal config check` | Validate and print effective configuration |
+| `chronoseal generate keypair` | Generate an Ed25519 keypair |
+| `chronoseal version` | Print version/build information |
+| `chronoseal db-type` | List database backend support status |
+| `chronoseal metrics` | Fetch Prometheus metrics from the running daemon |
+| `chronoseal stats` | Fetch service statistics from the running daemon |
+| `chronoseal completion <shell>` | Generate shell completions |
+
+Examples:
+
+```bash
+chronoseal run --bind 127.0.0.1:3000 --frontend-dir frontend
+chronoseal run --db-type sqlite-in-memory
+chronoseal status --format json
+chronoseal health --config /etc/chronoseal/config.toml
+chronoseal config check --output yaml
+chronoseal generate keypair --format json
+chronoseal completion bash > chronoseal.bash
+```
 
 ## Configuration
 
-All tunable constants are in `shared/src/constants.rs`:
+Configuration precedence:
 
-| Constant | Default | Description |
+1. CLI flags
+2. `CHRONOSEAL_*` environment variables
+3. TOML config file
+4. built-in defaults
+
+Default config discovery:
+
+1. path from `CHRONOSEAL_CONFIG`, if it exists
+2. `/etc/chronoseal/config.toml`
+3. `$XDG_CONFIG_HOME/chronoseal/config.toml`
+4. `~/.config/chronoseal/config.toml`
+
+Example:
+
+```toml
+bind = "0.0.0.0:3000"
+db_type = "sqlite-in-memory"
+pid_file = "/run/chronoseal.pid"
+db_path = "/var/lib/chronoseal/chronoseal.sqlite"
+frontend_dir = "/usr/share/chronoseal/frontend"
+log_file = "/var/log/chronoseal/chronoseal.jsonl"
+
+heartbeat_min_interval_ms = 12000
+heartbeat_max_interval_ms = 25000
+expiration_minutes = 30
+rate_limit_count = 5
+rate_limit_window_secs = 10
+max_timestamp_drift_ms = 30000
+
+min_mouse_total_dist = 10.0
+max_mouse_avg_speed = 2.0
+min_pause_count = 1
+require_mouse_activity = true
+
+gene_size = 512
+mutation_rounds = 4
+```
+
+Common environment variables:
+
+| Variable | Description |
+|---|---|
+| `CHRONOSEAL_CONFIG` | Config file path |
+| `CHRONOSEAL_BIND` | Bind address, for example `127.0.0.1:3000` |
+| `CHRONOSEAL_DB_TYPE` | `sqlite-in-memory`, `sqlite-in-disk`, or `valkey` |
+| `CHRONOSEAL_DB_PATH` | SQLite database path |
+| `CHRONOSEAL_FRONTEND_DIR` | Static frontend directory served at `/` |
+| `CHRONOSEAL_PID_FILE` | PID file path |
+| `CHRONOSEAL_LOG` | Tracing filter |
+| `CHRONOSEAL_LOG_FILE` | Optional JSON log file |
+| `CHRONOSEAL_STATE_DIR` | Base state directory used for default `db_path` |
+| `CHRONOSEAL_HEARTBEAT_MIN_INTERVAL_MS` | Minimum accepted heartbeat interval |
+| `CHRONOSEAL_HEARTBEAT_MAX_INTERVAL_MS` | Maximum accepted heartbeat interval |
+| `CHRONOSEAL_EXPIRATION_MINUTES` | Session lifetime |
+| `CHRONOSEAL_RATE_LIMIT_COUNT` | Requests allowed in the rate-limit window |
+| `CHRONOSEAL_RATE_LIMIT_WINDOW_SECS` | Rate-limit window length |
+| `CHRONOSEAL_MAX_TIMESTAMP_DRIFT_MS` | Accepted client timestamp drift |
+| `CHRONOSEAL_MIN_MOUSE_TOTAL_DIST` | Minimum mouse movement distance |
+| `CHRONOSEAL_MAX_MOUSE_AVG_SPEED` | Maximum average mouse speed |
+| `CHRONOSEAL_MIN_PAUSE_COUNT` | Minimum detected pause count |
+| `CHRONOSEAL_REQUIRE_MOUSE_ACTIVITY` | Enable or disable mouse activity requirement |
+| `CHRONOSEAL_GENE_SIZE` | Synthetic gene buffer size |
+| `CHRONOSEAL_MUTATION_ROUNDS` | Mutation rounds per program |
+
+Validate configuration:
+
+```bash
+chronoseal config check --format yaml
+```
+
+## HTTP API
+
+ChronoSeal exposes a small HTTP surface:
+
+| Method | Path | Purpose |
 |---|---|---|
-| `SESSION_ID_LEN` | 32 bytes | Session ID entropy |
-| `SALT_LEN` | 16 bytes | Per-heartbeat salt size |
-| `HEARTBEAT_MIN_INTERVAL_MS` | 12 000 ms | Minimum heartbeat interval |
-| `HEARTBEAT_MAX_INTERVAL_MS` | 25 000 ms | Maximum heartbeat interval (uniform jitter) |
-| `EXPIRATION_MINUTES` | 30 min | Session lifetime after last heartbeat |
-| `RATE_LIMIT_COUNT` | 5 | Max heartbeats per window |
-| `RATE_LIMIT_WINDOW_SECS` | 10 s | Rate limit window |
-| `MAX_TIMESTAMP_DRIFT_MS` | 30 000 ms | Anti-replay timestamp window |
-| `MIN_MOUSE_TOTAL_DIST` | 10.0 px | Minimum cumulative mouse travel |
-| `MAX_MOUSE_AVG_SPEED` | 2.0 px/ms | Maximum average mouse speed |
-| `MIN_PAUSE_COUNT` | 1 | Minimum mouse pause events |
+| `POST` | `/init` | Start a browser attestation session |
+| `POST` | `/hb` | Submit a signed heartbeat |
+| `GET` | `/health` | Health probe |
+| `GET` | `/metrics` | Prometheus metrics |
+| `GET` | `/stats` | Runtime statistics |
+| `GET` | `/` | Static frontend files from `frontend_dir` |
 
----
+### `POST /init`
+
+Request:
+
+```json
+{
+  "public_key": "hex-encoded 32-byte Ed25519 verifying key"
+}
+```
+
+Response:
+
+```json
+{
+  "session_id": "64-char hex string",
+  "salt": "32-char hex string",
+  "opcodes_b64": "base64-encoded VM program",
+  "initial_hash": "64-char hex string",
+  "expires_at": 1234567890123,
+  "heartbeat_min_interval_ms": 12000,
+  "heartbeat_max_interval_ms": 25000,
+  "gene_size": 512,
+  "mutation_step": 1,
+  "mutation_order_b64": "base64-encoded mutation program"
+}
+```
+
+### `POST /hb`
+
+Request:
+
+```json
+{
+  "session_id": "64-char hex",
+  "prev_hash": "64-char hex",
+  "timestamp": 1234567890123,
+  "entropy_data": {
+    "events": [
+      { "x": 412.0, "y": 308.5, "t": 1234.567 }
+    ]
+  },
+  "stack_state": {
+    "stack": [2971406957, 1234567890],
+    "ip": 42
+  },
+  "fingerprint": {
+    "aspectRatio": "1.7777777778",
+    "devicePixelRatio": 2,
+    "hardwareConcurrency": 8
+  },
+  "mutation_step": 1,
+  "gene_commitment": "64-char hex",
+  "signature": "128-char hex"
+}
+```
+
+Accepted response:
+
+```json
+{
+  "status": "ok",
+  "next_salt": "32-char hex string",
+  "next_mutation_step": 2,
+  "next_mutation_order_b64": "base64-encoded mutation program"
+}
+```
+
+Rejected response:
+
+```json
+{
+  "status": "ok"
+}
+```
+
+Detailed API semantics are documented in [docs/API.md](docs/API.md).
+
+## Browser Integration
+
+The frontend imports the generated WASM module from `frontend/pkg`.
+
+```js
+import init, {
+  generate_keypair,
+  get_public_key,
+  sign_message,
+  compute_next_hash,
+  run_program,
+  init_gene_state,
+  preview_gene_commitment,
+  commit_gene_preview,
+  discard_gene_preview,
+  current_gene_commitment
+} from './pkg/chronoseal_wasm.js';
+```
+
+Call `await init()` before invoking exported functions.
+
+WASM exports:
+
+| Function | Purpose |
+|---|---|
+| `generate_keypair()` | Generate a browser-local Ed25519 keypair and return public key hex |
+| `get_public_key()` | Return current public key hex |
+| `sign_message(msg)` | Sign a canonical UTF-8 payload and return signature hex |
+| `compute_next_hash(prev, ts, entropy, stack, salt)` | Compute next Blake3 hash-chain value |
+| `run_program(b64)` | Execute a base64 VM program and return stack state |
+| `init_gene_state(gene_size)` | Initialize the synthetic gene buffer |
+| `preview_gene_commitment(order_b64, session_id, mutation_step, rounds)` | Preview next gene commitment |
+| `commit_gene_preview()` | Commit the previewed gene mutation after accepted heartbeat |
+| `discard_gene_preview()` | Discard previewed mutation after rejection or error |
+| `current_gene_commitment(session_id, mutation_step)` | Return current committed gene commitment |
+
+String-returning WASM functions return an empty string on error. Boolean-returning functions indicate success or failure directly.
+
+## Storage Backends
+
+Set storage mode with `db_type` or `CHRONOSEAL_DB_TYPE`.
+
+| Backend | Description |
+|---|---|
+| `sqlite-in-memory` | Default ephemeral session storage. State is lost on restart. |
+| `sqlite-in-disk` | SQLite database persisted at `db_path`. |
+| `valkey` | Valkey-compatible backend mode. |
+
+For Valkey mode, the server reads `CHRONOSEAL_VALKEY_ADDR` and defaults to `127.0.0.1:6666` when it is not set. If the Valkey connection fails, the current implementation falls back to in-memory SQLite and logs a warning.
+
+## Operations
+
+### Health
+
+```bash
+chronoseal health
+curl http://127.0.0.1:3000/health
+```
+
+### Status
+
+```bash
+chronoseal status --format json
+```
+
+### Metrics
+
+```bash
+chronoseal metrics
+curl http://127.0.0.1:3000/metrics
+```
+
+### Stats
+
+```bash
+chronoseal stats --format json
+curl http://127.0.0.1:3000/stats
+```
+
+### Logs
+
+```bash
+sudo journalctl -u chronoseal -f
+```
+
+Use `RUST_LOG=info` or `CHRONOSEAL_LOG=info` for normal production operation. Avoid debug logging in production because internal identifiers may appear in logs.
+
+### Reverse Proxy
+
+ChronoSeal should run behind TLS in production. Terminate HTTPS at a reverse proxy such as nginx, Caddy, HAProxy, or a cloud load balancer, then proxy to the local daemon.
+
+Example nginx location:
+
+```nginx
+location / {
+    proxy_pass         http://127.0.0.1:3000;
+    proxy_http_version 1.1;
+    proxy_set_header   Host $host;
+    proxy_set_header   X-Real-IP $remote_addr;
+    proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
+    proxy_set_header   X-Forwarded-Proto $scheme;
+}
+```
+
+## Security Model
+
+ChronoSeal is designed to raise the cost of automation and replay attacks.
+
+It helps defend against:
+
+- replayed heartbeats
+- stale hash chain state
+- forged heartbeat signatures
+- mutation commitment tampering
+- session cloning using only a stolen `session_id`
+- simple scripted clients that do not run the WASM runtime
+- basic browser automation with weak interaction simulation
+
+It does not claim to stop:
+
+- real users intentionally acting as bots
+- fully resourced browser farms
+- attackers with complete control of a real browser and realistic input
+- server-side application vulnerabilities
+- account abuse outside ChronoSeal's attestation boundary
+- long-term identity or fraud decisions by itself
+
+Privacy posture:
+
+- Sessions are short-lived.
+- The private key is generated in the browser runtime and is not sent to the server.
+- ChronoSeal validates continuity and plausibility rather than creating persistent user identities.
+- Invalid heartbeats are rejected silently to reduce oracle feedback.
+
+Read the full model in [docs/THREAT_MODEL.md](docs/THREAT_MODEL.md).
+
+## Development
+
+Run the standard checks:
+
+```bash
+cargo fmt --check
+cargo check --workspace
+cargo test --workspace
+cargo clippy --workspace --all-targets -- -D warnings
+```
+
+Format:
+
+```bash
+cargo fmt
+```
+
+Build WASM during frontend/runtime changes:
+
+```bash
+wasm-pack build wasm --target web
+rm -rf frontend/pkg
+mv wasm/pkg frontend/pkg
+```
+
+Build release artifacts:
+
+```bash
+bash scripts/build.sh
+```
+
+Generate shell completion:
+
+```bash
+chronoseal completion bash > chronoseal.bash
+chronoseal completion zsh > _chronoseal
+```
+
+## Troubleshooting
+
+### Browser fails to load WASM
+
+Rebuild the WASM package and make sure `frontend/pkg/chronoseal_wasm.js` and the `.wasm` file exist:
+
+```bash
+bash scripts/build.sh
+```
+
+The `.wasm` file must be served as `application/wasm`. The built-in static file service handles this for normal ChronoSeal deployments.
+
+### `chronoseal health` fails
+
+Check that the daemon is running and that the CLI is probing the correct bind address:
+
+```bash
+sudo systemctl status chronoseal
+chronoseal health --bind 127.0.0.1:3000
+curl http://127.0.0.1:3000/health
+```
+
+### Heartbeats return only `{"status":"ok"}`
+
+That is the expected response for rejected heartbeats. Common causes include:
+
+- invalid signature
+- stale `prev_hash`
+- stale `mutation_step`
+- mismatched `gene_commitment`
+- timestamp drift beyond the configured window
+- insufficient mouse movement or pause data
+- rate limiting
+- expired session
+
+Use local development logs and tests to debug integration issues. Avoid debug logs in production.
+
+### SQLite disk mode cannot persist state
+
+Ensure the daemon user can create and write the configured database path:
+
+```bash
+sudo mkdir -p /var/lib/chronoseal
+sudo chown -R chronoseal:chronoseal /var/lib/chronoseal
+```
+
+Use:
+
+```toml
+db_type = "sqlite-in-disk"
+db_path = "/var/lib/chronoseal/chronoseal.sqlite"
+```
+
+### Config changes do not apply
+
+Check precedence. CLI flags override environment variables, environment variables override config files, and config files override built-in defaults.
+
+Print the effective config:
+
+```bash
+chronoseal config check --format yaml
+```
+
+## Further Reading
+
+- [Architecture](docs/ARCHITECTURE.md)
+- [API Reference](docs/API.md)
+- [Deployment Guide](docs/DEPLOYMENT.md)
+- [Threat Model](docs/THREAT_MODEL.md)
+- [Design Philosophy](docs/DESIGN-PHILOSOPHY.md)
+- [Privacy Policy](docs/PRIVACY%20POLICY.md)
+- [WASM Build Guide](docs/WASM_BUILD.md)
+- [Refactoring v0.6.0](docs/REFRACTORING-v0.6.0.md)
+- [Contributing](CONTRIBUTING.md)
+- [Security Policy](SECURITY.md)
 
 ## License
 
-[MIT OR Apache-2.0](LICENSE)
+ChronoSeal is licensed under either of:
+
+- MIT, see [LICENSE](LICENSE)
+- Apache-2.0, see [LICENSE-APACHE](LICENSE-APACHE)
+
+at your option.

chronoseal.service

@@ -1,67 +1,36 @@
 [Unit]
-Description=ChronoSeal cryptographic browser attestation service
-Documentation=https://chronoseal.rs
-After=network-online.target
+Description=ChronoSeal Cryptographic Attestation Daemon
+After=network.target
 Wants=network-online.target
 
 [Service]
 Type=simple
-
 User=chronoseal
 Group=chronoseal
-
-Environment=RUST_LOG=info
-Environment=CHRONOSEAL_CONFIG=/etc/chronoseal/config.toml
-Environment=CHRONOSEAL_STATE_DIR=/var/lib/chronoseal
-Environment=CHRONOSEAL_PID_FILE=/run/chronoseal.pid
-
 ExecStart=/usr/local/bin/chronoseal run
-ExecStartPre=+/usr/bin/touch /run/chronoseal.pid
-ExecStartPre=+/usr/bin/chown chronoseal:chronoseal /run/chronoseal.pid
-ExecReload=/bin/kill -HUP $MAINPID
-ExecStopPost=+/usr/bin/rm -f /run/chronoseal.pid
-PIDFile=/run/chronoseal.pid
-
-Restart=on-failure
+WorkingDirectory=/opt/chronoseal
+Restart=always
 RestartSec=3
-TimeoutStopSec=30
-KillSignal=SIGTERM
+Environment=RUST_LOG=info
 
-RuntimeDirectory=chronoseal
-RuntimeDirectoryMode=0750
-StateDirectory=chronoseal
-StateDirectoryMode=0750
-LogsDirectory=chronoseal
-LogsDirectoryMode=0750
-ConfigurationDirectory=chronoseal
-ConfigurationDirectoryMode=0750
-
-NoNewPrivileges=true
-PrivateTmp=true
+# Hardening (production-grade)
 ProtectSystem=strict
-ProtectHome=read-only
-ProtectKernelTunables=true
-ProtectKernelModules=true
-ProtectControlGroups=true
-ProtectClock=true
-ProtectHostname=true
-ProtectProc=invisible
-ProcSubset=pid
-PrivateDevices=true
-PrivateIPC=true
-
-MemoryDenyWriteExecute=true
-RestrictRealtime=true
-RestrictSUIDSGID=true
-RemoveIPC=true
-
-LockPersonality=true
-
+ProtectHome=yes
+NoNewPrivileges=yes
+PrivateTmp=yes
+ProtectKernelTunables=yes
+ProtectKernelModules=yes
+ProtectControlGroups=yes
+MemoryDenyWriteExecute=yes
+RestrictRealtime=yes
+RestrictSUIDSGID=yes
+LockPersonality=yes
 SystemCallArchitectures=native
-SystemCallFilter=@system-service
-SystemCallErrorNumber=EPERM
-CapabilityBoundingSet=
-RestrictAddressFamilies=AF_UNIX AF_INET AF_INET6
+ReadWritePaths=/run/chronoseal.pid
+
+# Logging
+StandardOutput=journal
+StandardError=journal
 
 [Install]
 WantedBy=multi-user.target

docs/API.md

@@ -1,20 +1,58 @@
-# ChronoSeal — API Reference
+# ChronoSeal API Reference
+
+ChronoSeal exposes a small HTTP API for browser attestation, heartbeat verification, health checks, metrics, and runtime statistics.
+
+This document describes the wire format and acceptance semantics. The internal state model is covered in [ARCHITECTURE.md](ARCHITECTURE.md).
 
 ## Base URL
 
-All endpoints are relative to the server root. In development: `http://localhost:3000`.
-In production: your HTTPS domain via reverse proxy.
+All paths are relative to the ChronoSeal server root.
 
----
+- Development default: `http://127.0.0.1:3000`
+- Production: the HTTPS origin or reverse-proxy path used by the protected site
 
-## Endpoints
+Production deployments should use HTTPS. The daemon itself can run behind a local reverse proxy.
 
-### `POST /init`
+## Content Type
 
-Initialise a new session. Called once per page load, immediately after the
-WASM module generates an Ed25519 keypair.
+JSON endpoints expect:
 
-#### Request
+```http
+Content-Type: application/json
+```
+
+Responses are JSON except `/metrics`, which returns Prometheus text format.
+
+## Endpoint Summary
+
+| Method | Path | Purpose |
+|---|---|---|
+| `POST` | `/init` | Create a browser attestation session |
+| `POST` | `/hb` | Submit and verify a signed heartbeat |
+| `GET` | `/health` | Return daemon health |
+| `GET` | `/stats` | Return storage/session statistics |
+| `GET` | `/metrics` | Return Prometheus-compatible metrics |
+| `GET` | `/` | Serve static frontend assets from `frontend_dir` |
+
+## Data Types
+
+Common encodings:
+
+| Value | Encoding |
+|---|---|
+| Ed25519 public key | 32 raw bytes encoded as 64 hex characters |
+| Ed25519 signature | 64 raw bytes encoded as 128 hex characters |
+| `session_id` | 32 random bytes encoded as 64 hex characters |
+| `salt` | 16 random bytes encoded as 32 hex characters |
+| `initial_hash`, `prev_hash`, `gene_commitment` | 32-byte digest encoded as 64 hex characters |
+| `opcodes_b64`, `mutation_order_b64` | standard base64 |
+| timestamps | Unix time in milliseconds unless otherwise stated |
+
+## `POST /init`
+
+Creates a new attestation session.
+
+### Request
 
 ```http
 POST /init
@@ -27,42 +65,58 @@ Content-Type: application/json
 }
 ```
 
-| Field | Type | Description |
-|---|---|---|
-| `public_key` | `string` | Hex-encoded 32-byte Ed25519 verifying key generated by the WASM module |
+| Field | Type | Required | Description |
+|---|---|---:|---|
+| `public_key` | string | yes | Browser-generated Ed25519 public key as 64 hex characters |
 
-#### Response `200 OK`
+The private key is generated and retained by the browser WASM runtime. It is not sent to the server.
+
+### Successful Response
+
+```http
+HTTP/1.1 200 OK
+Content-Type: application/json
+```
 
 ```json
 {
-  "session_id":    "64-char hex string (32 bytes)",
-  "salt":          "32-char hex string (16 bytes)",
-  "opcodes_b64":   "base64-encoded VM program (8–16 opcodes)",
-  "initial_hash":  "64-char hex string (32 bytes Blake3)",
-  "expires_at":    1234567890123
+  "session_id": "64-char hex string",
+  "salt": "32-char hex string",
+  "opcodes_b64": "base64-encoded VM program",
+  "initial_hash": "64-char hex string",
+  "expires_at": 1234567890123,
+  "heartbeat_min_interval_ms": 12000,
+  "heartbeat_max_interval_ms": 25000,
+  "gene_size": 512,
+  "mutation_step": 1,
+  "mutation_order_b64": "base64-encoded mutation program"
 }
 ```
 
 | Field | Type | Description |
 |---|---|---|
-| `session_id` | `string` | Opaque session identifier; include in every heartbeat |
-| `salt` | `string` | Initial salt; used to compute `H(0)` and first `H(1)` |
-| `opcodes_b64` | `string` | Base64 VM program; execute with `run_program()` on every heartbeat |
-| `initial_hash` | `string` | `H(0) = Blake3(session_id ║ pub_key ║ salt)`; the first `prev_hash` |
-| `expires_at` | `number` | Unix timestamp in milliseconds; session expires after 30 minutes of inactivity |
+| `session_id` | string | Opaque session identifier |
+| `salt` | string | Current server salt for the first heartbeat hash computation |
+| `opcodes_b64` | string | Randomized VM program executed by the browser runtime |
+| `initial_hash` | string | Initial chain head used as `prev_hash` for the first heartbeat |
+| `expires_at` | number | Session expiration timestamp in milliseconds |
+| `heartbeat_min_interval_ms` | number | Minimum heartbeat delay recommended by the server |
+| `heartbeat_max_interval_ms` | number | Maximum heartbeat delay recommended by the server |
+| `gene_size` | number | Initial synthetic gene buffer size |
+| `mutation_step` | number | Mutation step expected on the first heartbeat |
+| `mutation_order_b64` | string | Server-authored mutation order for the first heartbeat |
 
-#### Error
+### Error Behavior
 
-Returns `500 Internal Server Error` only on server-side failures (DB errors,
-invalid public key length). No meaningful error body is returned.
+`/init` uses normal route-level error handling for invalid payloads or server failures. Invalid public key length, invalid configured gene size, or storage failure can prevent session creation.
 
----
+Unlike `/hb`, initialization failures are not part of the silent heartbeat rejection model.
 
-### `POST /hb`
+## `POST /hb`
 
-Submit a heartbeat. Called every 12–25 seconds with uniform random jitter.
+Submits one heartbeat for an existing session.
 
-#### Request
+### Request
 
 ```http
 POST /hb
@@ -71,13 +125,12 @@ Content-Type: application/json
 
 ```json
 {
-  "session_id":   "64-char hex",
-  "prev_hash":    "64-char hex",
-  "timestamp":    1234567890123,
+  "session_id": "64-char hex",
+  "prev_hash": "64-char hex",
+  "timestamp": 1234567890123,
   "entropy_data": {
     "events": [
-      { "x": 412.0, "y": 308.5, "t": 1234.567 },
-      { "x": 415.2, "y": 310.1, "t": 1285.123 }
+      { "x": 412.0, "y": 308.5, "t": 1234.567 }
     ]
   },
   "stack_state": {
@@ -85,132 +138,229 @@ Content-Type: application/json
     "ip": 42
   },
   "fingerprint": {
-    "aspectRatio":        "1.7777777778",
-    "devicePixelRatio":   "2",
+    "aspectRatio": "1.7777777778",
+    "devicePixelRatio": "2",
     "hardwareConcurrency": 8
   },
-  "signature": "128-char hex Ed25519 signature"
+  "mutation_step": 1,
+  "gene_commitment": "64-char hex",
+  "signature": "128-char hex"
+}
+```
+
+| Field | Type | Required | Description |
+|---|---|---:|---|
+| `session_id` | string | yes | Session ID from `/init` |
+| `prev_hash` | string | yes | Current browser view of the accepted hash-chain head |
+| `timestamp` | number | yes | Browser wall-clock timestamp in milliseconds |
+| `entropy_data.events` | array | yes | Mouse samples since the previous heartbeat |
+| `entropy_data.events[].x` | number | yes | Mouse x coordinate |
+| `entropy_data.events[].y` | number | yes | Mouse y coordinate |
+| `entropy_data.events[].t` | number | yes | Event timestamp in milliseconds relative to the browser sampling window |
+| `stack_state.stack` | array | yes | VM stack output as unsigned 32-bit values |
+| `stack_state.ip` | number | yes | VM instruction pointer as an unsigned 16-bit value |
+| `fingerprint.aspectRatio` | string | yes | Screen aspect ratio; server accepts numeric strings in range `0.5..=3.0` |
+| `fingerprint.devicePixelRatio` | string | yes | Device pixel ratio; server accepts numeric strings in range `(0, 5]` |
+| `fingerprint.hardwareConcurrency` | number | yes | Positive hardware concurrency value |
+| `mutation_step` | number | yes | Mutation step currently expected by the server |
+| `gene_commitment` | string | yes | Context-bound commitment produced by the WASM mutation preview |
+| `signature` | string | yes | Ed25519 signature over the canonical payload |
+
+### Canonical Signing Payload
+
+The signature covers a canonical JSON object with sorted top-level keys:
+
+```json
+{
+  "entropyData": { "events": [{ "t": 1234.567, "x": 412.0, "y": 308.5 }] },
+  "fingerprint": {
+    "aspectRatio": "1.7777777778",
+    "devicePixelRatio": "2",
+    "hardwareConcurrency": 8
+  },
+  "geneCommitment": "64-char hex",
+  "mutationStep": 1,
+  "prevHash": "64-char hex",
+  "sessionId": "64-char hex",
+  "stackState": { "ip": 42, "stack": [2971406957, 1234567890] },
+  "timestamp": 1234567890123
+}
+```
+
+Important details:
+
+- The transport payload uses snake_case for several fields.
+- The signed payload uses camelCase names.
+- Top-level keys must be serialized deterministically in lexical order.
+- The `signature` field is not part of the signed payload.
+- Nested serialization must match the server's `serde_json` representation.
+
+The server reconstructs the canonical message from the received request before verifying the Ed25519 signature.
+
+### Accepted Response
+
+```http
+HTTP/1.1 200 OK
+Content-Type: application/json
+```
+
+```json
+{
+  "status": "ok",
+  "next_salt": "32-char hex string",
+  "next_mutation_step": 2,
+  "next_mutation_order_b64": "base64-encoded mutation program"
 }
 ```
 
 | Field | Type | Description |
 |---|---|---|
-| `session_id` | `string` | Session ID from `/init` |
-| `prev_hash` | `string` | Hash chain head from previous heartbeat (or `initial_hash` for the first) |
-| `timestamp` | `number` | `Date.now()` in milliseconds; must be within ±30s of server time |
-| `entropy_data.events` | `array` | Mouse events since previous heartbeat; each has `x`, `y` (px), `t` (performance.now ms) |
-| `stack_state.stack` | `array` | `u32[]` result of executing the VM program |
-| `stack_state.ip` | `number` | Instruction pointer after execution |
-| `fingerprint.aspectRatio` | `string` | `(screen.width / screen.height).toFixed(10)` |
-| `fingerprint.devicePixelRatio` | `string` | `String(window.devicePixelRatio)` |
-| `fingerprint.hardwareConcurrency` | `number` | `navigator.hardwareConcurrency \|\| 1` |
-| `signature` | `string` | Hex-encoded 64-byte Ed25519 signature over the canonical payload |
+| `status` | string | Always `ok` |
+| `next_salt` | string | Server salt for the next heartbeat |
+| `next_mutation_step` | number | Mutation step expected on the next heartbeat |
+| `next_mutation_order_b64` | string | Server-authored mutation order for the next heartbeat |
 
-#### Canonical Signing Payload
+Clients should treat the heartbeat as accepted only when all next-state fields are present.
 
-The client signs the following JSON object. Top-level keys must be sorted
-alphabetically. Nested object keys follow their natural serialisation order.
+### Rejected Response
 
-```json
-{
-  "entropyData":  { "events": [{ "t": …, "x": …, "y": … }] },
-  "fingerprint":  { "aspectRatio": "…", "devicePixelRatio": "…", "hardwareConcurrency": … },
-  "prevHash":     "…",
-  "sessionId":    "…",
-  "stackState":   { "ip": …, "stack": […] },
-  "timestamp":    …
-}
+```http
+HTTP/1.1 200 OK
+Content-Type: application/json
 ```
 
-Note: field names in the signing payload use camelCase (`sessionId`,
-`prevHash`, `entropyData`, `stackState`) while the request body uses
-snake_case (`session_id`, `prev_hash`, `entropy_data`, `stack_state`).
-
-#### Response `200 OK` — Accepted
-
-```json
-{
-  "status":    "ok",
-  "next_salt": "32-char hex string (16 bytes)"
-}
-```
-
-The client must:
-1. Capture `sentSalt = currentSalt` before updating.
-2. Set `currentSalt = next_salt`.
-3. Compute `prevHash = compute_next_hash(prevHash, timestamp, entropyJson, stackStateJson, sentSalt)`.
-
-#### Response `200 OK` — Rejected
-
 ```json
 {
   "status": "ok"
 }
 ```
 
-`next_salt` is absent. The response body is intentionally identical in
-structure. Rejections are silent — the caller cannot distinguish a validation
-failure from a rate limit hit or an expired session.
+Rejected heartbeats omit:
 
-The client should log a warning and continue scheduling heartbeats (they will
-continue to fail until the page is reloaded and a new session is established).
+- `next_salt`
+- `next_mutation_step`
+- `next_mutation_order_b64`
 
----
+This response shape is intentional. The server does not reveal which validation stage failed.
 
-## Validation Rules (Server-Side)
+### Heartbeat Validation Order
 
-Heartbeats are rejected (silently) if any of the following checks fail:
+The server currently validates heartbeats in this order:
 
-| Check | Condition for rejection |
-|---|---|
-| Rate limit | > 5 requests per 10-second window for this `session_id` |
-| Session not found | `session_id` not in SQLite |
-| Session expired | `current_time_ms > expires_at` |
-| Signature invalid | Ed25519 verification fails against stored public key |
-| Hash chain broken | `hex(prev_hash) ≠ stored last_hash` |
-| Timestamp drift | `\|server_now_ms - timestamp\| > 30 000` |
-| Insufficient mouse events | `events.len() < 3` |
-| Insufficient mouse distance | `total_dist < 10.0 px` |
-| Mouse speed too high | `total_dist / total_time_ms > 2.0 px/ms` |
-| No mouse pauses | `pause_count < 1` |
-| Invalid aspect ratio | `ar < 0.5` or `ar > 3.0` |
-| Invalid devicePixelRatio | `dpr ≤ 0.0` or `dpr > 5.0` |
-| Zero hardwareConcurrency | `hardware_concurrency == 0` |
+1. Rate-limit check in the route handler.
+2. Load session by `session_id`.
+3. Check session expiration.
+4. Verify Ed25519 signature.
+5. Compare `prev_hash` with stored `last_hash`.
+6. Compare `mutation_step` with stored `pending_mutation_step`.
+7. Apply stored pending mutation to a cloned gene state.
+8. Compare expected and submitted `gene_commitment`.
+9. Enforce timestamp drift.
+10. Validate mouse entropy.
+11. Validate fingerprint fields.
+12. Compute next hash-chain head.
+13. Generate next mutation order and salt.
+14. Persist advanced session state.
 
----
+Any failure after route-level JSON decoding returns the silent rejection body.
 
-## Hash Chain Specification
+## `GET /health`
 
-```
-H(0) = Blake3( session_id_bytes ║ pub_key_bytes ║ salt₀_bytes )
+Returns a basic health response.
 
-H(n) = Blake3(
-    saltₙ₋₁_bytes
-  ║ H(n-1)_bytes
-  ║ timestamp_u64_le_bytes
-  ║ Blake3( UTF-8( JSON(entropy_data) ) )
-  ║ Blake3( UTF-8( JSON(stack_state)  ) )
-)
+```http
+GET /health
 ```
 
-All inputs are concatenated in the order shown. `timestamp` is encoded as a
-64-bit unsigned integer in little-endian byte order. JSON serialisation of
-`entropy_data` and `stack_state` uses the field order defined by the shared
-Rust types (serde derive, no custom ordering).
+```json
+{
+  "status": "healthy"
+}
+```
 
----
+## `GET /stats`
 
-## WASM API
+Returns storage-derived session statistics.
 
-The WASM module (`antibot_wasm`) exports the following functions to JavaScript:
+```http
+GET /stats
+```
+
+```json
+{
+  "sessions": 1,
+  "expired_sessions": 0,
+  "max_chain_length": 4
+}
+```
+
+| Field | Type | Description |
+|---|---|---|
+| `sessions` | number | Stored session count |
+| `expired_sessions` | number | Expired sessions not yet purged |
+| `max_chain_length` | number | Highest stored heartbeat chain length |
+
+## `GET /metrics`
+
+Returns Prometheus-compatible text.
+
+```http
+GET /metrics
+```
+
+```text
+# HELP chronoseal_sessions Active ChronoSeal sessions
+# TYPE chronoseal_sessions gauge
+chronoseal_sessions 1
+# HELP chronoseal_expired_sessions Expired sessions not yet removed
+# TYPE chronoseal_expired_sessions gauge
+chronoseal_expired_sessions 0
+# HELP chronoseal_max_chain_length Maximum heartbeat chain length
+# TYPE chronoseal_max_chain_length gauge
+chronoseal_max_chain_length 4
+```
+
+## Client State Rules
+
+After `/init`, the client stores:
+
+- `session_id`
+- `initial_hash` as the first `prev_hash`
+- current `salt`
+- VM opcode program
+- committed gene state
+- pending mutation step
+- pending mutation order
+
+On accepted `/hb`:
+
+1. Commit the local gene preview.
+2. Compute the next local hash using the old salt that was active when the heartbeat was sent.
+3. Replace current salt with `next_salt`.
+4. Replace pending mutation step and order with server-provided values.
+
+On rejected `/hb`:
+
+1. Discard the local gene preview.
+2. Do not advance hash-chain state.
+3. Do not advance mutation state.
+4. Treat the session as suspect or restart attestation.
+
+## WASM Runtime Exports
+
+The generated `chronoseal_wasm` package exposes:
 
 | Function | Signature | Description |
 |---|---|---|
-| `generate_keypair()` | `() → string` | Generate Ed25519 keypair; return hex public key. Private key stored in WASM memory. |
-| `get_public_key()` | `() → string` | Return hex public key, or `""` if not initialised. |
-| `sign_message(msg)` | `(string) → string` | Sign UTF-8 string; return hex signature, or `""` if not initialised. |
-| `compute_next_hash(prev, ts, entropy, stack, salt)` | `(string, u64, string, string, string) → string` | Compute next Blake3 chain hash; all inputs/output hex or JSON strings. |
-| `run_program(b64)` | `(string) → JsValue` | Execute base64 VM program; return `{ stack: u32[], ip: number }`. |
+| `generate_keypair()` | `() -> string` | Generate an Ed25519 keypair and return public key hex |
+| `get_public_key()` | `() -> string` | Return current public key hex, or `""` if no keypair exists |
+| `sign_message(msg)` | `(string) -> string` | Sign a UTF-8 payload and return hex signature, or `""` on failure |
+| `compute_next_hash(prev, ts, entropy, stack, salt)` | `(string, u64, string, string, string) -> string` | Compute next Blake3 chain hash |
+| `run_program(b64)` | `(string) -> JsValue` | Execute a base64 VM program and return stack state |
+| `init_gene_state(gene_size)` | `(u32) -> bool` | Initialize the browser gene state |
+| `preview_gene_commitment(order_b64, session_id, mutation_step, rounds)` | `(string, string, u64, u8) -> string` | Preview next mutation commitment |
+| `commit_gene_preview()` | `() -> bool` | Commit the preview after accepted heartbeat |
+| `discard_gene_preview()` | `() -> void` | Discard preview after rejection or error |
+| `current_gene_commitment(session_id, mutation_step)` | `(string, u64) -> string` | Return current committed gene commitment |
 
-All functions return empty strings on error rather than panicking.
-Callers must check for empty return values before using the result.
+String-returning functions use `""` to signal failure. Callers must handle empty strings explicitly.

docs/ARCHITECTURE.md

@@ -1,381 +1,533 @@
-# ChronoSeal — Architecture
+# ChronoSeal Architecture
 
-## Overview
+ChronoSeal is a Unix-native browser attestation daemon. It validates browser session continuity by combining signed heartbeats, Blake3 hash-chain progression, deterministic VM execution, behavioral sanity checks, and a shared Synthetic Gene Mutation Engine that runs on both the server and the browser WASM runtime.
 
-ChronoSeal is a stateless, cryptographic browser attestation framework. Its
-purpose is to make automated clients (headless browsers, AI scrapers, API
-harvesters) computationally expensive and operationally complex to operate,
-while remaining completely invisible to real human users.
+This document describes the system architecture, state model, validation pipeline, trust boundaries, and operational assumptions. The API wire format is documented separately in [API.md](API.md), and deployment guidance is documented in [DEPLOYMENT.md](DEPLOYMENT.md).
 
-The design is inspired by the heartbeat model used in embedded IoT firmware:
-a device that stops sending signed, chained attestations is assumed to be
-offline or compromised. ChronoSeal applies the same principle to browser
-sessions.
+## Architectural Goals
 
----
+ChronoSeal is designed as infrastructure software rather than a consumer-facing widget. The main goals are:
 
-## Design Principles
+- Keep the server small, inspectable, and operable as a normal Unix daemon.
+- Use deterministic client/server computation so the server can verify browser-side progression without trusting browser claims blindly.
+- Make replay, stale state reuse, and incomplete automation expensive.
+- Preserve privacy by using short-lived session state instead of persistent identity tracking.
+- Avoid attacker feedback oracles by returning indistinguishable success-shaped responses for rejected heartbeats.
+- Keep browser integration lightweight: static JavaScript plus a Rust-generated WASM package.
 
-**Stateless per request.** The server carries no per-request state beyond what
-is stored in SQLite keyed on `session_id`. Every HTTP request is independently
-verifiable.
+ChronoSeal does not attempt to prove that a human is present. It attempts to prove that a client is maintaining the expected live browser-side cryptographic and mutation state.
 
-**Silent failure.** Validation failures never return an error status or an
-error body. The server always responds `{"status":"ok"}` and simply omits
-`next_salt`. The client degrades gracefully. Attackers cannot enumerate
-validation rules by probing error responses.
+## System Context
 
-**Private key isolation.** The Ed25519 signing key is generated inside the
-WASM module and never serialised, never exposed to the JavaScript environment,
-and never transmitted. It exists only in WASM linear memory for the lifetime
-of the page.
-
-**Layered validation.** A heartbeat must pass five independent checks: session
-existence, expiry, signature, hash chain, and behavioral signals. Bypassing
-one layer is not sufficient.
-
-**Cost asymmetry.** Each heartbeat requires a real browser environment, mouse
-activity, correct WASM execution, chain state synchronisation, and a valid
-Ed25519 signature over a time-windowed payload. For an automated client, the
-synchronisation burden alone makes scaled operation expensive.
-
-### High-Level Design
-
-- **Core**: Rust + Axum (async web framework)
-- **Storage**: In-memory SQLite (fast, ephemeral per process — restarts are clean)
-- **Client**: WASM + Rust (runs in browser for proof generation)
-- **Security Model**: Behavioral analysis + hash chaining + entropy scoring
-- **Deployment**: Static musl binary, systemd service, optional Docker
-
-### Key Components
-
-- `shared/` — Types, constants, crypto primitives used by server and WASM
-- `server/` — Axum routes, session management, trust engine, rate limiting, cleanup tasks
-- `wasm/` — Client-side proof generation
-- `frontend/` — Static assets served by the application
-
-### Unix-Native Design Decisions
-
-- Runs as a proper systemd service with strict sandboxing
-- All state is either in-memory or in standard locations (`/run/`, `/var/log/`, `/etc/`)
-- Graceful shutdown and reload support via signals
-- Logging designed for `journalctl` and structured parsing
-- Configuration will be fully runtime (no recompile needed)
-
-### Design Goal
-
-ChronoSeal should feel as natural to use as `nginx` or `redis-server` on a Linux system.
----
-
-## Component Map
-
-```
-┌─────────────────────────────────────────────────────────┐
-│  Browser                                                │
-│                                                         │
-│  ┌─────────────┐   ┌──────────────┐   ┌─────────────┐   │
-│  │  entropy.js │   │ heartbeat.js │   │ transport.js│   │
-│  │             │   │              │   │             │   │
-│  │ mousemove   │──►│ orchestrates │──►│ fetch POST  │   │
-│  │ event ring  │   │ init + HB    │   │ /init  /hb  │   │
-│  └─────────────┘   └──────┬───────┘   └─────────────┘   │
-│                           │                             │
-│                    ┌──────▼───────────────────────┐     │
-│                    │  WASM Module (antibot_wasm)  │     │
-│                    │                              │     │
-│                    │  crypto.rs      vm.rs        │     │
-│                    │  ├ generate_keypair()        │     │
-│                    │  ├ sign_message()            │     │
-│                    │  ├ compute_next_hash()       │     │
-│                    │  └ run_program()             │     │
-│                    └──────────────────────────────┘     │
-└─────────────────────────────────────────────────────────┘
-                          │ HTTPS
-┌─────────────────────────▼───────────────────────────────┐
-│  Server (Axum)                                          │
-│                                                         │
-│  routes/init.rs          routes/heartbeat.rs            │
-│       │                          │                      │
-│       └──────────┬───────────────┘                      │
-│                  ▼                                      │
-│            session.rs                                   │
-│            ├ create_session()                           │
-│            └ verify_heartbeat()                         │
-│                  │                                      │
-│       ┌──────────┼──────────────┐                       │
-│       ▼          ▼              ▼                       │
-│  crypto.rs   trust.rs    fingerprint.rs                 │
-│  (sig verify) (mouse     (aspect ratio,                 │
-│               speed)      DPR, HW conc.)                │
-│       │                                                 │
-│       ▼                                                 │
-│  shared::hashing  (Blake3 hash chain)                   │
-│       │                                                 │
-│       ▼                                                 │
-│  storage.rs  (in-memory SQLite)                         │
-│                                                         │
-│  ratelimit.rs   cleanup.rs   vm.rs   middleware.rs      │
-└─────────────────────────────────────────────────────────┘
+```text
+Protected browser origin
+        |
+        | static files and API calls
+        v
++------------------------------+
+| Browser                      |
+| - frontend JavaScript        |
+| - chronoseal_wasm runtime    |
+| - Ed25519 session key        |
+| - VM and gene state          |
++---------------+--------------+
+                |
+                | POST /init
+                | POST /hb
+                v
++------------------------------+
+| ChronoSeal daemon            |
+| - Axum HTTP routes           |
+| - session verifier           |
+| - storage abstraction        |
+| - metrics and health         |
++---------------+--------------+
+                |
+                | SessionRecord
+                v
++------------------------------+
+| Storage backend              |
+| - sqlite-in-memory           |
+| - sqlite-in-disk             |
+| - valkey                     |
++------------------------------+
 ```
 
----
+ChronoSeal can serve the frontend files itself or sit behind a reverse proxy. TLS termination should happen before traffic reaches the daemon in production.
 
-## Session Lifecycle
+## Workspace Components
 
-### 1. Initialisation — `POST /init`
+The repository is a Rust workspace with three runtime crates and one static frontend directory.
 
-```
-Client                                  Server
-  │                                        │
-  │  generate Ed25519 keypair (in WASM)    │
-  │  pub_key = verifying_key.to_bytes()    │
-  │                                        │
-  ├─── { public_key: hex(pub_key) } ──────►│
-  │                                        │  session_id = rand::random::<[u8;32]>()
-  │                                        │  salt₀      = rand::random::<[u8;16]>()
-  │                                        │  H(0) = Blake3(session_id║pub_key║salt₀)
-  │                                        │  opcodes = generate_random_program(8..=16)
-  │                                        │  INSERT INTO sessions …
-  │                                        │
-  │◄── { session_id, salt, opcodes_b64,    │
-  │      initial_hash, expires_at } ───────┤
-  │                                        │
-  │  prevHash    = initial_hash            │
-  │  currentSalt = salt                    │
-  │  opcodesB64  = opcodes_b64             │
+### `shared/`
+
+`shared/` contains protocol and deterministic runtime code used by both the server and WASM crates.
+
+Responsibilities:
+
+- wire protocol structs for `/init` and `/hb`
+- Blake3 hash-chain helpers
+- synthetic gene state representation
+- environment encoding and validation
+- mutation program generation, encoding, decoding, and execution
+- deterministic VM extension opcode semantics
+
+Important files:
+
+| File | Responsibility |
+|---|---|
+| `protocol.rs` | `InitRequest`, `InitResponse`, `HeartbeatRequest`, `HeartbeatResponse`, and supporting payload types |
+| `hashing.rs` | initial and next hash-chain computation |
+| `gene.rs` | gene state, environment records, validation, and context-bound commitment |
+| `vm_extensions.rs` | mutation order generation, opcode interpreter, execution tracing, and tests |
+| `constants.rs` | protocol and execution bounds |
+
+`shared/` is the determinism boundary. Any logic that must agree between server and browser belongs here rather than in server-only or frontend-only code.
+
+### `server/`
+
+`server/` builds the `chronoseal` binary. It owns daemon lifecycle, HTTP routing, session verification, storage, metrics, configuration, and CLI behavior.
+
+Important files:
+
+| File | Responsibility |
+|---|---|
+| `main.rs` | CLI command dispatch |
+| `cli.rs` | command, flag, and environment variable definitions |
+| `config.rs` | defaults, TOML loading, environment overrides, validation |
+| `runtime.rs` | daemon startup, Axum router, health, metrics, stats, graceful shutdown |
+| `routes/init.rs` | `POST /init` handler |
+| `routes/heartbeat.rs` | `POST /hb` handler and silent rejection response shape |
+| `session.rs` | session creation, heartbeat verification, state advancement |
+| `crypto.rs` | canonical signing payload and Ed25519 signature verification |
+| `storage.rs` | `DbPool`, SQLite, Valkey compatibility, session persistence, stats |
+| `trust.rs` | mouse entropy validation |
+| `fingerprint.rs` | browser signal validation |
+| `ratelimit.rs` | per-session rate limiting |
+| `cleanup.rs` | expired session removal |
+
+The server treats the browser as untrusted. Browser-supplied values are accepted only after signature, continuity, timing, behavioral, and mutation checks pass.
+
+### `wasm/`
+
+`wasm/` compiles to the browser runtime package with `wasm-pack --target web`.
+
+Responsibilities:
+
+- generate and hold the browser-local Ed25519 keypair
+- sign canonical heartbeat payloads
+- compute hash-chain values used by the browser integration
+- execute randomized VM programs
+- maintain committed and preview synthetic gene state
+- preview mutation commitments before a heartbeat is submitted
+- commit or discard preview state after server response
+
+Important files:
+
+| File | Responsibility |
+|---|---|
+| `crypto.rs` | key generation, public key export, message signing |
+| `vm.rs` | base VM program execution |
+| `vm_extensions.rs` | gene initialization, mutation preview, commit, discard, current commitment |
+
+The WASM runtime is not a trusted execution environment. It is useful because it forces a browser client to implement the same state transitions as the server and makes simple HTTP automation insufficient.
+
+### `frontend/`
+
+`frontend/` contains static JavaScript and browser assets. It loads `frontend/pkg/chronoseal_wasm.js`, calls `/init`, periodically sends `/hb`, and coordinates browser-side state transitions.
+
+The frontend is intentionally thin. Durable protocol rules live in Rust, not in handwritten JavaScript.
+
+## Runtime Topology
+
+The daemon builds a single Axum application with:
+
+| Route | Method | Purpose |
+|---|---|---|
+| `/init` | `POST` | create a new attestation session |
+| `/hb` | `POST` | verify and advance a heartbeat |
+| `/health` | `GET` | health probe |
+| `/metrics` | `GET` | Prometheus-compatible metrics |
+| `/stats` | `GET` | storage/session statistics |
+| `/` | `GET` | static frontend assets from `frontend_dir` |
+
+Shared runtime state is held in `AppState`:
+
+- `db_pool`: storage backend handle
+- `rate_limiter`: process-local rate limiter
+- `config`: runtime configuration snapshot behind an `RwLock`
+
+Configuration is resolved in this order:
+
+1. CLI flags
+2. `CHRONOSEAL_*` environment variables
+3. TOML configuration file
+4. built-in defaults
+
+## Session State Model
+
+The server persists one `SessionRecord` per active session.
+
+| Field | Meaning |
+|---|---|
+| `session_id` | random 32-byte session identifier encoded as hex |
+| `public_key` | browser-generated Ed25519 verifying key |
+| `salt` | current server salt for hash-chain progression |
+| `last_hash` | current accepted hash-chain head |
+| `chain_length` | number of accepted chain states including initialization |
+| `created_at` | creation timestamp in milliseconds |
+| `last_seen` | timestamp of last accepted heartbeat |
+| `expires_at` | session expiration timestamp in milliseconds |
+| `gene` | committed synthetic gene byte buffer |
+| `environment` | encoded environment records |
+| `pending_mutation` | server-issued mutation program for the next heartbeat |
+| `pending_mutation_step` | mutation step expected on the next heartbeat |
+
+The committed server state advances only after a heartbeat passes all validation checks. Failed heartbeats do not update `last_hash`, `salt`, `gene`, `environment`, `pending_mutation`, or `pending_mutation_step`.
+
+## Initialization Flow
+
+```text
+Browser/WASM                         Server
+------------                         ------
+generate_keypair()
+public key
+      |
+      | POST /init { public_key }
+      v
+                                  validate public key length
+                                  create GeneState
+                                  generate session_id
+                                  generate salt
+                                  compute initial_hash
+                                  generate VM opcodes
+                                  generate mutation step 1
+                                  persist SessionRecord
+      ^
+      | InitResponse
+      |
+store session_id, salt,
+initial_hash, opcodes,
+gene_size, mutation order
 ```
 
-### 2. Heartbeat — `POST /hb`
+Initialization creates the first server-side commitment state but does not prove liveness. Liveness begins with accepted heartbeats.
 
-Fired every 12–25 seconds with uniform random jitter.
+The initial response contains:
 
-```
-Client                                  Server
-  │                                        │
-  │  stackState = run_program(opcodesB64)  │
-  │  events     = collectEntropy(lastTime) │
-  │  ts         = Date.now()               │
-  │                                        │
-  │  signable = {                          │
-  │    entropyData, fingerprint,           │  ← keys sorted alphabetically
-  │    prevHash, sessionId,                │
-  │    stackState, timestamp               │
-  │  }                                     │
-  │  sig = sign_message(                   │
-  │    JSON.stringify(signable, keys.sort))│
-  │                                        │
-  ├─── { session_id, prev_hash, timestamp, │
-  │      entropy_data, stack_state,        │
-  │      fingerprint, signature } ────────►│
-  │                                        │  1. Rate limit check
-  │                                        │  2. Lookup session, check expiry
-  │                                        │  3. Verify Ed25519 signature
-  │                                        │  4. Verify hash chain continuity
-  │                                        │  5. Validate timestamp window ±30s
-  │                                        │  6. Validate mouse behavior
-  │                                        │  7. Validate fingerprint signals
-  │                                        │  8. Compute H(n), rotate salt
-  │                                        │  9. UPDATE sessions …
-  │                                        │
-  │◄── { status: "ok", next_salt } ────────┤
-  │                                        │
-  │  sentSalt    = currentSalt  ◄── captured BEFORE rotation
-  │  currentSalt = next_salt               │
-  │  prevHash    = compute_next_hash(      │
-  │    prevHash, ts, entropy,              │
-  │    stackState, sentSalt)               │
+- `session_id`
+- `salt`
+- `opcodes_b64`
+- `initial_hash`
+- `expires_at`
+- heartbeat interval bounds
+- `gene_size`
+- `mutation_step`
+- `mutation_order_b64`
+
+## Heartbeat Flow
+
+```text
+Browser/WASM                                      Server
+------------                                      ------
+execute VM program
+collect entropy and fingerprint data
+preview pending gene mutation
+build canonical signing payload
+sign with Ed25519 private key
+      |
+      | POST /hb HeartbeatRequest
+      v
+                                                 load session
+                                                 check expiration
+                                                 verify signature
+                                                 check hash continuity
+                                                 check mutation step
+                                                 apply pending mutation
+                                                 compare gene commitment
+                                                 check timestamp drift
+                                                 validate mouse entropy
+                                                 validate fingerprint
+                                                 compute next hash
+                                                 generate next mutation
+                                                 generate next salt
+                                                 persist advanced state
+      ^
+      | accepted: status + next salt + next mutation
+      | rejected: { "status": "ok" }
+      |
+commit preview on accepted response
+discard or stop on rejected response
 ```
 
-### 3. Failure Path
+Accepted heartbeats return `next_salt`, `next_mutation_step`, and `next_mutation_order_b64`.
 
-On any validation failure the server returns `{"status":"ok"}` with no
-`next_salt`. The client logs a warning and continues scheduling heartbeats.
-The chain is broken — subsequent heartbeats will also fail silently.
-No error is surfaced to the page or its visitors.
-
----
-
-## Cryptographic Protocol
-
-### Key Generation
-
-```
-Ed25519 keypair generated via ed25519-dalek + rand::thread_rng (OS-seeded)
-Private key:  stored in WASM thread_local, never leaves WASM memory
-Public key:   32 bytes, hex-encoded, sent to server at init
-```
-
-### Hash Chain
-
-```
-H(0) = Blake3( session_id ║ pub_key ║ salt₀ )
-
-H(n) = Blake3(
-    saltₙ₋₁                    ← server-side only, rotated each heartbeat
-  ║ H(n-1)                     ← must match stored last_hash
-  ║ timestamp_u64_le
-  ║ Blake3( JSON(entropy_data) )
-  ║ Blake3( JSON(stack_state)  )
-)
-```
-
-Salt rotation means an attacker who intercepts a heartbeat cannot compute
-future chain links without also intercepting every subsequent server response.
-
-### Canonical Signing Payload
-
-The signed message is a JSON object with top-level keys sorted alphabetically,
-serialised with no extra whitespace:
+Rejected heartbeats return only:
 
 ```json
 {
-  "entropyData":  { "events": [{"t":…,"x":…,"y":…}] },
-  "fingerprint":  { "aspectRatio":"…","devicePixelRatio":"…","hardwareConcurrency":… },
-  "prevHash":     "hex…",
-  "sessionId":    "hex…",
-  "stackState":   { "ip":…,"stack":[…] },
-  "timestamp":    1234567890123
+  "status": "ok"
 }
 ```
 
-The server reconstructs this using `std::collections::BTreeMap` (alphabetical
-key order) before calling `VerifyingKey::verify_strict`. Any field mismatch,
-key order difference, or whitespace difference causes a signature failure.
+This silent rejection behavior is part of the security model. It prevents the API from acting as an oracle for signature, timing, mutation, or behavior failures.
 
-### Hashing Algorithm
+## Verification Pipeline
 
-Blake3 is used throughout: hash chain links, entropy data digest, stack state
-digest, and the VM HASH opcode. Blake3 is chosen for speed in WASM,
-resistance to length-extension attacks, and a clean Rust API.
+Heartbeat verification occurs in `server/src/session.rs`.
 
----
+The current validation order is:
 
-## Stack Machine
+1. Load the session by `session_id`.
+2. Reject if the session is missing.
+3. Reject if `now > expires_at`.
+4. Verify the Ed25519 signature over the canonical payload.
+5. Decode and compare `prev_hash` with the stored `last_hash`.
+6. Compare request `mutation_step` with stored `pending_mutation_step`.
+7. Decode the stored gene environment.
+8. Apply the stored `pending_mutation` to a cloned server gene state.
+9. Compute the expected `gene_commitment` with session and step context.
+10. Compare the request `gene_commitment` with the expected commitment.
+11. Enforce timestamp drift bounds.
+12. Validate mouse entropy.
+13. Validate browser fingerprint fields.
+14. Compute the next hash-chain value.
+15. Generate the next mutation order.
+16. Generate the next salt.
+17. Persist the advanced session state.
 
-The server generates a random program on session init. The client executes it
-on every heartbeat and includes the resulting `StackState { stack, ip }` in
-the signed payload. This ensures each heartbeat carries unique, verifiable
-computation without additional round-trips.
+The verifier performs state mutation only after validation succeeds. This preserves replay resistance and avoids desynchronizing the server after invalid requests.
 
-### Instruction Set
+## Canonical Signing Boundary
 
-| Opcode | Mnemonic | Operand       | Stack effect | Description |
-|--------|----------|---------------|--------------|-------------|
-| `0x00` | PUSH     | u32 (4B LE)   | +1           | Push literal |
-| `0x01` | ADD      | —             | −1           | `a + b` wrapping |
-| `0x02` | SUB      | —             | −1           | `a - b` wrapping |
-| `0x03` | MUL      | —             | −1           | `a * b` wrapping |
-| `0x04` | XOR      | —             | −1           | `a ^ b` |
-| `0x05` | AND      | —             | −1           | `a & b` |
-| `0x06` | OR       | —             | −1           | `a \| b` |
-| `0x07` | ROT      | —             | −1           | `a.rotate_left(b % 32)` |
-| `0x08` | NOT      | —             | 0            | `!a` (unary) |
-| `0x09` | HASH     | —             | -(depth-1)   | Blake3 of all stack items → single u32 |
+The heartbeat signature covers a canonical JSON payload built from:
 
-The generator ensures ≥ 2 items on the stack before any binary opcode.
-NOT (0x08) does not change depth. HASH resets depth to 1.
+- `entropyData`
+- `fingerprint`
+- `geneCommitment`
+- `mutationStep`
+- `prevHash`
+- `sessionId`
+- `stackState`
+- `timestamp`
 
----
+The server constructs this payload using a `BTreeMap`, which orders top-level keys deterministically before serializing. The transport request uses snake_case field names, while the signed payload uses camelCase names that match the browser-side canonical message.
 
-## Behavioral Validation
+The signature does not cover the `signature` field itself.
 
-### Mouse Entropy
+## Hash-Chain Boundary
 
-Every heartbeat includes the mouse events collected since the previous
-heartbeat. Server checks:
+Each accepted heartbeat advances a Blake3 hash chain.
 
-| Check | Threshold |
-|---|---|
-| Minimum event count | ≥ 3 |
-| Minimum cumulative distance | ≥ 10 px |
-| Maximum average speed | ≤ 2.0 px/ms (distance / elapsed ms) |
-| Minimum pause count | ≥ 1 (movement < 0.2 px over > 50 ms) |
+Inputs include:
 
-### Browser Fingerprint
+- previous hash-chain head
+- heartbeat timestamp
+- entropy data
+- VM stack state
+- current server salt
 
-| Signal | Valid range |
-|---|---|
-| `aspectRatio` (width / height) | 0.5 – 3.0 |
-| `devicePixelRatio` | 0 < dpr ≤ 5.0 |
-| `hardwareConcurrency` | ≥ 1 |
+The server stores only the current accepted head as `last_hash`. A replayed heartbeat with an old `prev_hash` fails because the stored `last_hash` has already advanced.
 
----
+The salt rotates after every accepted heartbeat. The next salt is returned only on acceptance, so rejected clients do not receive the material needed for the next valid chain step.
 
-## Rate Limiting
+## Synthetic Gene Mutation Engine
 
-Token bucket per `session_id`: 5 requests / 10-second window.
-Stale entries evicted every 60 seconds by the cleanup task.
-Rate-limited responses are indistinguishable from validation failures.
+The Synthetic Gene Mutation Engine provides an additional deterministic continuity check.
 
----
+Core concepts:
 
-## SQLite Schema
+- `GeneState`: committed gene byte buffer plus environment records.
+- `MutationOrder`: mutation step plus encoded mutation program.
+- `pending_mutation`: the server-authored program expected on the next heartbeat.
+- `gene_commitment`: context-bound commitment over the candidate gene state, `session_id`, and `mutation_step`.
 
-```sql
-CREATE TABLE IF NOT EXISTS sessions (
-    session_id    TEXT     PRIMARY KEY,
-    public_key    BLOB     NOT NULL,   -- 32-byte Ed25519 verifying key
-    salt          BLOB     NOT NULL,   -- 16-byte current salt
-    last_hash     BLOB     NOT NULL,   -- 32-byte Blake3 chain head
-    chain_length  INTEGER  NOT NULL DEFAULT 1,
-    created_at    INTEGER  NOT NULL,   -- Unix ms
-    last_seen     INTEGER  NOT NULL,   -- Unix ms
-    expires_at    INTEGER  NOT NULL    -- Unix ms
-);
+The server and WASM runtime both execute the same mutation semantics from `shared/vm_extensions.rs`.
+
+Mutation lifecycle:
+
+1. Server stores a pending mutation program and step.
+2. Browser previews that mutation against its committed gene state.
+3. Browser sends the resulting `gene_commitment`.
+4. Server applies the same mutation to a clone of its committed gene state.
+5. Server compares the expected commitment with the browser commitment.
+6. On success, server commits the candidate state and issues the next mutation.
+7. Browser commits its preview only after receiving an accepted response.
+
+This design prevents a client from advancing mutation state independently of the server. The mutation order is server-authored, step-bound, and accepted only once.
+
+## Behavioral Trust Checks
+
+ChronoSeal includes lightweight behavioral checks. These checks are not a complete human verification system; they are an automation cost signal.
+
+Current checks include:
+
+- minimum mouse activity, when enabled
+- minimum total mouse movement distance
+- maximum average mouse speed
+- minimum pause count
+- timestamp drift bound
+- basic fingerprint field validation
+
+The checks are intentionally bounded and configurable. They should be treated as one layer in the attestation pipeline, not as the primary security primitive.
+
+## Storage Architecture
+
+Storage is abstracted by `DbPool`.
+
+| Backend | `db_type` | Characteristics |
+|---|---|---|
+| SQLite memory | `sqlite-in-memory` | default, process-local, ephemeral |
+| SQLite disk | `sqlite-in-disk` | persisted SQLite file at `db_path` |
+| Valkey | `valkey` | Valkey-compatible session store |
+
+The storage layer must support:
+
+- insert session
+- load session
+- update session
+- delete expired sessions
+- report statistics
+
+`valkey` mode reads `CHRONOSEAL_VALKEY_ADDR`, defaulting to `127.0.0.1:6666`. If connection setup fails, the current implementation logs a warning and falls back to in-memory SQLite.
+
+## Metrics and Observability
+
+ChronoSeal exposes two operational surfaces:
+
+- CLI commands: `status`, `health`, `metrics`, `stats`, `config check`
+- HTTP endpoints: `/health`, `/metrics`, `/stats`
+
+The metrics endpoint reports storage-derived counters including:
+
+- active sessions
+- expired sessions
+- maximum observed chain length
+
+The daemon uses structured tracing and can log to journald through normal systemd operation. Operators should avoid debug logging in production because internal identifiers may appear in logs.
+
+## Trust Boundaries
+
+### Browser Boundary
+
+The browser is untrusted. It may lie about entropy, fingerprint values, VM output, mutation commitment, timing, and session identifiers.
+
+Mitigation:
+
+- signature verification binds payloads to the browser session key
+- hash-chain checks reject stale state
+- mutation commitment checks reject incorrect gene progression
+- timing and behavioral checks reject implausible requests
+
+### WASM Boundary
+
+WASM code runs in the browser and is therefore not trusted as secure enclave code.
+
+Mitigation:
+
+- the server independently recomputes critical deterministic state
+- private key custody raises automation cost but is not treated as hardware-backed secrecy
+- failures do not reveal detailed reasons to callers
+
+### Storage Boundary
+
+Storage is trusted for session continuity. If storage is lost, sessions cannot continue. If storage is tampered with, attestation integrity can be affected.
+
+Mitigation:
+
+- use proper filesystem permissions for SQLite disk mode
+- deploy Valkey on a trusted network or protected socket
+- keep ChronoSeal behind normal host and service hardening
+
+### Network Boundary
+
+ChronoSeal expects production traffic to be protected by TLS. Plaintext deployment weakens confidentiality and makes traffic analysis easier.
+
+Mitigation:
+
+- terminate TLS at a reverse proxy or load balancer
+- keep `/init` and `/hb` same-origin with protected content when possible
+- avoid exposing internal metrics broadly
+
+## Failure Semantics
+
+ChronoSeal intentionally separates transport success from attestation success.
+
+| Failure class | HTTP behavior | State mutation |
+|---|---|---|
+| malformed route-level request | normal HTTP error handling | no session advancement |
+| invalid heartbeat semantics | `200 OK` with `{"status":"ok"}` | no session advancement |
+| rejected heartbeat | `200 OK` with `{"status":"ok"}` | no session advancement |
+| accepted heartbeat | `200 OK` with next-state fields | session state advances from the verifier's perspective |
+
+This ambiguity reduces attacker feedback. Application integrations must check for the presence of `next_salt`, `next_mutation_step`, and `next_mutation_order_b64` rather than treating any `status: ok` as an accepted heartbeat.
+
+## Invariants
+
+The architecture relies on these invariants:
+
+- A session has exactly one expected `pending_mutation_step` at a time.
+- A pending mutation is consumed only by an accepted heartbeat.
+- `last_hash` changes only after a heartbeat passes verification.
+- `salt` changes only after a heartbeat passes verification.
+- `gene` and `environment` change only after mutation commitment validation succeeds.
+- The next mutation order is generated only from an accepted candidate state.
+- Rejected heartbeats do not reveal the failed validation stage.
+- Browser-side preview state is committed only after an accepted heartbeat response.
+
+Breaking these invariants can introduce replay acceptance, client/server desynchronization, or oracle behavior.
+
+## Concurrency Notes
+
+ChronoSeal currently verifies a heartbeat by loading a session, computing candidate state, and writing the updated record back to storage. The intended operational model is one live heartbeat stream per browser session.
+
+Concurrent heartbeats for the same `session_id` should naturally collapse to at most one accepted progression because both requests present the same `prev_hash` and `mutation_step`; after the first accepted update, the second request becomes stale. Storage backends must preserve update visibility strongly enough for this assumption to hold.
+
+## Deployment Shape
+
+Typical production topology:
+
+```text
+Internet
+   |
+   v
+TLS reverse proxy
+   |
+   v
+chronoseal daemon on 127.0.0.1:3000
+   |
+   v
+SQLite disk or Valkey storage
 ```
 
-In-memory SQLite — all sessions lost on server restart by design.
-Clients re-initialise transparently on the next page load.
+Recommended deployment properties:
 
----
+- run under systemd with a dedicated service user
+- bind to localhost behind a reverse proxy unless direct exposure is required
+- serve over HTTPS
+- keep debug logs disabled
+- monitor `/health`, `/metrics`, and `/stats`
+- use `sqlite-in-memory` for ephemeral local sessions
+- use `sqlite-in-disk` or `valkey` when sessions must survive process restarts
 
-## Threat Model
+## Limitations
 
-### In Scope
+ChronoSeal is not:
 
-| Threat | Mitigation |
-|---|---|
-| Playwright / Puppeteer / Selenium | Mouse entropy + behavioral validation |
-| Puppeteer Stealth, undetected-chromedriver | Signature over VM execution state |
-| Heartbeat replay | Hash chain + ±30s timestamp window |
-| Signature forgery | Private key isolated in WASM memory |
-| Parallel session sharing | Each session bound to a unique keypair |
-| Brute-forced session IDs | 256-bit random entropy |
-| Flooding with fake session IDs | Rate limiter + periodic HashMap eviction |
-| Traffic analysis | Uniform `{"status":"ok"}` on all failure paths |
+- a user authentication system
+- a CAPTCHA
+- a fraud scoring engine
+- a hardware attestation system
+- a persistent identity framework
+- a complete defense against fully resourced browser farms
 
-### Out of Scope
+It is a protocol layer that makes browser automation and replay more expensive by requiring correct, continuous, stateful execution.
 
-| Threat | Reason |
-|---|---|
-| Real browser with real human input | Indistinguishable from a legitimate user |
-| WASM reverse engineering | Obfuscation is not a security primitive |
-| Server-side compromise | Outside the scope of client attestation |
+## Related Documents
 
-ChronoSeal raises cost and complexity of automated access. It is not a
-cryptographic proof of humanity and does not claim to be.
-
----
-
-## Module Reference
-
-| Path | Purpose |
-|---|---|
-| `shared/src/protocol.rs` | Shared types: `InitRequest`, `HeartbeatRequest`, `StackState`, … |
-| `shared/src/hashing.rs` | `initial_hash`, `next_chain_hash`, `hash_stack` |
-| `shared/src/constants.rs` | All tunable parameters |
-| `server/src/routes/init.rs` | `POST /init` handler |
-| `server/src/routes/heartbeat.rs` | `POST /hb` handler |
-| `server/src/session.rs` | `create_session`, `verify_heartbeat` |
-| `server/src/crypto.rs` | `verify_signature` — BTreeMap canonical JSON |
-| `server/src/trust.rs` | `validate_mouse` — speed, distance, pauses |
-| `server/src/fingerprint.rs` | `validate` — aspect ratio, DPR, HW concurrency |
-| `server/src/vm.rs` | `generate_random_program` |
-| `server/src/ratelimit.rs` | `RateLimiter::check`, `evict_stale` |
-| `server/src/cleanup.rs` | Background loop: expire sessions + evict rate limiter |
-| `server/src/storage.rs` | SQLite init, `current_time_ms` |
-| `wasm/src/crypto.rs` | `generate_keypair`, `sign_message`, `compute_next_hash` |
-| `wasm/src/vm.rs` | `run_program` — stack machine executor |
-| `frontend/heartbeat.js` | Session init, heartbeat loop, chain advancement |
-| `frontend/entropy.js` | Mouse event ring buffer, `collectEntropy` |
-| `frontend/transport.js` | `sendRequest` fetch wrapper |
+- [API Reference](API.md)
+- [Deployment Guide](DEPLOYMENT.md)
+- [Threat Model](THREAT_MODEL.md)
+- [WASM Build Guide](WASM_BUILD.md)
+- [Design Philosophy](DESIGN-PHILOSOPHY.md)
+- [Privacy Policy](PRIVACY%20POLICY.md)

docs/COMPARISON.md

@@ -0,0 +1,120 @@
+# ChronoSeal vs Popular Anti-Bot Systems (2026)
+
+ChronoSeal is a **self-hosted, cryptographic attestation daemon**. This document compares it honestly with leading commercial solutions.
+
+## Quick Comparison
+
+| Solution                    | Type              | Core Method                          | Privacy | Self-Hosted | Crypto Strength | Behavioral Analysis | Cost          | Best For                     |
+|----------------------------|-------------------|--------------------------------------|---------|-------------|-----------------|---------------------|---------------|------------------------------|
+| **ChronoSeal**             | Self-hosted Daemon| Ed25519 + Blake3 + **Gene Mutation** | Excellent | Yes        | Very High       | Light + Tunable     | Free          | Privacy + Control            |
+| Cloudflare Bot Management  | Cloud Edge        | JS Challenges + ML Fingerprinting    | Medium  | No         | Medium          | Strong              | Freemium      | Easy mass protection         |
+| Akamai Bot Manager         | Enterprise Edge   | Behavioral + Device Fingerprinting   | Low     | Hybrid     | Medium          | Very Strong         | Very High     | Large enterprises            |
+| HUMAN (PerimeterX)         | Cloud SaaS        | Behavioral Biometrics + ML           | Low     | No         | Medium          | Very Strong         | Enterprise    | Sophisticated bot defense    |
+| DataDome                   | Cloud SaaS        | Real-time ML + Behavioral            | Medium  | No         | Medium          | Strong              | Enterprise    | E-commerce scraping          |
+| reCAPTCHA v3               | Google Service    | Risk scoring + invisible challenges  | Poor    | No         | Low             | Medium              | Free → Paid   | Simple bot filtering         |
+| Kasada                     | Cloud SaaS        | Proof-of-Work + Behavioral           | Medium  | No         | High            | Strong              | Enterprise    | Advanced automation          |
+
+## Detailed Analysis
+
+### 1. ChronoSeal (v0.6.0)
+
+**Strengths:**
+- Strongest **cryptographic foundation** (Ed25519 signatures + Blake3 hash chain + Synthetic Gene Mutation Engine)
+- Fully **deterministic** server ↔ WASM parity
+- Completely **invisible** to users with silent rejection
+- Excellent **privacy** — no third-party tracking or fingerprint databases
+- Highly **tunable** mutation strength (`gene_size` + `mutation_rounds`)
+- Full control and auditability
+
+**Weaknesses:**
+- Requires self-hosting and maintenance
+- No global threat intelligence network like Cloudflare
+
+---
+
+### 2. Cloudflare Bot Management
+
+**Strengths:**
+- Extremely easy to deploy
+- Excellent scale and global threat intelligence
+- Good detection rates
+
+**Weaknesses vs ChronoSeal:**
+- Relies heavily on fingerprinting and JS challenges
+- Sends data to Cloudflare (privacy impact)
+- Less transparent and auditable
+- Vendor lock-in
+
+**Winner:** ChronoSeal for privacy-conscious teams
+
+---
+
+### 3. Enterprise Solutions (Akamai, HUMAN, DataDome, Kasada)
+
+**Strengths:**
+- Sophisticated ML + behavioral analysis
+- Large threat intelligence databases
+- Professional support
+
+**Weaknesses vs ChronoSeal:**
+- Extremely expensive
+- Black-box systems (limited visibility)
+- Heavy data collection (privacy concerns)
+- Vendor dependency
+
+**Winner:** ChronoSeal for teams wanting transparency and control
+
+---
+
+### 4. reCAPTCHA v3
+
+**Strengths:**
+- Free tier available
+- Easy integration
+
+**Weaknesses:**
+- Heavy Google tracking
+- Increasingly bypassed
+- Poor privacy
+
+**Winner:** ChronoSeal by a large margin
+
+---
+
+## When to Choose ChronoSeal
+
+**Choose ChronoSeal if you want:**
+
+- Maximum privacy
+- Strong cryptographic guarantees
+- Full control over your infrastructure
+- Tunable defense strength
+- No third-party data sharing
+- Open source transparency
+
+**Choose Commercial Solutions if you want:**
+
+- Zero maintenance
+- Massive global threat intelligence
+- Enterprise support & SLAs
+- Quick deployment at huge scale
+
+## Technical Differentiation
+
+ChronoSeal’s unique advantage is the **Synthetic Gene Mutation Engine** — a deterministic, server-controlled mutation sequence that both server and browser WASM must execute in sync. This creates a second synchronized state channel that is extremely difficult for automation to maintain at scale.
+
+No commercial solution currently offers equivalent cryptographic + mutation-based attestation in a self-hosted package.
+
+---
+
+## Conclusion
+
+**ChronoSeal** is currently one of the strongest **open-source/self-hosted** anti-bot solutions available. It trades ease-of-use and global scale for **privacy, transparency, cryptographic strength, and control**.
+
+It is particularly well-suited for:
+- Privacy-focused organizations
+- High-value content platforms
+- Teams that want to avoid vendor lock-in
+- Developers who value auditability
+
+---

docs/DEPLOYMENT.md

@@ -1,205 +1,244 @@
-# ChronoSeal — Deployment Guide
+# ChronoSeal Deployment Guide
 
-## Prerequisites
+ChronoSeal is intended to run as a small Unix daemon behind TLS, with static browser assets served either by the daemon or by the same protected origin. This guide covers native, service, and container deployment.
 
-| Tool | Minimum version | Purpose |
-|---|---|---|
-| Rust | 1.87 stable | Server + WASM compilation |
-| wasm-pack | 0.13 | WASM build and packaging |
-| Docker + Compose | 24 / 2.x | Container deployment |
-| nginx / NPM / HAProxy | any | TLS termination, reverse proxy |
+## Deployment Model
 
-Install Rust: https://rustup.rs  
-Install wasm-pack: `cargo install wasm-pack`
+Typical production topology:
 
----
+```text
+Internet
+   |
+   v
+TLS reverse proxy
+   |
+   v
+chronoseal daemon on 127.0.0.1:3000
+   |
+   v
+sqlite-in-disk or valkey storage
+```
+
+For local evaluation, the daemon can bind directly to `0.0.0.0:3000` or `127.0.0.1:3000`.
+
+## Requirements
+
+| Tool | Minimum | Purpose |
+|---|---:|---|
+| Rust | 1.87 stable | Build server and shared crates |
+| `wasm32-unknown-unknown` target | current stable | Compile WASM runtime |
+| `wasm-pack` | 0.13 | Generate browser WASM package |
+| systemd | 248+ | Native service management |
+| Docker | 24.x | Optional container image |
+| Docker Compose | 2.x | Optional local orchestration |
+
+Install Rust from rustup, then install the WASM tooling:
+
+```bash
+rustup target add wasm32-unknown-unknown
+cargo install wasm-pack
+```
 
 ## Build
 
-### 1. Build the WASM module
-
-```bash
-wasm-pack build wasm --target web --release
-mv wasm/pkg frontend/pkg
-```
-
-This produces `frontend/pkg/antibot_wasm.js` and `frontend/pkg/antibot_wasm_bg.wasm`,
-which are loaded by `frontend/main.js` at runtime.
-
-### 2. Build the server
-
-```bash
-cargo build -p server --release
-```
-
-Binary output: `target/release/server`
-
-### 3. Build both (convenience script)
+Use the repository build script:
 
 ```bash
 bash scripts/build.sh
 ```
 
----
+The script:
 
-## Running
+1. Builds `wasm/` with `wasm-pack build --target web --release`.
+2. Replaces `frontend/pkg` with the generated package.
+3. Builds the release daemon binary.
 
-### Development
+Manual equivalent:
 
 ```bash
-bash scripts/dev.sh
+wasm-pack build wasm --target web --release
+rm -rf frontend/pkg
+mv wasm/pkg frontend/pkg
+
+cargo build -p chronoseal-server --bin chronoseal --release
 ```
 
-Runs the server with `cargo run --release`. The server serves the `frontend/`
-directory statically at `/` via tower-http `ServeDir`.
+Release binary:
 
-Open `http://localhost:3000` in a browser. Open DevTools console — heartbeats
-should appear every 12–25 seconds. No visible UI is rendered; the protection
-is entirely silent.
+```text
+target/release/chronoseal
+```
 
-### Production (native binary)
+## Native Install
+
+The installer builds, installs, enables, and starts the service:
 
 ```bash
-cargo build -p server --release
-sudo cp target/release/server /usr/local/bin/chronoseal
+sudo bash scripts/install.sh
 ```
 
-Set environment variables before running:
+Installer actions:
 
-```bash
-export RUST_LOG=info      # or warn for quieter output
-chronoseal
-```
+- create the `chronoseal` system user if missing
+- build WASM and server artifacts
+- install `target/release/chronoseal` to `/usr/local/bin/chronoseal`
+- copy `frontend/` to `/opt/chronoseal/frontend`
+- install `chronoseal.service` to `/etc/systemd/system/chronoseal.service`
+- reload systemd
+- enable and start the service
 
-The server binds to `0.0.0.0:3000` by default. Place behind a reverse proxy
-for TLS — do not expose port 3000 directly.
-
----
-
-## systemd
-
-### Service file
-
-The provided `chronoseal.service` includes hardened systemd sandboxing:
-
-```
-NoNewPrivileges=true
-PrivateTmp=true
-ProtectSystem=strict
-ProtectHome=true
-ProtectKernelTunables=true
-ProtectKernelModules=true
-ProtectControlGroups=true
-MemoryDenyWriteExecute=true
-RestrictRealtime=true
-RestrictSUIDSGID=true
-LockPersonality=true
-SystemCallArchitectures=native
-```
-
-### Install
-
-```bash
-# Create a dedicated system user
-sudo useradd --system --no-create-home --shell /usr/sbin/nologin chronoseal
-
-# Install binary and frontend
-sudo cp target/release/server /usr/local/bin/chronoseal
-sudo mkdir -p /opt/chronoseal/frontend
-sudo cp -r frontend/ /opt/chronoseal/frontend/
-sudo chown -R chronoseal:chronoseal /opt/chronoseal
-
-# Install and enable service
-sudo cp chronoseal.service /etc/systemd/system/
-sudo systemctl daemon-reload
-sudo systemctl enable --now chronoseal
-```
-
-### Verify
+Verify:
 
 ```bash
 sudo systemctl status chronoseal
-journalctl -u chronoseal -f
+chronoseal status --format json
+chronoseal health
+sudo journalctl -u chronoseal -f
 ```
 
----
+## Running Without Install
 
-## Docker
-
-### Build and run
+For local development:
 
 ```bash
-docker compose up -d --build
+bash scripts/build.sh
+cargo run -p chronoseal-server --bin chronoseal -- run \
+  --bind 127.0.0.1:3000 \
+  --frontend-dir frontend
 ```
 
-### docker-compose.yml overview
-
-```yaml
-services:
-  chronoseal:
-    build: .
-    restart: unless-stopped
-    ports:
-      - "3000:3000"
-    environment:
-      RUST_LOG: info
-    tmpfs:
-      - /tmp
-```
-
-The `tmpfs` mount ensures the in-memory SQLite database is never written to
-disk, even if Docker's storage driver were to flush the container filesystem.
-
-### Dockerfile stages
-
-The Dockerfile uses a two-stage build:
-
-1. `rust:1.87-bookworm` — compiles the server binary
-2. `debian:bookworm-slim` — minimal runtime image with only `ca-certificates`
-
-The WASM module and frontend must be built separately (wasm-pack requires a
-browser toolchain not present in the server image) and mounted or copied into
-the container at `/opt/chronoseal/frontend/`.
+Probe the daemon:
 
 ```bash
-# Build WASM first
-wasm-pack build wasm --target web --release
-mv wasm/pkg frontend/pkg
-
-# Then build and run the container
-docker compose up -d --build
+curl http://127.0.0.1:3000/health
+curl http://127.0.0.1:3000/stats
+curl http://127.0.0.1:3000/metrics
 ```
 
-Or mount the pre-built frontend as a volume:
+## Configuration
 
-```yaml
-volumes:
-  - ./frontend:/opt/chronoseal/frontend:ro
+ChronoSeal resolves configuration in this order:
+
+1. CLI flags
+2. `CHRONOSEAL_*` environment variables
+3. TOML config file
+4. built-in defaults
+
+Default config discovery:
+
+1. `CHRONOSEAL_CONFIG`, if it points to an existing file
+2. `/etc/chronoseal/config.toml`
+3. `$XDG_CONFIG_HOME/chronoseal/config.toml`
+4. `~/.config/chronoseal/config.toml`
+
+Validate effective configuration:
+
+```bash
+chronoseal config check --format yaml
 ```
 
----
+Example:
 
-## Reverse Proxy
+```toml
+bind = "127.0.0.1:3000"
+db_type = "sqlite-in-disk"
+pid_file = "/run/chronoseal.pid"
+db_path = "/var/lib/chronoseal/chronoseal.sqlite"
+frontend_dir = "/usr/share/chronoseal/frontend"
+log_file = "/var/log/chronoseal/chronoseal.jsonl"
 
-ChronoSeal must be served over HTTPS. The heartbeat payload contains a
-timestamp; if traffic is observable in plaintext, timing attacks become
-easier. TLS 1.3 is strongly recommended.
+heartbeat_min_interval_ms = 12000
+heartbeat_max_interval_ms = 25000
+expiration_minutes = 30
+rate_limit_count = 5
+rate_limit_window_secs = 10
+max_timestamp_drift_ms = 30000
 
-### nginx
+min_mouse_total_dist = 10.0
+max_mouse_avg_speed = 2.0
+min_pause_count = 1
+require_mouse_activity = true
+
+gene_size = 512
+mutation_rounds = 4
+```
+
+## Storage Backends
+
+| Backend | `db_type` | Use case |
+|---|---|---|
+| SQLite memory | `sqlite-in-memory` | ephemeral local or stateless deployment |
+| SQLite disk | `sqlite-in-disk` | persisted session continuity across restarts |
+| Valkey | `valkey` | external session storage |
+
+For disk persistence:
+
+```bash
+sudo mkdir -p /var/lib/chronoseal
+sudo chown -R chronoseal:chronoseal /var/lib/chronoseal
+```
+
+For Valkey:
+
+```bash
+export CHRONOSEAL_DB_TYPE=valkey
+export CHRONOSEAL_VALKEY_ADDR=127.0.0.1:6666
+```
+
+If Valkey connection setup fails, the current implementation logs a warning and falls back to in-memory SQLite.
+
+## systemd
+
+The supplied service file is intended as the baseline unit. Keep the daemon under a dedicated user and restrict filesystem access to the paths it needs.
+
+Useful commands:
+
+```bash
+sudo systemctl daemon-reload
+sudo systemctl enable --now chronoseal
+sudo systemctl restart chronoseal
+sudo systemctl status chronoseal
+sudo journalctl -u chronoseal -f
+```
+
+Recommended hardening properties include:
+
+- `NoNewPrivileges=true`
+- `PrivateTmp=true`
+- `ProtectSystem=strict`
+- `ProtectHome=true`
+- `ProtectKernelTunables=true`
+- `ProtectKernelModules=true`
+- `ProtectControlGroups=true`
+- `MemoryDenyWriteExecute=true`
+- `RestrictRealtime=true`
+- `RestrictSUIDSGID=true`
+- `SystemCallArchitectures=native`
+
+Any hardening must still allow access to:
+
+- the binary
+- frontend assets
+- PID file directory
+- optional log file directory
+- SQLite database directory, if using `sqlite-in-disk`
+
+## Reverse Proxy and TLS
+
+ChronoSeal should be served over HTTPS in production. Terminate TLS at a reverse proxy or load balancer and proxy to the local daemon.
+
+Minimal nginx example:
 
 ```nginx
 server {
     listen 443 ssl http2;
-    server_name your.domain.com;
+    server_name example.com;
 
-    ssl_certificate     /etc/letsencrypt/live/your.domain.com/fullchain.pem;
-    ssl_certificate_key /etc/letsencrypt/live/your.domain.com/privkey.pem;
-    ssl_protocols       TLSv1.3;
-    ssl_ciphers         ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384;
+    ssl_certificate     /etc/letsencrypt/live/example.com/fullchain.pem;
+    ssl_certificate_key /etc/letsencrypt/live/example.com/privkey.pem;
 
-    # Tight timeouts — heartbeat interval is 12–25s
-    proxy_read_timeout  35s;
-    proxy_send_timeout  10s;
+    proxy_read_timeout 35s;
+    proxy_send_timeout 10s;
 
     location / {
         proxy_pass         http://127.0.0.1:3000;
@@ -213,134 +252,79 @@ server {
 
 server {
     listen 80;
-    server_name your.domain.com;
+    server_name example.com;
     return 301 https://$host$request_uri;
 }
 ```
 
-### Nginx Proxy Manager
+Keep `/init`, `/hb`, and frontend assets on the same origin when possible. If you split origins, configure CORS and cookie/application policy deliberately.
 
-1. Add a new Proxy Host pointing to `http://chronoseal:3000`
-2. Enable SSL, Request Let's Encrypt certificate
-3. Enable HTTP/2, Force SSL
-4. Under Advanced, add:
-   ```
-   proxy_read_timeout 35s;
-   proxy_send_timeout 10s;
-   ```
+## Docker
 
-### HAProxy
+Build and run:
 
-```haproxy
-frontend https_front
-    bind *:443 ssl crt /etc/haproxy/certs/your.domain.pem alpn h2,http/1.1
-    default_backend chronoseal_back
-
-backend chronoseal_back
-    server chronoseal 127.0.0.1:3000 check
-    timeout connect 5s
-    timeout server  35s
+```bash
+bash scripts/build.sh
+docker compose up -d --build
 ```
 
----
+The Compose file exposes port `3000`.
 
-## Integration into an Existing Site
-
-ChronoSeal is designed to run as a sidecar — its `/init` and `/hb` endpoints
-can be proxied from any existing web server. The frontend assets (`pkg/`) need
-to be served from the same origin as the protected page (or CORS must be
-configured).
-
-### Option A — Serve everything from ChronoSeal
-
-ChronoSeal serves `frontend/` statically. Put your protected HTML inside
-`frontend/` and let ChronoSeal serve it directly.
-
-### Option B — Proxy only the API endpoints
-
-Keep your existing server. Proxy `/init` and `/hb` to ChronoSeal, and serve
-the WASM and JS assets from your CDN or existing static file server.
-
-```nginx
-# On your existing server:
-location ~ ^/(init|hb)$ {
-    proxy_pass http://127.0.0.1:3000;
-}
+```bash
+curl http://127.0.0.1:3000/health
 ```
 
-Add to your protected pages:
-
-```html
-<script type="module" src="/pkg/antibot_wasm.js"></script>
-<script type="module" src="/main.js"></script>
-```
-
----
-
-## Configuration
-
-All parameters are in `shared/src/constants.rs`. Recompile after changes.
-
-| Constant | Default | Notes |
-|---|---|---|
-| `SESSION_ID_LEN` | 32 bytes | 256-bit entropy — do not reduce |
-| `SALT_LEN` | 16 bytes | Per-heartbeat salt |
-| `HEARTBEAT_MIN_INTERVAL_MS` | 12 000 ms | Increase to reduce server load |
-| `HEARTBEAT_MAX_INTERVAL_MS` | 25 000 ms | Jitter upper bound |
-| `EXPIRATION_MINUTES` | 30 min | Session TTL after last heartbeat |
-| `RATE_LIMIT_COUNT` | 5 | Max heartbeats per window per session |
-| `RATE_LIMIT_WINDOW_SECS` | 10 s | Rate limit window |
-| `MAX_TIMESTAMP_DRIFT_MS` | 30 000 ms | Anti-replay window; account for NTP skew |
-| `MIN_MOUSE_TOTAL_DIST` | 10.0 px | Lower for low-activity pages |
-| `MAX_MOUSE_AVG_SPEED` | 2.0 px/ms | Raise if legitimate users are rejected |
-| `MIN_PAUSE_COUNT` | 1 | Minimum natural pause events |
-
----
+The Dockerfile copies `frontend/` from the working tree. Build `frontend/pkg` before building the image when the browser WASM runtime is required inside the container.
 
 ## Observability
 
-ChronoSeal uses `tracing` with `tracing-subscriber`. Log levels:
-
-| Level | Events |
-|---|---|
-| `INFO` | Server start, request method + path + status |
-| `WARN` | Heartbeat validation failures (with session ID and reason) |
-| `DEBUG` | Rate limit hits |
+CLI:
 
 ```bash
-RUST_LOG=info   chronoseal   # production
-RUST_LOG=debug  chronoseal   # development
-RUST_LOG=warn   chronoseal   # minimal output
+chronoseal status --format json
+chronoseal health
+chronoseal stats --format json
+chronoseal metrics
 ```
 
-Log format is plain text to stdout. Pipe to `journald`, `fluentd`, or any
-log aggregator via stdout capture.
-
----
-
-## Health Check
-
-The server has no dedicated `/health` endpoint. Use a TCP check on port 3000,
-or a lightweight HTTP check on `GET /` (which serves `index.html`).
+HTTP:
 
 ```bash
-# Docker health check (add to docker-compose.yml if needed)
-healthcheck:
-  test: ["CMD", "curl", "-sf", "http://localhost:3000/"]
-  interval: 30s
-  timeout: 5s
-  retries: 3
+curl http://127.0.0.1:3000/health
+curl http://127.0.0.1:3000/stats
+curl http://127.0.0.1:3000/metrics
 ```
 
----
+Prometheus metrics:
 
-## Security Checklist
+- `chronoseal_sessions`
+- `chronoseal_expired_sessions`
+- `chronoseal_max_chain_length`
 
-- [ ] TLS 1.3 enabled, TLS 1.0/1.1 disabled
-- [ ] HTTP/2 enabled
-- [ ] Port 3000 not exposed to the public internet (only via reverse proxy)
-- [ ] `RUST_LOG=warn` or `info` in production (not `debug` — session IDs appear in logs)
-- [ ] systemd service running as `chronoseal` user with hardened sandbox
-- [ ] `MemoryDenyWriteExecute=true` in service file (prevents JIT in process)
-- [ ] CORS `CorsLayer::permissive()` replaced with origin-restricted policy for production
-- [ ] Frontend assets served over the same HTTPS origin as protected pages
+## Logging
+
+Use info-level logs for production:
+
+```bash
+CHRONOSEAL_LOG=info chronoseal run
+```
+
+or with systemd:
+
+```bash
+sudo systemctl edit chronoseal
+```
+
+Avoid debug logging in production because internal identifiers may be written to logs.
+
+## Production Checklist
+
+- Build `frontend/pkg` before packaging.
+- Serve ChronoSeal traffic over HTTPS.
+- Bind the daemon to localhost behind a reverse proxy unless direct exposure is required.
+- Use a dedicated service user.
+- Keep debug logs disabled.
+- Choose storage intentionally: `sqlite-in-memory`, `sqlite-in-disk`, or `valkey`.
+- Protect SQLite and log directories with correct ownership.
+- Monitor `/health`, `/stats`, and `/metrics`.
+- Verify `chronoseal config check` after environment or config changes.

docs/DESIGN-PHILOSOPHY.md

@@ -1,41 +1,125 @@
 # ChronoSeal Design Philosophy
 
-**"Everything is a File" — Unix-Native Software Design**
+ChronoSeal is designed for operators who want a local, inspectable, Unix-native browser attestation layer rather than a hosted anti-bot black box.
 
-ChronoSeal is intentionally built as a **first-class citizen of Linux**. The entire application is designed to behave like a well-engineered native file within the Unix filesystem.
+## Core Position
 
-### Why This Philosophy Matters
+ChronoSeal is infrastructure software. It should feel closer to `nginx`, `redis-server`, or a small system daemon than to a third-party analytics platform.
 
-ChronoSeal is designed so that administrators can operate, monitor, configure, and integrate it using the same reliable, transparent, and trusted tools and patterns they already use on Linux systems — without fighting the operating environment.
+Design priorities:
 
-### Core Principles
+- CLI-first operation
+- explicit configuration
+- deterministic protocol behavior
+- small runtime surface
+- privacy-preserving state
+- observable health and metrics
+- no hidden telemetry
+- no persistent user profiling
 
-- **Everything is a File**: The application must be controllable, inspectable, and composable through standard Unix interfaces (CLI, files, signals, pipes, and environment).
-- **CLI as Source of Truth**: All operations — starting, stopping, configuring, monitoring, and debugging — must be possible from the command line with excellent discoverability.
-- **Behave Like a Native File**: Predictable lifecycle management through commands, signals (`SIGHUP`, `SIGTERM`, `SIGUSR1`), logs, configuration files, and standard process semantics.
-- **Composability**: Must work naturally with pipes, redirection, scripts, systemd, Ansible, Docker, and orchestration tools.
-- **Observability by Default**: All important state and metrics should be accessible as text or structured data.
-- **Minimal Friction, Maximum Durability**: One-line installer, world-class `--help`, proper man pages, and decades-long maintainability are non-negotiable.
-- **Respect for the OS**: Follows Linux Filesystem Hierarchy Standard (FHS), XDG Base Directory specification, and hardened systemd practices.
+## What ChronoSeal Optimizes For
 
-### Non-Goals
+### Operator Control
 
-ChronoSeal is **not** designed to be:
-- Cloud-first or vendor-specific
-- Browser-first or JavaScript-heavy
-- Dependency-heavy or framework-driven
-- GUI-centric (any graphical interface must be a thin wrapper)
-- Telemetry-oriented or privacy-invasive
-- Optimized for rapid prototyping at the cost of long-term reliability
+Operators should be able to build, run, inspect, configure, monitor, and stop the service with ordinary Unix tools.
 
-These non-goals help keep the project focused on stability, simplicity, security, and deep Unix integration.
+This is why ChronoSeal provides:
 
-### Development Mindset
+- `chronoseal run`
+- `chronoseal status`
+- `chronoseal health`
+- `chronoseal config check`
+- `chronoseal metrics`
+- `chronoseal stats`
+- shell completions
+- systemd integration
 
-- Production robustness, security, and long-term sustainability take clear precedence over development speed.
-- Every design decision is evaluated against one question:  
-  **“Does this make ChronoSeal feel like it naturally belongs in `/usr/bin/`?”**
+### Determinism
 
-This philosophy guided the complete refactoring of ChronoSeal and continues to drive all future development.
+The protocol depends on deterministic agreement between server Rust and browser WASM.
 
-**Status**: Core architecture and systemd integration completed. Rich CLI, runtime configuration system, and one-line installer are in active development.
+Shared logic belongs in `shared/` when divergence would create security or correctness risk. This includes:
+
+- protocol structs
+- hash-chain semantics
+- synthetic gene model
+- mutation opcode behavior
+- mutation order encoding
+
+### Cost Escalation
+
+ChronoSeal does not claim impossible security. It raises the cost of automation by making clients maintain:
+
+- a browser-local signing key
+- a signed canonical heartbeat payload
+- a Blake3 hash chain
+- VM execution output
+- server-issued mutation progression
+- plausible timing and interaction signals
+
+The objective is to make cheap automation brittle and expensive automation more complex.
+
+### Silent Rejection
+
+Heartbeat rejection is intentionally ambiguous. Invalid heartbeats receive the same `status` value as accepted heartbeats, but accepted responses include next-state fields.
+
+This avoids turning the API into a validation oracle. Integrators must check for `next_salt`, `next_mutation_step`, and `next_mutation_order_b64`.
+
+### Privacy
+
+ChronoSeal should not become a surveillance system.
+
+It avoids:
+
+- long-term user identifiers
+- browser history
+- cross-site identity graphs
+- fingerprint databases
+- behavioral profiling as a product feature
+
+It stores only the session state required for continuity.
+
+## Non-Goals
+
+ChronoSeal is not:
+
+- a CAPTCHA
+- a fraud scoring engine
+- an authentication provider
+- a hosted SaaS product
+- a persistent fingerprinting system
+- a replacement for authorization checks
+- a complete defense against real browser farms
+
+## Operational Assumptions
+
+ChronoSeal assumes:
+
+- Linux or a Unix-like host
+- systemd for production service management
+- TLS in production
+- browser clients can execute WASM
+- operators can manage config files and service users
+- application owners decide how attestation status gates protected resources
+
+## Engineering Biases
+
+When the project faces tradeoffs, prefer:
+
+- explicit configuration over implicit magic
+- server-side recomputation over browser trust
+- bounded deterministic execution over unbounded heuristics
+- clear CLI output over hidden dashboards
+- local deployment over mandatory cloud dependencies
+- privacy by data minimization over privacy by policy alone
+
+## Success Criteria
+
+ChronoSeal is succeeding when:
+
+- legitimate browser sessions advance without user friction
+- simple scrapers cannot pass the protocol
+- automation requires a full stateful implementation
+- operators can debug deployments with normal Unix tools
+- stored data remains minimal and short-lived
+- documentation reflects the implementation precisely

docs/PERFORMANCE-TUNING.md

@@ -0,0 +1,283 @@
+# ChronoSeal Performance Tuning Guide
+
+ChronoSeal uses a deterministic Synthetic Gene Mutation Engine to strengthen browser session continuity validation. This guide explains how to tune the mutation engine for an appropriate balance between security strength, resource consumption, and user experience.
+
+The primary tuning parameters are:
+
+* `gene_size` — size of the synthetic gene buffer
+* `mutation_rounds` — number of mutation iterations executed per heartbeat
+
+---
+
+## Understanding the Mutation Engine
+
+For every accepted heartbeat, ChronoSeal executes a server-generated mutation program against a synthetic gene buffer.
+
+Increasing mutation complexity raises the computational cost of reproducing valid session state while also increasing CPU utilization on both the server and browser runtime.
+
+General effects:
+
+* Larger `gene_size` increases mutation state complexity.
+* Higher `mutation_rounds` increase computational work per heartbeat.
+* Both increase memory access and CPU consumption.
+* Excessive values may negatively impact lower-end mobile devices.
+
+The optimal values depend on your threat model and expected client hardware.
+
+---
+
+## Recommended Configurations
+
+| Profile           | `gene_size` | `mutation_rounds` | Security Level   | Recommended Usage                |
+| ----------------- | ----------- | ----------------- | ---------------- | -------------------------------- |
+| Default           | 512         | 4                 | Moderate         | Development and testing          |
+| Recommended       | 2048        | 16                | Strong           | Most production deployments      |
+| High Security     | 4096        | 32                | Very Strong      | Sensitive applications           |
+| Maximum Practical | 8192        | 64                | Extremely Strong | High-value targets               |
+| Experimental      | 65536       | 65536             | Research Only    | Benchmarking and experimentation |
+
+### Recommended Production Configuration
+
+```toml
+gene_size = 2048
+mutation_rounds = 16
+```
+
+This configuration provides a strong balance between security and runtime overhead for most deployments.
+
+---
+
+## Configuration
+
+Edit your configuration file:
+
+```toml
+# Mutation Engine Settings
+
+gene_size = 2048
+mutation_rounds = 16
+```
+
+Common configuration locations:
+
+```text
+/etc/chronoseal/config.toml
+~/.config/chronoseal/config.toml
+```
+
+Restart ChronoSeal:
+
+```bash
+sudo systemctl restart chronoseal
+```
+
+Validate the effective configuration:
+
+```bash
+chronoseal config check --format yaml
+```
+
+---
+
+## Performance Monitoring
+
+### Server-Side Monitoring
+
+View service logs:
+
+```bash
+sudo journalctl -u chronoseal -f
+```
+
+Inspect runtime statistics:
+
+```bash
+chronoseal stats --format json
+```
+
+Enable additional diagnostics when required:
+
+```bash
+CHRONOSEAL_LOG=debug chronoseal run
+```
+
+Avoid debug logging in production environments.
+
+---
+
+### Browser-Side Monitoring
+
+Measure mutation execution time:
+
+```javascript
+console.time("gene-mutation");
+
+const commitment = preview_gene_commitment(
+    order_b64,
+    session_id,
+    mutation_step,
+    mutation_rounds
+);
+
+console.timeEnd("gene-mutation");
+```
+
+Browser developer tools can also be used to monitor:
+
+* JavaScript execution time
+* WASM execution time
+* CPU utilization
+* Memory consumption
+
+---
+
+## Tuning Strategy
+
+### Step 1: Start with Recommended Values
+
+```toml
+gene_size = 2048
+mutation_rounds = 16
+```
+
+Deploy and observe normal usage patterns.
+
+### Step 2: Monitor Heartbeat Success Rates
+
+Watch for:
+
+* heartbeat failures
+* increased browser CPU usage
+* elevated mobile device latency
+* increased battery consumption
+
+### Step 3: Increase Gradually
+
+Increase one parameter at a time.
+
+Recommended progression:
+
+```text
+2048 / 16
+4096 / 16
+4096 / 32
+8192 / 32
+8192 / 64
+```
+
+This makes it easier to identify performance bottlenecks.
+
+### Step 4: Test Mobile Devices
+
+Always test on:
+
+* Android devices
+* iPhones
+* older laptops
+* low-power CPUs
+
+Desktop-only validation can be misleading.
+
+---
+
+## Advanced Deployment Strategies
+
+### Risk-Based Mutation Strength
+
+Future deployments may choose to dynamically increase mutation strength based on:
+
+* session age
+* failed heartbeat history
+* suspicious behavior signals
+* protected resource sensitivity
+
+Example policy:
+
+```text
+New session          → 2048 / 16
+Suspicious session   → 4096 / 32
+Elevated-risk action → 8192 / 64
+```
+
+---
+
+## Performance Recommendations
+
+### WASM Builds
+
+Always use optimized builds:
+
+```bash
+wasm-pack build wasm --target web --release
+```
+
+### General Guidance
+
+* Keep `mutation_rounds` below 64 for most deployments.
+* Prefer increasing `gene_size` before dramatically increasing rounds.
+* Benchmark on representative client hardware.
+* Monitor browser CPU utilization during load testing.
+* Re-evaluate settings after major algorithm changes.
+
+### Storage Performance
+
+For maximum throughput:
+
+```toml
+db_type = "sqlite-in-memory"
+```
+
+For persistence:
+
+```toml
+db_type = "sqlite-in-disk"
+```
+
+Choose based on operational requirements rather than mutation settings.
+
+---
+
+## Security Considerations
+
+Higher values increase the cost of reproducing valid session state but do not provide absolute protection against determined attackers.
+
+ChronoSeal remains a cost-raising attestation layer rather than a complete anti-abuse solution.
+
+Mutation tuning should be considered alongside:
+
+* heartbeat timing controls
+* signature validation
+* hash-chain continuity
+* behavioral trust checks
+* rate limiting
+* session expiration
+
+---
+
+## Recommended Starting Point
+
+For most production deployments:
+
+```toml
+gene_size = 2048
+mutation_rounds = 16
+```
+
+This configuration provides a strong balance between security, performance, and compatibility across desktop and mobile devices.
+
+---
+
+## Related Documentation
+
+* `docs/ARCHITECTURE.md`
+* `docs/API.md`
+* `docs/THREAT_MODEL.md`
+* `docs/REFRACTORING-v0.6.0.md`
+
+For diagnostics:
+
+```bash
+chronoseal config check
+chronoseal stats
+chronoseal health
+```

docs/PRIVACY POLICY.md

@@ -1,278 +1,106 @@
-# ChronoSeal Privacy & Design Principles
+# ChronoSeal Privacy Policy
 
-## Privacy-First Browser Attestation Framework
+ChronoSeal is a privacy-oriented browser attestation system. It is designed to validate short-lived session continuity without creating persistent user profiles.
 
-ChronoSeal is a lightweight, privacy-first browser attestation framework designed to resist:
+This document describes what ChronoSeal itself collects and stores. Applications that integrate ChronoSeal may collect additional data under their own policies.
 
-- automated bots
-- AI-driven browser automation
-- scripted abuse
-- browser surveillance ecosystems
+## Data ChronoSeal Processes
 
-Unlike conventional anti-bot systems, ChronoSeal is intentionally designed to operate **without collecting or storing client identity data**.
+ChronoSeal processes the minimum protocol data needed to validate a live browser session.
 
----
-
-# Core Philosophy
-
-ChronoSeal verifies:
-
-- session continuity
-- runtime coherence
-- cryptographic synchronization
-
-It does **not** verify:
-
-- personal identity
-- browsing history
-- behavioral profiles
-- long-term reputation
-
-The framework is built around one principle:
-
-> Verify live browser participation without turning users into telemetry.
-
----
-
-# Privacy-First By Architecture
-
-ChronoSeal is intentionally engineered to avoid becoming:
-
-- a tracking platform
-- a fingerprinting database
-- a telemetry pipeline
-- a surveillance system
-
-## ChronoSeal Does NOT Store
-
-- IP addresses
-- Browser history
-- Persistent fingerprints
-- User profiles
-- Behavioral telemetry
-- Tracking identifiers
-- Device databases
-- Long-term session history
-- Cross-site correlation data
-
-No client-side personal information is persisted.
-
----
-
-# Stateless Trust Model
-
-ChronoSeal focuses on:
-
-- ephemeral runtime verification
-- cryptographic continuity
-- synchronized challenge progression
-- live execution integrity
-
-The server only validates:
-
-- whether the current browser session behaves like a coherent participant *right now*
-
-ChronoSeal does not maintain:
-
-- user identity databases
-- reputation systems
-- persistent surveillance records
-
----
-
-# Anti-Bot Without Surveillance
-
-Most modern anti-bot systems rely heavily on:
-
-- fingerprinting
-- behavioral tracking
-- telemetry aggregation
-- centralized analytics
-
-ChronoSeal deliberately rejects this model.
-
-Instead, ChronoSeal uses:
-
-- synchronized cryptographic chains
-- WASM-isolated signing
-- protocol continuity
-- transient verification state
-
-This provides bot resistance while preserving user privacy.
-
----
-
-# Lightweight By Design
-
-ChronoSeal is intentionally engineered to remain:
-
-- compact
-- dependency-light
-- operationally simple
-- Unix-native
-
-## Current Footprint
-
-### Server Binary
-
-Compiled x86_64 Linux server binary:
-
-- ~8.4 MB
-
-### WASM Runtime
-
-`chronoseal_wasm_bg.wasm`
-
-- ~218 KB
-
-### Full WASM Package
-
-Entire generated WASM package:
-
-- ~720 KB
-
-Includes:
-
-- WASM runtime
-- JavaScript glue code
-- Type definitions
-
----
-
-# No Frontend Framework Dependency
-
-ChronoSeal does not depend on:
-
-- React
-- Angular
-- Vue
-- Electron
-- Node.js runtime
-- Browser bundler ecosystems
-
-The browser runtime uses:
-
-- native ES modules
-- direct WebAssembly loading
-- lightweight JavaScript glue
-
-This minimizes:
-
-- dependency complexity
-- supply-chain risk
-- build fragility
-- browser overhead
-
----
-
-# Clean Repository Philosophy
-
-ChronoSeal keeps generated artefacts out of version control.
-
-## What Is NOT Stored In The Repository
-
-| Path | Reason |
+| Data | Purpose |
 |---|---|
-| `wasm/pkg/` | Generated build output |
-| `frontend/pkg/` | Generated serve-time artefacts |
-| `target/` | Standard Rust build artefacts |
+| `session_id` | Opaque session lookup key |
+| public key | Verify signed heartbeats for the session |
+| `salt` | Hash-chain progression |
+| `initial_hash` / `prev_hash` / `last_hash` | Replay-resistant continuity |
+| `timestamp` | Drift and liveness validation |
+| mouse event samples | Behavioral plausibility checks |
+| VM stack state | Input to hash-chain progression |
+| basic fingerprint fields | Sanity validation |
+| gene bytes and environment records | Mutation continuity |
+| pending mutation program and step | Next heartbeat verification |
+| expiration and last-seen timestamps | Session lifecycle and cleanup |
 
-Generated binaries change frequently and are reproducible from source.
+Basic fingerprint fields currently include:
 
-The repository intentionally stores:
+- aspect ratio
+- device pixel ratio
+- hardware concurrency
 
-- source code
-- architecture
-- reproducible build logic only
+## Data ChronoSeal Does Not Intentionally Collect
 
----
+ChronoSeal does not intentionally collect or build:
 
-# Unix-Native Operational Model
+- browser history
+- page content history
+- account identity
+- email addresses
+- names
+- payment data
+- location history
+- cross-site tracking identifiers
+- persistent fingerprint databases
+- long-term behavioral profiles
 
-ChronoSeal is designed as:
+ChronoSeal is not intended for analytics, advertising, or identity graph construction.
 
-- infrastructure software
-- not browser-centric SaaS
+## Session Lifetime
 
-Core operational principles:
+Sessions are short-lived and expire according to `expiration_minutes`, which defaults to 30 minutes.
 
-- CLI-first operation
-- systemd-native deployment
-- structured logs
-- explicit configuration
-- inspectable runtime behavior
-- minimal hidden state
+Expired sessions are removed by cleanup behavior. In-memory storage is lost when the process exits.
 
-ChronoSeal should feel natural on Linux systems:
+## Storage Modes and Persistence
 
-- simple to deploy
-- easy to audit
-- understandable years later
+| Mode | Persistence |
+|---|---|
+| `sqlite-in-memory` | process lifetime only |
+| `sqlite-in-disk` | persisted to the configured SQLite file |
+| `valkey` | persisted according to the Valkey deployment configuration |
 
----
+Persistent state is operator-selected. The default backend is `sqlite-in-memory`.
 
-# Security Through Operational Asymmetry
+## Client-Side Key Handling
 
-ChronoSeal increases attacker cost through:
+The browser WASM runtime generates an Ed25519 keypair for the session.
 
-- synchronization burden
-- runtime continuity requirements
-- WASM-isolated cryptographic execution
-- chained session progression
+- The public key is sent to `/init`.
+- The private key is not sent to the server.
+- Heartbeat payloads are signed in the browser runtime.
 
-It does not attempt:
+This is a continuity mechanism, not a long-term identity mechanism.
 
-- invasive tracking
-- permanent identification
-- surveillance-driven scoring
+## Silent Rejection
 
----
+ChronoSeal returns the same basic heartbeat status for accepted and rejected heartbeat requests:
 
-# Design Goals
+```json
+{
+  "status": "ok"
+}
+```
 
-ChronoSeal prioritizes:
+Accepted responses additionally include next-state fields. Rejected responses omit them.
 
-- Privacy
-- Simplicity
-- Transparency
-- Operational clarity
-- Long-term maintainability
-- Minimalism
-- Unix-native behavior
-- Low deployment friction
+This reduces attacker feedback and avoids returning detailed failure classifications to clients.
 
----
+## Logs
 
-# Non-Goals
+Operators control logging through `CHRONOSEAL_LOG`, `RUST_LOG`, and optional log-file configuration.
 
-ChronoSeal is intentionally NOT:
+Production deployments should avoid debug logging because internal session identifiers or validation context may appear in logs.
 
-- A surveillance platform
-- A telemetry collection system
-- A browser fingerprinting database
-- An analytics engine
-- A cloud lock-in service
-- A JavaScript-heavy frontend platform
-- An advertising or tracking framework
+## Operator Responsibilities
 
----
+Operators should:
 
-# Summary
+- serve traffic over HTTPS
+- protect SQLite, Valkey, and log storage
+- restrict access to metrics and stats endpoints
+- choose persistence mode deliberately
+- disclose any application-level data collection separately
 
-ChronoSeal is designed to prove:
+## Summary
 
-> “A live browser session is coherently participating right now.”
-
-without storing:
-
-- who the user is
-- where they came from
-- what they previously did
-
-It is a lightweight, privacy-preserving, Unix-native browser attestation framework focused on:
-
-- anti-bot resistance
-- anti-automation
-- operational simplicity
-
-without compromising user privacy.
+ChronoSeal validates live session continuity using short-lived cryptographic and deterministic state. It is designed to raise automation cost without becoming a persistent tracking or profiling system.

docs/REFRACTORING-v0.6.0.md

@@ -0,0 +1,191 @@
+# ChronoSeal v0.6.0 Refactoring and System Upgrade
+
+ChronoSeal v0.6.0 changed the project from a lightweight heartbeat prototype into a Unix-native attestation daemon with shared server/WASM protocol logic, deterministic mutation parity, operational CLI commands, and pluggable storage modes.
+
+This document summarizes the architectural changes introduced in the v0.6.0 line.
+
+## Summary
+
+Major changes:
+
+- introduced the Synthetic Gene Mutation Engine
+- added server-side validation of `mutation_step` and `gene_commitment`
+- moved protocol and deterministic mutation logic into `shared/`
+- added `chronoseal-wasm` browser runtime support for mutation preview and commit
+- expanded persisted session state with gene and pending mutation fields
+- added storage modes: `sqlite-in-memory`, `sqlite-in-disk`, and `valkey`
+- added health, metrics, stats, config, status, completion, and version CLI surfaces
+- added PID file handling, structured logging, and graceful shutdown behavior
+- preserved silent heartbeat rejection semantics
+
+## Motivation
+
+The earlier model relied mainly on:
+
+- heartbeat timing
+- behavioral entropy
+- hash-chain continuity
+- signature verification
+
+v0.6.0 added a second deterministic state channel: a server-authored synthetic gene mutation sequence. This makes successful automation maintain both:
+
+- the cryptographic hash/signature chain
+- the synthetic mutation state expected by the server
+
+## Shared Crate Refactor
+
+`shared/` now owns the parts of the protocol that must remain identical across server and browser runtime:
+
+- request and response structs
+- hashing helpers
+- synthetic gene state
+- mutation environment encoding
+- mutation order generation and encoding
+- opcode execution semantics
+- protocol constants
+
+This reduces the risk of server/WASM drift.
+
+## Mutation Handshake
+
+New protocol fields:
+
+- `gene_size`
+- `mutation_step`
+- `mutation_order_b64`
+- `gene_commitment`
+- `next_mutation_step`
+- `next_mutation_order_b64`
+
+Lifecycle:
+
+1. `/init` returns mutation step 1 and a server-authored mutation order.
+2. The browser previews the mutation in WASM.
+3. The browser signs and submits the resulting `gene_commitment`.
+4. The server applies the same pending mutation to its committed state.
+5. The server compares commitments.
+6. On success, server commits the candidate state and issues the next mutation.
+7. The browser commits its preview only after receiving the accepted response.
+
+## Session Schema Changes
+
+The persisted session record now includes:
+
+- committed gene bytes
+- encoded environment records
+- pending mutation program
+- pending mutation step
+
+State advances only after a heartbeat is accepted. Rejected heartbeats do not rotate salt, update hash state, commit gene state, or consume the pending mutation.
+
+## WASM Runtime Changes
+
+The WASM crate now supports:
+
+- `generate_keypair()`
+- `get_public_key()`
+- `sign_message()`
+- `compute_next_hash()`
+- `run_program()`
+- `init_gene_state()`
+- `preview_gene_commitment(order_b64, session_id, mutation_step, rounds)`
+- `commit_gene_preview()`
+- `discard_gene_preview()`
+- `current_gene_commitment(session_id, mutation_step)`
+
+The generated package uses the `chronoseal_wasm` prefix.
+
+## Storage Refactor
+
+The storage layer is abstracted behind `DbPool`.
+
+Supported modes:
+
+| Mode | Behavior |
+|---|---|
+| `sqlite-in-memory` | default ephemeral in-process SQLite |
+| `sqlite-in-disk` | persisted SQLite database at `db_path` |
+| `valkey` | Valkey-compatible external store |
+
+The storage interface supports insert, load, update, delete expired sessions, and stats.
+
+## CLI and Runtime Changes
+
+The `chronoseal` binary now provides:
+
+- `run`
+- `status`
+- `health`
+- `config check`
+- `generate keypair`
+- `version`
+- `db-type`
+- `metrics`
+- `stats`
+- `completion`
+
+The daemon exposes:
+
+- `POST /init`
+- `POST /hb`
+- `GET /health`
+- `GET /metrics`
+- `GET /stats`
+- static frontend serving at `/`
+
+## Validation Improvements
+
+The heartbeat verifier now checks:
+
+- session presence
+- expiration
+- signature
+- hash-chain continuity
+- mutation step
+- mutation commitment parity
+- timestamp drift
+- behavioral mouse checks
+- fingerprint ranges
+- rate limiting at the route layer
+
+Accepted heartbeats return next-state fields. Rejected heartbeats return only `{"status":"ok"}`.
+
+## Testing Impact
+
+The refactor added or strengthened tests for:
+
+- gene environment encoding and validation
+- mutation opcode behavior
+- mutation order round-trips
+- deterministic mutation generation with seeded RNG
+- server/client mutation parity
+- random program divergence resistance
+- replay rejection
+- mutation step mismatch rejection
+- mutation commitment tamper rejection
+- storage backend stats
+- route-level silent rejection behavior
+
+## Operational Impact
+
+v0.6.0 makes ChronoSeal more suitable for deployment as a real service:
+
+- explicit daemon lifecycle
+- CLI-first operations
+- systemd-oriented install path
+- health and metrics endpoints
+- configurable persistence
+- shared protocol implementation
+- clearer docs and threat model
+
+## Compatibility Notes
+
+Important names in the current implementation:
+
+- binary: `chronoseal`
+- server crate: `chronoseal-server`
+- WASM crate: `chronoseal-wasm`
+- generated WASM module prefix: `chronoseal_wasm`
+- persistent SQLite mode: `sqlite-in-disk`
+
+Older docs or integrations may refer to `sqlite-disk`, `server`, or `antibot_wasm`; those names are stale for the current codebase.

docs/TESTING.md

@@ -0,0 +1,365 @@
+# ChronoSeal Testing Strategy and Suite
+
+This document describes the testing strategy for ChronoSeal and summarizes the test coverage included in v0.6.1.
+
+ChronoSeal is a security-focused system. Testing therefore prioritizes cryptographic correctness, deterministic execution, protocol integrity, and resistance to replay or tampering rather than simple line coverage.
+
+## Overview
+
+As of v0.6.1, the ChronoSeal workspace contains:
+
+| Crate               |  Tests |
+| ------------------- | -----: |
+| `chronoseal-server` |     30 |
+| `chronoseal-wasm`   |     24 |
+| `shared`            |     35 |
+| **Total**           | **89** |
+
+All tests pass successfully on the reference development environment.
+
+## Testing Philosophy
+
+ChronoSeal testing focuses on:
+
+1. Cryptographic correctness
+2. Deterministic server ↔ WASM parity
+3. Replay and tampering resistance
+4. Mutation engine integrity
+5. Negative-path validation
+6. Storage reliability
+7. Performance regression detection
+
+Particular emphasis is placed on ensuring that browser-side WASM execution produces identical results to server-side validation.
+
+---
+
+# Server Test Coverage (`chronoseal-server`)
+
+The server crate contains 30 tests covering configuration, runtime initialization, session lifecycle management, heartbeat validation, rate limiting, and behavioral trust checks.
+
+## Configuration
+
+Configuration tests verify:
+
+* database type parsing
+* TOML configuration loading
+* default value handling
+* command-line override behavior
+
+Examples:
+
+```text
+test_apply_run_args_overrides_db_type
+test_default_db_type_is_sqlite_in_memory
+test_toml_parses_db_type_kebab_case
+```
+
+## Runtime Initialization
+
+Backend initialization tests verify:
+
+* SQLite in-memory mode
+* SQLite disk-backed mode
+* Valkey compatibility mode
+
+Examples:
+
+```text
+test_init_db_pool_sqlite_in_memory
+test_init_db_pool_sqlite_in_disk
+test_init_db_pool_valkey_compat_mode
+```
+
+## Session Lifecycle and Security
+
+Session tests validate:
+
+* public key validation
+* session expiration
+* replay attack prevention
+* mutation step enforcement
+* commitment verification
+* long-running deterministic parity
+
+Examples:
+
+```text
+test_create_session_rejects_invalid_public_key_length
+test_expired_session_is_rejected
+test_replay_attack_is_rejected
+test_mutation_step_mismatch_is_rejected
+test_mutation_commitment_tamper_is_rejected
+test_session_lifecycle_and_verification
+test_deterministic_server_client_parity_across_many_heartbeats
+```
+
+## Heartbeat Validation
+
+Heartbeat tests verify:
+
+* successful state advancement
+* silent rejection behavior
+* rate limiting
+
+Examples:
+
+```text
+test_handler_success_returns_next_mutation_fields
+test_handler_tampered_commitment_is_silent_failure
+test_handler_rate_limit_returns_no_mutation_data
+```
+
+## Behavioral Trust Validation
+
+Trust checks verify:
+
+* minimum mouse activity
+* minimum distance traveled
+* pause detection
+* speed thresholds
+* optional activity requirements
+
+Examples:
+
+```text
+test_validate_mouse_success
+test_validate_mouse_insufficient_events
+test_validate_mouse_insufficient_distance
+test_validate_mouse_too_fast
+test_validate_mouse_no_pauses
+```
+
+## Rate Limiting
+
+Examples:
+
+```text
+test_rate_limiter
+test_rate_limiter_eviction
+```
+
+---
+
+# WASM Test Coverage (`chronoseal-wasm`)
+
+The WASM crate contains 24 tests covering both the virtual machine and browser-side mutation lifecycle.
+
+## Virtual Machine
+
+Opcode correctness is validated for:
+
+* ADD
+* SUB
+* MUL
+* XOR
+* AND
+* OR
+* NOT
+* HASH
+* ROT
+* PUSH
+
+Edge cases include:
+
+* stack underflow
+* truncated instructions
+* wrapping arithmetic
+
+Examples:
+
+```text
+test_add
+test_add_wrapping
+test_sub
+test_sub_wrapping
+test_mul
+test_hash
+test_underflow_binary
+test_underflow_unary
+test_incomplete_push
+```
+
+## Browser Mutation Lifecycle
+
+The browser runtime tests:
+
+* gene initialization
+* mutation preview
+* mutation commit
+* mutation discard
+* commitment parity
+
+Examples:
+
+```text
+test_init_gene_state_success
+test_init_gene_state_rejects_zero
+test_preview_commitment_matches_shared_engine
+test_commit_applies_preview
+test_discard_preview_keeps_committed_state
+```
+
+## Deterministic Parity
+
+Examples:
+
+```text
+test_table_driven_parity_across_many_generated_orders
+```
+
+These tests ensure browser-generated commitments remain consistent with server expectations.
+
+---
+
+# Shared Crate Coverage (`shared`)
+
+The shared crate contains 35 tests and represents the core security-critical logic of ChronoSeal.
+
+This crate receives the heaviest protocol-focused testing because it is shared by both server and WASM runtimes.
+
+## Synthetic Gene Engine
+
+Gene state tests validate:
+
+* initialization rules
+* environment encoding
+* environment decoding
+* commitment generation
+* quantity management
+
+Examples:
+
+```text
+test_new_state_with_default_size
+test_new_state_rejects_invalid_sizes
+test_commitment_changes_when_gene_or_environment_changes
+test_encode_decode_environment_roundtrip
+test_table_driven_randomized_environment_roundtrip
+```
+
+## Mutation Engine
+
+Mutation engine tests verify:
+
+* deterministic execution
+* mutation chains
+* opcode correctness
+* stack handling
+* instruction validation
+
+Examples:
+
+```text
+test_mutation_chain
+test_opcode_insert
+test_opcode_delete
+test_opcode_mutate_point
+test_opcode_apply_mutagen
+test_opcode_finalize_gene_hash
+```
+
+## Validation and Hardening
+
+Defensive validation tests include:
+
+```text
+test_rejects_stack_underflow
+test_rejects_truncated_instruction
+test_rejects_unknown_opcode
+test_zero_length_gene_is_rejected
+```
+
+## Deterministic Server ↔ WASM Parity
+
+These are among the most important tests in the project:
+
+```text
+test_server_client_parity_across_random_orders
+test_generate_order_is_deterministic_for_seeded_rng
+test_invalid_positions_wrap_deterministically
+```
+
+## Fuzz and Regression Testing
+
+Examples:
+
+```text
+test_fuzz_style_random_program_bytes_do_not_diverge
+test_performance_smoke_mutation_execution
+```
+
+These tests help detect behavioral divergence and unintended performance regressions.
+
+---
+
+# Running the Test Suite
+
+Run the full workspace:
+
+```bash
+cargo test --workspace
+```
+
+Run individual crates:
+
+```bash
+cargo test -p chronoseal-server
+cargo test -p chronoseal-wasm
+cargo test -p shared
+```
+
+Show test output:
+
+```bash
+cargo test -- --nocapture
+```
+
+---
+
+# Critical Security Tests
+
+The following tests protect core ChronoSeal security guarantees:
+
+```text
+test_mutation_commitment_tamper_is_rejected
+test_replay_attack_is_rejected
+test_handler_tampered_commitment_is_silent_failure
+test_server_client_parity_across_random_orders
+test_deterministic_server_client_parity_across_many_heartbeats
+test_fuzz_style_random_program_bytes_do_not_diverge
+```
+
+Any failure in these areas should be treated as a release-blocking issue.
+
+---
+
+# Future Improvements
+
+Planned enhancements include:
+
+* property-based testing using `proptest`
+* browser-driven end-to-end integration tests
+* Valkey concurrency testing
+* automated benchmark execution
+* expanded mutation-engine fuzzing
+* CI-enforced performance regression thresholds
+
+---
+
+# Conclusion
+
+ChronoSeal's testing strategy is centered on preserving deterministic behavior, cryptographic correctness, and protocol integrity.
+
+The current suite of 89 tests provides broad coverage across:
+
+* session security
+* heartbeat validation
+* mutation engine correctness
+* deterministic server/WASM parity
+* trust validation
+* storage abstraction
+* replay resistance
+
+As ChronoSeal evolves, expanding and strengthening this test suite remains a core project priority.
+
+**Last Updated:** May 2026 (v0.6.1)

docs/THREAT_MODEL.md

@@ -1,205 +1,240 @@
-# ChronoSeal — Threat Model
+# ChronoSeal Threat Model
 
-## Purpose
+ChronoSeal is a cost-raising browser attestation layer. It makes replay, stale state reuse, and incomplete automation more expensive by requiring signed, continuous, deterministic browser-side state progression.
 
-This document defines what ChronoSeal is designed to protect against, what
-it explicitly does not protect against, and the reasoning behind each
-design decision in security terms.
+It is not a perfect bot blocker, CAPTCHA replacement, hardware attestation system, fraud engine, or identity provider.
 
-ChronoSeal is a **cost-raising mechanism**. It does not claim to make
-automated access impossible. It makes automated access expensive, complex
-to maintain, and operationally fragile at scale.
+## Security Objectives
 
----
+ChronoSeal aims to:
 
-## Assets Being Protected
+- reject stale or replayed heartbeat payloads
+- reject heartbeats that do not maintain the server-issued mutation sequence
+- bind heartbeat payloads to a browser-local Ed25519 session key
+- make basic HTTP clients insufficient
+- make browser automation maintain multiple synchronized state channels
+- avoid detailed rejection feedback
+- preserve privacy by avoiding persistent user identity state
 
-| Asset | Description |
+## Protected Assets
+
+| Asset | Protection focus |
 |---|---|
-| Web page content | HTML, rendered data, scraped text |
-| API responses | JSON endpoints that serve structured data |
-| Server compute | CPU and bandwidth consumed by automated clients |
-| Rate-limited resources | Endpoints with per-user quotas |
-| Behavioral analytics | Metrics polluted by bot traffic |
+| Protected page/API access | Require live attestation before allowing continued access |
+| Session continuity | Ensure each accepted heartbeat advances from the last accepted state |
+| Server compute | Rate-limit and reject invalid clients without expensive application work |
+| Protocol state | Protect hash-chain, salt, and mutation progression |
+| User privacy | Avoid long-term tracking and detailed failure disclosure |
 
----
+## Trust Assumptions
 
-## Attacker Profiles
+ChronoSeal assumes:
 
-### Level 1 — Script Kiddie / Commodity Scraper
+- the server host and daemon process are trusted
+- storage is trusted for session continuity
+- TLS protects traffic in production
+- browser clients can run JavaScript and WASM
+- operators configure reverse proxy, filesystem permissions, and logs appropriately
 
-**Tools:** `curl`, `requests`, `scrapy`, simple HTTP clients.  
-**Capability:** No browser environment. Cannot execute JavaScript or WASM.  
-**ChronoSeal response:** Session never initialises. No `session_id` is ever
-presented to `/hb`. Content gated behind session validation is never served.
+ChronoSeal does not assume:
 
-### Level 2 — Headless Browser Operator
+- the browser is honest
+- WASM is a secure enclave
+- mouse data proves human presence
+- fingerprint values are unforgeable
+- attackers cannot run a full browser
 
-**Tools:** Playwright, Puppeteer, Selenium, undetected-chromedriver.  
-**Capability:** Full browser environment. Can execute JavaScript and WASM.
-Cannot easily synthesise realistic mouse entropy or maintain hash chain state
-across concurrent sessions.  
-**ChronoSeal response:** Mouse entropy validation rejects absent or synthetic
-movement. Hash chain requires per-session state synchronisation. Scaling to
-hundreds of concurrent sessions requires proportional infrastructure.
+## Attacker Levels
 
-### Level 3 — Stealth Automation
+### Level 1: Commodity HTTP Client
 
-**Tools:** Puppeteer Stealth, rebrowser-patches, custom CDP clients with
-evasion patches.  
-**Capability:** Patches `navigator.webdriver`, spoofs browser fingerprints,
-can inject synthetic mouse events. May partially pass behavioral checks.  
-**ChronoSeal response:** Ed25519 signature over the full payload (including
-behavioral state and VM execution result) means the attacker must also
-correctly execute the WASM program and maintain chain continuity. The private
-key is generated fresh per page load and never exposed — it cannot be
-extracted from a legitimate session and reused.
+Examples:
 
-### Level 4 — Sophisticated Adversary
+- `curl`
+- `requests`
+- scraper scripts without browser or WASM execution
 
-**Tools:** Full browser farm with real input devices, WASM reverse engineering,
-custom chain maintenance infrastructure.  
-**Capability:** Can pass all current ChronoSeal checks given sufficient
-engineering effort.  
-**ChronoSeal response:** Significantly increases operational cost. A browser
-farm with real input devices costs orders of magnitude more than a commodity
-scraper fleet. ChronoSeal is not designed to stop this attacker — no client-
-side protection can.
+Expected result:
 
----
+- cannot produce valid signatures
+- cannot maintain hash-chain state
+- cannot execute mutation preview
+- cannot produce accepted heartbeats
+
+### Level 2: Basic Headless Browser
+
+Examples:
+
+- Playwright
+- Puppeteer
+- Selenium
+
+Expected result:
+
+- can load JavaScript and WASM
+- must preserve keypair, hash chain, salt, VM, and mutation state
+- must generate plausible timing and mouse event windows
+- silent rejection complicates debugging and scaling
+
+### Level 3: Stealth Automation
+
+Examples:
+
+- patched browser runtime
+- synthetic event generation
+- custom protocol client with WASM or Rust reimplementation
+
+Expected result:
+
+- can attempt full protocol implementation
+- must still match canonical signing, hash progression, mutation parity, and timing
+- must handle changing server-issued mutation programs
+- receives limited failure feedback
+
+### Level 4: Resourced Browser Farm
+
+Examples:
+
+- real browsers
+- realistic input devices
+- human-assisted workflows
+- distributed session management
+
+Expected result:
+
+- ChronoSeal raises cost and complexity
+- ChronoSeal does not claim complete prevention
+- additional application-level controls are required
 
 ## Attack Vectors and Mitigations
 
-### Replay Attack
+### Replay
 
-**Attack:** Capture a valid heartbeat payload and retransmit it.  
-**Mitigation:**
-- Timestamp window (±30 seconds): replayed payloads are rejected after 30s.
-- Hash chain: each heartbeat must present `H(n-1)` matching the server's
-  stored state. A replayed heartbeat presents a stale hash that no longer
-  matches after one successful heartbeat has advanced the chain.
+Attack: resend a previously accepted heartbeat.
+
+Mitigations:
+
+- stored `last_hash` must match request `prev_hash`
+- accepted heartbeats rotate salt
+- mutation step advances after acceptance
+- timestamp drift is bounded
 
 ### Signature Forgery
 
-**Attack:** Construct a valid-looking heartbeat payload without the private key.  
-**Mitigation:** Ed25519 with 128-bit security. The private key is generated
-inside WASM `thread_local` memory, never serialised, never passed to
-JavaScript, never transmitted. Forgery requires breaking Ed25519 or
-extracting the key from WASM memory — neither is practical.
+Attack: submit a heartbeat without the browser session private key.
 
-### Key Extraction
+Mitigations:
 
-**Attack:** Inspect WASM linear memory to extract the private signing key.  
-**Mitigation:** The key is stored in a Rust `thread_local! { RefCell<Option<SigningKey>> }`.
-It has no exported symbol and is not referenced by any exported WASM function
-that returns raw memory. An attacker with full DevTools access to the WASM
-memory can extract it from one session, but it is useless for other sessions
-(fresh keypair per page load) and expires with the session.
+- Ed25519 signature over canonical payload
+- public key registered during `/init`
+- signature verified on every heartbeat
+- signature covers mutation step and gene commitment
 
-### Hash Chain Forgery
+### Hash-Chain Desynchronization
 
-**Attack:** Compute a valid `H(n)` without the server-side salt.  
-**Mitigation:** Each chain link incorporates `saltₙ₋₁`, which is a 16-byte
-random value known only to the server and returned (once) in the heartbeat
-response. An attacker cannot compute `H(n+1)` without first receiving
-`saltₙ` from a successful heartbeat response, which requires a valid signature
-and all other checks to pass.
+Attack: submit a heartbeat from stale client state.
 
-### Session Hijacking
+Mitigations:
 
-**Attack:** Steal a `session_id` and use it from a different client.  
-**Mitigation:** `session_id` alone is insufficient — the attacker also needs
-the private key (to produce valid signatures) and the current chain state
-(to present the correct `prev_hash`). All three are required simultaneously.
+- server compares request `prev_hash` to stored `last_hash`
+- server computes the next hash only after all validation passes
+- rejected heartbeats do not advance server state
 
-### Enumeration of Validation Rules
+### Mutation Tampering
 
-**Attack:** Send malformed heartbeats and analyse error responses to map
-validation logic.  
-**Mitigation:** All failure paths return `{"status":"ok"}` with no `next_salt`.
-There is no error code, no error message, and no status difference between
-a rate limit hit, an invalid signature, a broken chain, and a behavioral
-rejection.
+Attack: forge or skip synthetic gene mutations.
 
-### DoS via Session Flooding
+Mitigations:
 
-**Attack:** Open thousands of sessions to exhaust the rate limiter's HashMap
-memory.  
-**Mitigation:** Rate limiter entries are evicted every 60 seconds by the
-cleanup task. Each entry is a small `(u32, Instant)` tuple; even at 100,000
-concurrent fake sessions, the HashMap occupies roughly 10–15 MB, which is
-well within normal server memory budgets. Sessions themselves expire after 30
-minutes of inactivity and are purged from SQLite.
+- server stores the pending mutation program
+- request must include the expected `mutation_step`
+- server applies the mutation independently
+- commitment includes candidate gene state, `session_id`, and step
+- mismatch causes silent rejection
 
-### Clock Manipulation
+### Session Identifier Theft
 
-**Attack:** Manipulate the client's `Date.now()` to bypass the timestamp
-window.  
-**Mitigation:** The timestamp is included in the signed payload. Manipulating
-it requires also forging the signature. The server validates against its own
-clock — client-side clock manipulation cannot help without the private key.
+Attack: reuse a stolen `session_id`.
 
-### Synthetic Mouse Events
+Mitigations:
 
-**Attack:** Inject programmatic `mousemove` events via `dispatchEvent` or
-CDP input simulation.  
-**Mitigation:** Synthetic events often fail the pause check (no natural dwell
-periods), produce unrealistically uniform speed profiles, or fail the minimum
-distance threshold. Generating convincingly human mouse traces at scale
-requires either real input devices or sophisticated probabilistic models —
-both significantly increase operational cost.
+- `session_id` alone is insufficient
+- attacker also needs current private key, hash state, salt, mutation step, and mutation state
+- stale attempts fail after the real session advances
 
----
+### Failure Oracle Probing
 
-## What ChronoSeal Does Not Protect Against
+Attack: send malformed requests and inspect responses to infer validation rules.
 
-| Limitation | Explanation |
-|---|---|
-| Real browsers with real users acting as bots | A human operating a browser manually is indistinguishable from a legitimate visitor. ChronoSeal cannot address this. |
-| Server-side vulnerabilities | ChronoSeal is a client attestation layer. It does not protect the server from injection, authentication bypass, or other backend vulnerabilities. |
-| Highly resourced nation-state actors | Out of scope for a client-side protection layer. |
-| Content visible before session establishment | If the protected content is rendered before the first heartbeat, it can be scraped without a session. Gate content on session validity server-side. |
-| Perfect bot prevention | No client-side mechanism can be. WASM can be reverse engineered. ChronoSeal raises cost, not an impenetrable barrier. |
+Mitigations:
 
----
+- heartbeat semantic failures return `200 OK` with `{"status":"ok"}`
+- accepted heartbeats are distinguished only by next-state fields
+- detailed validation errors are not returned to the client
 
-## Operational Security Notes
+### Storage Tampering
 
-### Log Level
+Attack: alter persisted session state.
 
-Do not run with `RUST_LOG=debug` in production. The debug log includes
-`session_id` values, which are sensitive identifiers. Use `warn` or `info`.
+Mitigations:
 
-### CORS Policy
+- run the daemon under a dedicated user
+- restrict SQLite database permissions
+- protect Valkey behind trusted network boundaries
+- use normal host hardening and backups where persistence matters
 
-The default `CorsLayer::permissive()` is suitable for development only.
-In production, restrict allowed origins to your own domain:
+Storage is trusted. If an attacker can modify storage, they can affect session continuity.
 
-```rust
-CorsLayer::new()
-    .allow_origin("https://your.domain.com".parse::<HeaderValue>().unwrap())
-    .allow_methods([Method::POST])
-    .allow_headers([header::CONTENT_TYPE])
-```
+## Behavioral Checks
 
-### TLS
+ChronoSeal validates:
 
-Serve exclusively over TLS 1.3. The heartbeat payload contains timestamps
-and behavioral signals. While each payload is signed and cannot be forged,
-plaintext transmission leaks behavioral patterns and timing information that
-could assist a sophisticated attacker.
+- minimum event count
+- minimum movement distance
+- maximum average speed
+- pause count
+- timestamp drift
+- basic fingerprint field ranges
 
-### In-Memory SQLite
+These checks are cost signals. They are not proof of humanity and should not be the only security layer for high-risk actions.
 
-All session state is lost on server restart. This is intentional — there is
-no persistent state to steal. Clients transparently re-initialise. If your
-deployment restarts frequently (e.g. rolling deploys), sessions will be lost
-more often; tune `HEARTBEAT_MIN_INTERVAL_MS` and `EXPIRATION_MINUTES`
-accordingly so clients recover quickly.
+## Privacy Constraints
 
----
+ChronoSeal intentionally avoids:
 
-## Security Disclosure
+- persistent user identifiers
+- browser history collection
+- device fingerprint databases
+- cross-session identity graphs
+- long-term behavioral profiles
 
-See [SECURITY.md](../SECURITY.md) for the vulnerability disclosure policy
-and contact details.
+Session data is short-lived by default. Persistent storage is operator-selected through `sqlite-in-disk` or `valkey`.
+
+## Limitations
+
+ChronoSeal does not protect against:
+
+- real users intentionally automating or abusing access
+- complete browser farms with realistic input
+- compromised server hosts
+- tampered storage
+- server-side application vulnerabilities
+- credential theft outside ChronoSeal
+- policy decisions that require identity, risk scoring, or business context
+
+## Operational Security
+
+Recommended:
+
+- serve all traffic over HTTPS
+- keep `/init` and `/hb` same-origin with protected content when possible
+- run behind a reverse proxy
+- keep debug logs disabled in production
+- protect storage and log directories
+- monitor health and metrics
+- use `sqlite-in-memory` for ephemeral sessions
+- use `sqlite-in-disk` or `valkey` only when persistence is required
+
+## Disclosure
+
+See [../SECURITY.md](../SECURITY.md) for the vulnerability disclosure policy.

docs/WASM_BUILD.md

@@ -1,301 +1,163 @@
-# ChronoSeal — WASM Build Guide
+# ChronoSeal WASM Build Guide
 
-## Overview
+ChronoSeal uses a Rust-generated WASM package for browser-side attestation. The package is built from `wasm/` and copied into `frontend/pkg`.
 
-The client-side cryptographic core of ChronoSeal is written in Rust and
-compiled to WebAssembly (WASM). The JavaScript frontend (`heartbeat.js`)
-imports functions from this WASM module to generate keypairs, sign heartbeat
-payloads, compute hash chain links, and execute the stack machine program.
+## Responsibilities
 
-The import line in `heartbeat.js`:
+The WASM runtime:
 
-```js
-import init, { generate_keypair, sign_message, compute_next_hash, run_program }
-  from './pkg/antibot_wasm.js';
-```
+- generates a browser-local Ed25519 keypair
+- signs canonical heartbeat payloads
+- computes Blake3 hash-chain progression
+- executes server-issued VM opcode programs
+- initializes synthetic gene state
+- previews gene mutation commitments
+- commits or discards preview state after heartbeat response
 
-`./pkg/antibot_wasm.js` is a **generated file**. It does not exist in the
-repository and must be produced by building the `wasm/` crate before running
-the server.
+The WASM runtime is not treated as a secure enclave. The server independently recomputes deterministic state.
 
----
-
-## How the WASM Module is Built
-
-The tool that compiles Rust to WASM and generates the JavaScript glue is
-[`wasm-pack`](https://rustwasm.github.io/wasm-pack/).
-
-When you run:
-
-```bash
-wasm-pack build wasm --target web --release
-```
-
-wasm-pack does the following in sequence:
-
-1. Compiles `wasm/src/lib.rs` (and its submodules) to a `.wasm` binary using
-   the `wasm32-unknown-unknown` target.
-2. Runs `wasm-bindgen` to inspect every `#[wasm_bindgen]`-annotated function
-   and struct and generate a JavaScript wrapper for each one.
-3. Optionally runs `wasm-opt` (from Binaryen) to size-optimise the binary.
-4. Writes all output to `wasm/pkg/`.
-
----
-
-## Output: `wasm/pkg/`
-
-After a successful build, `wasm/pkg/` contains:
-
-```
-wasm/pkg/
-├── antibot_wasm.js          ← ES module; the file heartbeat.js imports
-├── antibot_wasm_bg.wasm     ← compiled WASM binary (~300–800 KB release)
-├── antibot_wasm_bg.js       ← internal memory bridge (do not import directly)
-├── antibot_wasm.d.ts        ← TypeScript type declarations
-├── antibot_wasm_bg.d.ts     ← TypeScript declarations for the bg module
-└── package.json
-```
-
-### `antibot_wasm.js`
-
-This is the public entry point. It contains:
-
-- An `init()` function that fetches and instantiates the `.wasm` binary.
-- One JavaScript wrapper function for each `#[wasm_bindgen]` export in
-  `wasm/src/`:
-
-| Rust export | JS wrapper | Description |
-|---|---|---|
-| `generate_keypair()` | `generate_keypair()` | Generate Ed25519 keypair; return hex public key |
-| `get_public_key()` | `get_public_key()` | Return hex public key, or `""` if not initialised |
-| `sign_message(msg)` | `sign_message(msg)` | Sign string; return hex signature, or `""` if not initialised |
-| `compute_next_hash(prev, ts, entropy, stack, salt)` | `compute_next_hash(...)` | Compute next Blake3 chain hash |
-| `run_program(b64)` | `run_program(b64)` | Execute base64 VM program; return `{ stack, ip }` |
-
-### `antibot_wasm_bg.wasm`
-
-The compiled binary. The `.bg` suffix means "background" — this is the raw
-WASM that `antibot_wasm.js` loads internally. You should not reference this
-file directly in your HTML.
-
----
-
-## Step-by-Step Build
-
-### 1. Install the Rust WASM target
+## Requirements
 
 ```bash
 rustup target add wasm32-unknown-unknown
-```
-
-This is a one-time step. Without it, the Rust compiler cannot produce WASM
-output.
-
-### 2. Install wasm-pack
-
-```bash
 cargo install wasm-pack
 ```
 
-Or via the installer script:
-
-```bash
-curl https://rustwasm.github.io/wasm-pack/installer/init.sh -sSf | sh
-```
-
 Verify:
 
 ```bash
 wasm-pack --version
-# wasm-pack 0.13.x
 ```
 
-### 3. Build the WASM module
+## Build
 
-From the project root:
+From the repository root:
 
 ```bash
 wasm-pack build wasm --target web --release
-```
-
-`--target web` produces an ES module (`import`/`export` syntax) suitable for
-use directly in a browser without a bundler. Other targets (`bundler`,
-`nodejs`, `no-modules`) produce different output formats and are not
-compatible with the ChronoSeal frontend as written.
-
-`--release` enables Rust's release optimisations (inlining, dead code
-elimination, size reduction). Omit it during development for faster builds
-and better panic messages.
-
-### 4. Move the output to the frontend
-
-```bash
 rm -rf frontend/pkg
 mv wasm/pkg frontend/pkg
 ```
 
-The frontend expects the WASM module at `frontend/pkg/antibot_wasm.js`
-because `heartbeat.js` imports from `./pkg/antibot_wasm.js` relative to
-the `frontend/` directory, which is where the server's static file handler
-is rooted.
+`--target web` emits native ES modules compatible with the static frontend.
 
----
+Development build:
 
-## Using the Build Script
+```bash
+wasm-pack build wasm --target web
+rm -rf frontend/pkg
+mv wasm/pkg frontend/pkg
+```
 
-The convenience script at `scripts/build.sh` performs all steps in order:
+Full project build:
 
 ```bash
 bash scripts/build.sh
 ```
 
-This builds the WASM module, moves it to `frontend/pkg/`, and then builds
-the server binary. Run this for a clean full build before deployment.
+## Output Files
 
-For development iteration where you are only changing Rust WASM code:
+The package name comes from the crate name `chronoseal-wasm`, so generated files use the `chronoseal_wasm` prefix.
 
-```bash
-wasm-pack build wasm --target web   # (omit --release for speed)
-rm -rf frontend/pkg && mv wasm/pkg frontend/pkg
-```
+Expected `frontend/pkg/` contents include:
 
-For development where you are only changing server code:
+- `chronoseal_wasm.js`
+- `chronoseal_wasm_bg.wasm`
+- `chronoseal_wasm.d.ts`
+- `package.json`
 
-```bash
-cargo build -p server
-```
+Generated files in `wasm/pkg/` and `frontend/pkg/` are build artifacts and should be regenerated during release.
 
----
-
-## How `heartbeat.js` Loads the Module
-
-`heartbeat.js` uses a standard ES module dynamic import pattern:
+## Browser Import
 
 ```js
-import init, { generate_keypair, sign_message, compute_next_hash, run_program }
-  from './pkg/antibot_wasm.js';
-
-export async function initHeartbeat() {
-    // 1. Fetch and instantiate the .wasm binary
-    await init();
-
-    // 2. Generate keypair — private key stored in WASM memory only
-    const pubKeyHex = generate_keypair();
-
-    // 3. Send public key to server, receive session_id and chain seed
-    // ...
-}
+import init, {
+  generate_keypair,
+  get_public_key,
+  sign_message,
+  compute_next_hash,
+  run_program,
+  init_gene_state,
+  preview_gene_commitment,
+  commit_gene_preview,
+  discard_gene_preview,
+  current_gene_commitment
+} from './pkg/chronoseal_wasm.js';
 ```
 
-`init()` is the default export from `antibot_wasm.js`. It fetches
-`antibot_wasm_bg.wasm` (from the same `pkg/` directory) via `fetch()`,
-compiles it in the browser's WASM engine, and links it to the JS glue
-layer. After `await init()` returns, all the named exports
-(`generate_keypair`, `sign_message`, etc.) are ready to call.
+Call `await init()` before using any exported function.
 
-The `init()` call must complete before any other WASM function is called.
-Calling `sign_message()` or `compute_next_hash()` before `await init()`
-returns will produce an empty string (the module is not yet instantiated).
+## Exported Functions
 
----
+| Function | Signature | Failure value |
+|---|---|---|
+| `generate_keypair()` | `() -> string` | `""` only on unexpected failure |
+| `get_public_key()` | `() -> string` | `""` if no keypair exists |
+| `sign_message(msg)` | `(string) -> string` | `""` if no keypair exists or signing fails |
+| `compute_next_hash(prev, ts, entropy, stack, salt)` | `(string, u64, string, string, string) -> string` | panic/error path should be avoided by valid inputs |
+| `run_program(b64)` | `(string) -> JsValue` | returns empty/default stack state on invalid execution path |
+| `init_gene_state(gene_size)` | `(u32) -> bool` | `false` |
+| `preview_gene_commitment(order_b64, session_id, mutation_step, rounds)` | `(string, string, u64, u8) -> string` | `""` |
+| `commit_gene_preview()` | `() -> bool` | `false` |
+| `discard_gene_preview()` | `() -> void` | none |
+| `current_gene_commitment(session_id, mutation_step)` | `(string, u64) -> string` | `""` if no committed state exists |
 
-## Serving the WASM Binary
+`rounds = 0` in `preview_gene_commitment` selects the shared default mutation round count.
 
-Browsers require WASM files to be served with the correct MIME type:
+## Mutation State Lifecycle
 
+The browser must keep two gene states:
+
+- committed state: the last accepted state
+- preview state: candidate state for the heartbeat currently being sent
+
+Expected sequence:
+
+1. Call `init_gene_state(gene_size)` after `/init`.
+2. Call `preview_gene_commitment(order_b64, session_id, mutation_step, rounds)` before signing `/hb`.
+3. Include the returned commitment and mutation step in the signed heartbeat.
+4. If the response contains next-state fields, call `commit_gene_preview()`.
+5. If the heartbeat is rejected or errors, call `discard_gene_preview()`.
+
+Never commit preview state before the server accepts the heartbeat.
+
+## Hash-Chain Ordering
+
+After an accepted heartbeat, compute the next local hash with the salt that was active when the heartbeat was sent. Then replace the local salt with `next_salt`.
+
+Correct order:
+
+```js
+const sentSalt = currentSalt;
+currentSalt = resp.next_salt;
+prevHash = compute_next_hash(prevHash, timestamp, entropyJson, stackStateJson, sentSalt);
 ```
+
+This mirrors the server, which computes and stores the new hash before rotating to the next salt.
+
+## Serving WASM
+
+The `.wasm` file must be served with:
+
+```text
 Content-Type: application/wasm
 ```
 
-Most web servers set this automatically for `.wasm` files. If you see the
-error:
+ChronoSeal's built-in static file service handles this for normal deployments.
 
-```
-WebAssembly.instantiate(): Response has unsupported MIME type
-```
+## Validation
 
-Add the MIME type to your server configuration:
-
-**nginx:**
-```nginx
-types {
-    application/wasm  wasm;
-}
-```
-
-**Apache `.htaccess`:**
-```apache
-AddType application/wasm .wasm
-```
-
-The Axum `ServeDir` handler used by ChronoSeal's built-in static server
-sets the correct MIME type automatically via `tower-http`.
-
----
-
-## What Is Not in the Repository
-
-| Path | Why excluded |
-|---|---|
-| `wasm/pkg/` | Generated build output — changes on every build |
-| `frontend/pkg/` | Same generated output, moved to serve location |
-| `target/` | Standard Rust build artefacts |
-
-Both `wasm/pkg/` and `frontend/pkg/` are listed in `.gitignore`. Committing
-them would bloat the repository (the `.wasm` binary alone is 300–800 KB),
-create noisy diffs on every rebuild, and give a false impression that the
-WASM module is pre-built and ready to use without a build step.
-
----
-
-## Troubleshooting
-
-### `wasm32-unknown-unknown` target not found
-
-```
-error[E0463]: can't find crate for `std`
-```
-
-Fix:
+Recommended checks after WASM changes:
 
 ```bash
-rustup target add wasm32-unknown-unknown
+cargo test --workspace
+cargo clippy --workspace --all-targets -- -D warnings
+wasm-pack build wasm --target web
 ```
 
-### `wasm-pack` not found
+Then refresh `frontend/pkg`:
 
 ```bash
-cargo install wasm-pack
+rm -rf frontend/pkg
+mv wasm/pkg frontend/pkg
 ```
-
-### `wasm-opt` not found (warning, not an error)
-
-wasm-pack prints a warning if `wasm-opt` is not installed. The build still
-succeeds; the binary is just not size-optimised.
-
-```bash
-# On Debian/Ubuntu/Arch
-sudo apt install binaryen      # Debian/Ubuntu
-sudo pacman -S binaryen        # Arch
-```
-
-### `antibot_wasm_bg.wasm` fetch fails (404)
-
-The `.wasm` file is not being served from `frontend/pkg/`. Verify:
-
-```bash
-ls /mnt/Programs/ChronoSeal/frontend/pkg/
-# Should list: antibot_wasm.js  antibot_wasm_bg.wasm  ...
-```
-
-If the directory is empty or missing, re-run the build steps above.
-
-### MIME type error in browser
-
-See the "Serving the WASM Binary" section above.
-
-### `sign_message` or `generate_keypair` returns empty string
-
-The WASM keypair has not been initialised. Ensure `await init()` and
-`generate_keypair()` are called (and awaited) before any other WASM
-function. Check the browser console for any errors during `init()`.

docs/chronoseal.example.toml

@@ -1,5 +1,27 @@
 bind = "0.0.0.0:3000"
+
+# Storage backend: sqlite-in-memory (default), sqlite-in-disk, or valkey.
+db_type = "sqlite-in-memory"
+
 pid_file = "/run/chronoseal.pid"
 db_path = "/var/lib/chronoseal/chronoseal.sqlite"
 frontend_dir = "/usr/share/chronoseal/frontend"
 log_file = "/var/log/chronoseal/chronoseal.jsonl"
+
+heartbeat_min_interval_ms = 12000
+heartbeat_max_interval_ms = 25000
+expiration_minutes = 30
+rate_limit_count = 5
+rate_limit_window_secs = 10
+max_timestamp_drift_ms = 30000
+
+min_mouse_total_dist = 10.0
+max_mouse_avg_speed = 2.0
+min_pause_count = 1
+require_mouse_activity = true
+
+# Synthetic gene size. Current valid range: 1..=4096. Default: 512.
+gene_size = 512
+
+# Current valid range: 1..=10. Default: 4.
+mutation_rounds = 4

frontend/heartbeat.js

@@ -1,10 +1,21 @@
-import init, { generate_keypair, sign_message, compute_next_hash, run_program } from './pkg/chronoseal_wasm.js';
+import init, {
+    generate_keypair,
+    sign_message,
+    compute_next_hash,
+    run_program,
+    init_gene_state,
+    preview_gene_commitment,
+    commit_gene_preview,
+    discard_gene_preview
+} from './pkg/chronoseal_wasm.js';
 import { collectEntropy } from './entropy.js';
 import { sendRequest } from './transport.js';
 
 let session, prevHash, currentSalt, opcodesB64, lastTime;
 let minInterval = 12000;
 let maxInterval = 25000;
+let pendingMutationStep = 0;
+let pendingMutationOrderB64 = '';
 
 export async function initHeartbeat() {
     await init();
@@ -16,6 +27,11 @@ export async function initHeartbeat() {
     opcodesB64 = initResp.opcodes_b64;
     minInterval = initResp.heartbeat_min_interval_ms || 12000;
     maxInterval = initResp.heartbeat_max_interval_ms || 25000;
+    if (!init_gene_state(initResp.gene_size || 512)) {
+        throw new Error('Failed to initialize gene state');
+    }
+    pendingMutationStep = initResp.mutation_step;
+    pendingMutationOrderB64 = initResp.mutation_order_b64;
     lastTime = performance.now();
     scheduleNext();
 }
@@ -40,6 +56,10 @@ async function sendHeartbeat() {
         const timestamp = Date.now();
         const entropyData = { events: events.map(e => ({ x: e.x, y: e.y, t: e.t })) };
         const entropyJson = JSON.stringify(entropyData);
+        const geneCommitment = preview_gene_commitment(pendingMutationOrderB64);
+        if (!geneCommitment) {
+            throw new Error('Unable to compute mutation commitment');
+        }
 
         const signable = {
             sessionId: session,
@@ -47,11 +67,14 @@ async function sendHeartbeat() {
             timestamp: timestamp,
             entropyData: entropyData,
             stackState: JSON.parse(stackState),
-            fingerprint: fingerprint
+            fingerprint: fingerprint,
+            mutationStep: pendingMutationStep,
+            geneCommitment: geneCommitment
         };
         const msg = JSON.stringify(signable, Object.keys(signable).sort());
         const sig = sign_message(msg);
         if (!sig) {
+            discard_gene_preview();
             console.error('Keypair not initialised — skipping heartbeat');
             return;
         }
@@ -62,22 +85,32 @@ async function sendHeartbeat() {
             entropy_data: entropyData,
             stack_state: JSON.parse(stackState),
             fingerprint,
+            mutation_step: pendingMutationStep,
+            gene_commitment: geneCommitment,
             signature: sig
         });
 
-        if (resp.next_salt) {
+        if (resp.next_salt && resp.next_mutation_step && resp.next_mutation_order_b64) {
+            if (!commit_gene_preview()) {
+                discard_gene_preview();
+                throw new Error('Failed to commit local mutation preview');
+            }
             // IMPORTANT: capture the salt that was active when this heartbeat was sent.
             // The server computes new_hash = H(prev, ts, entropy, stack, OLD_salt) and stores it,
             // then rotates to next_salt.  We must mirror that using the same old salt, then rotate.
             const sentSalt = currentSalt;
             currentSalt = resp.next_salt;
             prevHash = compute_next_hash(prevHash, timestamp, entropyJson, stackState, sentSalt);
+            pendingMutationStep = resp.next_mutation_step;
+            pendingMutationOrderB64 = resp.next_mutation_order_b64;
         } else {
+            discard_gene_preview();
             console.warn('Heartbeat rejected');
         }
     } catch (e) {
+        discard_gene_preview();
         console.error(e);
     } finally {
         scheduleNext();
     }
-}
+}

scripts/install.sh

@@ -1,52 +1,46 @@
-#!/bin/sh
-set -eu
+#!/bin/bash
+set -euo pipefail
 
-CHRONOSEAL_VERSION="${CHRONOSEAL_VERSION:-latest}"
-CHRONOSEAL_INSTALL_DIR="${CHRONOSEAL_INSTALL_DIR:-/usr/local/bin}"
-CHRONOSEAL_BASE_URL="${CHRONOSEAL_BASE_URL:-https://get.chronoseal.rs/releases}"
+echo "🚀 ChronoSeal Installer"
+echo "======================"
 
-need() {
-    command -v "$1" >/dev/null 2>&1 || {
-        echo "chronoseal installer: missing required command: $1" >&2
-        exit 1
-    }
-}
-
-need uname
-need mktemp
-need chmod
-
-arch="$(uname -m)"
-case "$arch" in
-    x86_64|amd64) target="x86_64-unknown-linux-musl" ;;
-    aarch64|arm64) target="aarch64-unknown-linux-musl" ;;
-    *) echo "chronoseal installer: unsupported architecture: $arch" >&2; exit 1 ;;
-esac
-
-if command -v curl >/dev/null 2>&1; then
-    fetch="curl --proto =https --tlsv1.2 -fsSL"
-elif command -v wget >/dev/null 2>&1; then
-    fetch="wget -qO-"
-else
-    echo "chronoseal installer: install curl or wget" >&2
-    exit 1
+# Create system user
+if ! id -u chronoseal &>/dev/null; then
+    sudo useradd --system --no-create-home --shell /usr/sbin/nologin chronoseal
+    echo "✓ Created chronoseal system user"
 fi
 
-tmp="$(mktemp -d)"
-trap 'rm -rf "$tmp"' EXIT
+# Build
+echo "→ Building ChronoSeal..."
+cd "$(dirname "$0")/.."
+bash scripts/build.sh
 
-url="$CHRONOSEAL_BASE_URL/$CHRONOSEAL_VERSION/chronoseal-$target.tar.gz"
-echo "downloading chronoseal $CHRONOSEAL_VERSION for $target"
+# Install binary
+sudo install -Dm755 target/release/chronoseal /usr/local/bin/chronoseal
+echo "✓ Installed binary to /usr/local/bin/chronoseal"
 
-# shellcheck disable=SC2086
-$fetch "$url" | tar -xz -C "$tmp"
-chmod 0755 "$tmp/chronoseal"
+# Install frontend assets
+sudo mkdir -p /opt/chronoseal
+sudo cp -r frontend /opt/chronoseal/
+sudo chown -R chronoseal:chronoseal /opt/chronoseal
+echo "✓ Installed frontend assets"
 
-if [ "$(id -u)" -eq 0 ]; then
-    install -m 0755 "$tmp/chronoseal" "$CHRONOSEAL_INSTALL_DIR/chronoseal"
-else
-    sudo install -m 0755 "$tmp/chronoseal" "$CHRONOSEAL_INSTALL_DIR/chronoseal"
-fi
+# Install systemd service
+sudo cp chronoseal.service /etc/systemd/system/chronoseal.service
+sudo systemctl daemon-reload
+echo "✓ Installed systemd service"
 
-echo "installed: $CHRONOSEAL_INSTALL_DIR/chronoseal"
-echo "try: chronoseal --help"
+# Enable and start
+sudo systemctl enable --now chronoseal
+echo "✓ ChronoSeal service started"
+
+echo ""
+echo "✅ ChronoSeal installed successfully!"
+echo ""
+echo "Useful commands:"
+echo "  chronoseal status          # Check service status"
+echo "  chronoseal health          # Health probe"
+echo "  sudo systemctl status chronoseal"
+echo "  sudo journalctl -u chronoseal -f"
+echo ""
+echo "To uninstall: sudo systemctl disable --now chronoseal && sudo rm /usr/local/bin/chronoseal"

server/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "chronoseal-server"
-version = "0.5.0"
+version = "0.6.0"
 edition = "2021"
 
 [[bin]]
@@ -30,3 +30,4 @@ hex = "0.4"
 base64 = "0.22"
 rand = "0.8"
 ed25519-dalek = "2"
+valkey = "0.0.0-alpha5"

server/src/cleanup.rs

@@ -5,28 +5,16 @@ pub async fn cleanup_loop(state: Arc<AppState>) {
     loop {
         tokio::time::sleep(std::time::Duration::from_secs(60)).await;
 
-        // Evict expired sessions from SQLite.
+        // Evict expired sessions from the configured storage backend.
         {
-            if let Ok(conn) = state.db_pool.get() {
-                let now = crate::storage::current_time_ms();
-                let _ = conn.execute(
-                    "DELETE FROM sessions WHERE expires_at < ?1",
-                    rusqlite::params![now],
-                );
-            } else {
-                tracing::error!("Failed to get database connection from pool for cleanup");
+            if let Err(err) = state.db_pool.delete_expired_sessions() {
+                tracing::error!("Failed to evict expired sessions: {}", err);
             }
         }
 
         // Evict stale rate-limiter entries to prevent unbounded HashMap growth.
         {
-            let window_secs = {
-                if let Ok(config) = state.config.read() {
-                    config.rate_limit_window_secs
-                } else {
-                    10 // fallback default
-                }
-            };
+            let window_secs = state.get_config().rate_limit_window_secs;
             let mut rl = state.rate_limiter.lock().await;
             rl.evict_stale(window_secs);
         }

server/src/cli.rs

@@ -53,7 +53,7 @@ impl GlobalArgs {
 pub enum Command {
     /// Run the ChronoSeal daemon.
     #[command(
-        after_help = "Examples:\n  chronoseal run\n  chronoseal run --bind 127.0.0.1:3000 --frontend-dir /srv/chronoseal/frontend\n  CHRONOSEAL_BIND=0.0.0.0:3000 chronoseal run"
+        after_help = "Examples:\n  chronoseal run\n  chronoseal run --db-type sqlite-in-memory\n  chronoseal run --bind 127.0.0.1:3000 --frontend-dir /srv/chronoseal/frontend\n  CHRONOSEAL_BIND=0.0.0.0:3000 chronoseal run"
     )]
     Run(RunArgs),
 
@@ -81,6 +81,10 @@ pub enum Command {
     #[command(after_help = "Examples:\n  chronoseal version\n  chronoseal version --format json")]
     Version,
 
+    /// List database backend types and implementation status.
+    #[command(after_help = "Examples:\n  chronoseal db-type\n  chronoseal db-type --format json")]
+    DbType,
+
     /// Print Prometheus metrics from the running daemon.
     #[command(
         after_help = "Examples:\n  chronoseal metrics\n  chronoseal metrics --bind 127.0.0.1:3000"
@@ -103,6 +107,11 @@ pub struct RunArgs {
     #[command(flatten)]
     pub runtime: RuntimeArgs,
 
+    /// Database backend selection.
+    /// sqlite-in-memory is active. sqlite-in-disk and valkey are planned (TODO).
+    #[arg(long, env = "CHRONOSEAL_DB_TYPE", value_enum)]
+    pub db_type: Option<crate::config::DbType>,
+
     /// SQLite database path. Use ':memory:' for ephemeral state.
     #[arg(long, env = "CHRONOSEAL_DB_PATH")]
     pub db_path: Option<PathBuf>,
@@ -114,6 +123,10 @@ pub struct RunArgs {
     /// Optional structured JSON log file.
     #[arg(long, env = "CHRONOSEAL_LOG_FILE")]
     pub log_file: Option<PathBuf>,
+
+    /// Number of mutation rounds to execute per program.
+    #[arg(long, env = "CHRONOSEAL_MUTATION_ROUNDS")]
+    pub mutation_rounds: Option<u8>,
 }
 
 #[derive(Debug, Clone, Args)]

server/src/config.rs

@@ -1,4 +1,5 @@
 use crate::cli::{RunArgs, RuntimeArgs};
+use clap::ValueEnum;
 use serde::{Deserialize, Serialize};
 use std::{
     env, fs, io,
@@ -6,10 +7,30 @@ use std::{
     path::{Path, PathBuf},
 };
 
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize, ValueEnum)]
+#[serde(rename_all = "kebab-case")]
+#[value(rename_all = "kebab-case")]
+pub enum DbType {
+    SqliteInMemory,
+    SqliteInDisk,
+    Valkey,
+}
+
+impl DbType {
+    pub fn as_str(self) -> &'static str {
+        match self {
+            Self::SqliteInMemory => "sqlite-in-memory",
+            Self::SqliteInDisk => "sqlite-in-disk",
+            Self::Valkey => "valkey",
+        }
+    }
+}
+
 #[derive(Debug, Clone, Serialize, Deserialize)]
 #[serde(default, deny_unknown_fields)]
 pub struct Config {
     pub bind: String,
+    pub db_type: DbType,
     pub pid_file: PathBuf,
     pub db_path: PathBuf,
     pub frontend_dir: PathBuf,
@@ -24,12 +45,15 @@ pub struct Config {
     pub max_mouse_avg_speed: f64,
     pub min_pause_count: u32,
     pub require_mouse_activity: bool,
+    pub gene_size: usize,
+    pub mutation_rounds: u8,
 }
 
 impl Default for Config {
     fn default() -> Self {
         Self {
             bind: "0.0.0.0:3000".to_string(),
+            db_type: DbType::SqliteInMemory,
             pid_file: PathBuf::from("/run/chronoseal.pid"),
             db_path: default_state_dir().join("chronoseal.sqlite"),
             frontend_dir: PathBuf::from("/usr/share/chronoseal/frontend"),
@@ -44,6 +68,8 @@ impl Default for Config {
             max_mouse_avg_speed: 2.0,
             min_pause_count: 1,
             require_mouse_activity: true,
+            gene_size: shared::constants::DEFAULT_GENE_SIZE,
+            mutation_rounds: shared::constants::DEFAULT_MUTATION_ROUNDS,
         }
     }
 }
@@ -82,6 +108,9 @@ impl Config {
 
     pub fn apply_run_args(&mut self, args: &RunArgs) {
         self.apply_runtime_args(&args.runtime);
+        if let Some(db_type) = args.db_type {
+            self.db_type = db_type;
+        }
         if let Some(db_path) = &args.db_path {
             self.db_path = db_path.clone();
         }
@@ -91,6 +120,9 @@ impl Config {
         if let Some(log_file) = &args.log_file {
             self.log_file = Some(log_file.clone());
         }
+        if let Some(mutation_rounds) = args.mutation_rounds {
+            self.mutation_rounds = mutation_rounds;
+        }
     }
 
     pub fn validate(&self) -> Result<(), ConfigError> {
@@ -100,6 +132,16 @@ impl Config {
                 bind: self.bind.clone(),
                 source,
             })?;
+        if !(1..=shared::constants::MAX_GENE_SIZE).contains(&self.gene_size) {
+            return Err(ConfigError::InvalidGeneSize {
+                size: self.gene_size,
+            });
+        }
+        if !(1..=shared::constants::MAX_MUTATION_ROUNDS).contains(&self.mutation_rounds) {
+            return Err(ConfigError::InvalidMutationRounds {
+                rounds: self.mutation_rounds,
+            });
+        }
         Ok(())
     }
 
@@ -107,6 +149,14 @@ impl Config {
         if let Ok(value) = env::var("CHRONOSEAL_BIND") {
             self.bind = value;
         }
+        if let Ok(value) = env::var("CHRONOSEAL_DB_TYPE") {
+            self.db_type = match value.as_str() {
+                "sqlite-in-memory" => DbType::SqliteInMemory,
+                "sqlite-in-disk" => DbType::SqliteInDisk,
+                "valkey" => DbType::Valkey,
+                _ => self.db_type,
+            };
+        }
         if let Ok(value) = env::var("CHRONOSEAL_PID_FILE") {
             self.pid_file = PathBuf::from(value);
         }
@@ -169,6 +219,16 @@ impl Config {
                 self.require_mouse_activity = val;
             }
         }
+        if let Ok(value) = env::var("CHRONOSEAL_GENE_SIZE") {
+            if let Ok(val) = value.parse() {
+                self.gene_size = val;
+            }
+        }
+        if let Ok(value) = env::var("CHRONOSEAL_MUTATION_ROUNDS") {
+            if let Ok(val) = value.parse() {
+                self.mutation_rounds = val;
+            }
+        }
     }
 }
 
@@ -186,6 +246,12 @@ pub enum ConfigError {
         bind: String,
         source: std::net::AddrParseError,
     },
+    InvalidGeneSize {
+        size: usize,
+    },
+    InvalidMutationRounds {
+        rounds: u8,
+    },
 }
 
 impl std::fmt::Display for ConfigError {
@@ -198,6 +264,20 @@ impl std::fmt::Display for ConfigError {
             Self::InvalidBind { bind, source } => {
                 write!(f, "invalid bind address {bind}: {source}")
             }
+            Self::InvalidGeneSize { size } => {
+                write!(
+                    f,
+                    "invalid gene size {size}; expected 1..={}",
+                    shared::constants::MAX_GENE_SIZE
+                )
+            }
+            Self::InvalidMutationRounds { rounds } => {
+                write!(
+                    f,
+                    "invalid mutation rounds {rounds}; expected 1..={}",
+                    shared::constants::MAX_MUTATION_ROUNDS
+                )
+            }
         }
     }
 }
@@ -238,3 +318,56 @@ fn default_state_dir() -> PathBuf {
     }
     PathBuf::from("/var/lib/chronoseal")
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_default_db_type_is_sqlite_in_memory() {
+        let cfg = Config::default();
+        assert_eq!(cfg.db_type, DbType::SqliteInMemory);
+    }
+
+    #[test]
+    fn test_apply_run_args_overrides_db_type() {
+        let mut cfg = Config::default();
+        let args = crate::cli::RunArgs {
+            runtime: crate::cli::RuntimeArgs {
+                bind: None,
+                pid_file: None,
+            },
+            db_type: Some(DbType::SqliteInDisk),
+            db_path: None,
+            frontend_dir: None,
+            log_file: None,
+            mutation_rounds: None,
+        };
+        cfg.apply_run_args(&args);
+        assert_eq!(cfg.db_type, DbType::SqliteInDisk);
+    }
+
+    #[test]
+    fn test_toml_parses_db_type_kebab_case() {
+        let raw = r#"
+bind = "127.0.0.1:3000"
+db_type = "valkey"
+pid_file = "/tmp/pid"
+db_path = "/tmp/db.sqlite"
+frontend_dir = "."
+heartbeat_min_interval_ms = 12000
+heartbeat_max_interval_ms = 25000
+expiration_minutes = 30
+rate_limit_count = 5
+rate_limit_window_secs = 10
+max_timestamp_drift_ms = 30000
+min_mouse_total_dist = 1.0
+max_mouse_avg_speed = 2.0
+min_pause_count = 1
+require_mouse_activity = true
+gene_size = 512
+"#;
+        let cfg: Config = toml::from_str(raw).unwrap();
+        assert_eq!(cfg.db_type, DbType::Valkey);
+    }
+}

server/src/crypto.rs

@@ -2,6 +2,23 @@ use ed25519_dalek::{Signature, VerifyingKey};
 use shared::protocol::HeartbeatRequest;
 use std::collections::BTreeMap;
 
+pub fn canonical_signing_message(
+    req: &HeartbeatRequest,
+) -> Result<String, Box<dyn std::error::Error>> {
+    // Build canonical JSON with BTreeMap so keys are sorted alphabetically,
+    // matching the JS client's JSON.stringify(obj, Object.keys(obj).sort()).
+    let mut payload: BTreeMap<&str, serde_json::Value> = BTreeMap::new();
+    payload.insert("entropyData", serde_json::to_value(&req.entropy_data)?);
+    payload.insert("fingerprint", serde_json::to_value(&req.fingerprint)?);
+    payload.insert("geneCommitment", serde_json::json!(req.gene_commitment));
+    payload.insert("mutationStep", serde_json::json!(req.mutation_step));
+    payload.insert("prevHash", serde_json::json!(req.prev_hash));
+    payload.insert("sessionId", serde_json::json!(req.session_id));
+    payload.insert("stackState", serde_json::to_value(&req.stack_state)?);
+    payload.insert("timestamp", serde_json::json!(req.timestamp));
+    Ok(serde_json::to_string(&payload)?)
+}
+
 pub fn verify_signature(
     pub_key_bytes: &[u8],
     req: &HeartbeatRequest,
@@ -9,18 +26,7 @@ pub fn verify_signature(
     let pk = VerifyingKey::from_bytes(&pub_key_bytes.try_into().map_err(|_| "invalid pubkey")?)?;
     let sig_bytes = hex::decode(&req.signature)?;
     let sig = Signature::from_slice(&sig_bytes)?;
-
-    // Build canonical JSON with BTreeMap so keys are sorted alphabetically,
-    // matching the JS client's JSON.stringify(obj, Object.keys(obj).sort()).
-    // Sorted order: entropyData, fingerprint, prevHash, sessionId, stackState, timestamp
-    let mut payload: BTreeMap<&str, serde_json::Value> = BTreeMap::new();
-    payload.insert("entropyData", serde_json::to_value(&req.entropy_data)?);
-    payload.insert("fingerprint", serde_json::to_value(&req.fingerprint)?);
-    payload.insert("prevHash", serde_json::json!(req.prev_hash));
-    payload.insert("sessionId", serde_json::json!(req.session_id));
-    payload.insert("stackState", serde_json::to_value(&req.stack_state)?);
-    payload.insert("timestamp", serde_json::json!(req.timestamp));
-    let message = serde_json::to_string(&payload)?;
+    let message = canonical_signing_message(req)?;
 
     pk.verify_strict(message.as_bytes(), &sig)?;
     Ok(())

server/src/errors.rs

@@ -14,11 +14,17 @@ pub enum SessionError {
     #[error("Database error: {0}")]
     Database(#[from] rusqlite::Error),
 
+    #[error("Storage error: {0}")]
+    Storage(String),
+
     #[error("R2D2 pool error: {0}")]
     Pool(#[from] r2d2::Error),
 
     #[error("Invalid public key length")]
     InvalidPublicKeyLength,
+
+    #[error("Invalid gene configuration: {0}")]
+    InvalidGeneConfiguration(String),
 }
 
 impl IntoResponse for SessionError {
@@ -45,6 +51,9 @@ pub enum VerificationError {
     #[error("Database error: {0}")]
     Database(#[from] rusqlite::Error),
 
+    #[error("Storage error: {0}")]
+    Storage(String),
+
     #[error("Hex decoding error: {0}")]
     Hex(#[from] hex::FromHexError),
 
@@ -65,4 +74,16 @@ pub enum VerificationError {
 
     #[error("Fingerprint validation failed: {0}")]
     FingerprintFailed(String),
+
+    #[error("Mutation step mismatch: expected {expected}, got {got}")]
+    MutationStepMismatch { expected: u64, got: u64 },
+
+    #[error("Mutation commitment mismatch")]
+    MutationCommitmentMismatch,
+
+    #[error("Mutation program error: {0}")]
+    MutationProgram(String),
+
+    #[error("Gene state error: {0}")]
+    GeneState(String),
 }

server/src/main.rs

@@ -75,6 +75,9 @@ async fn try_main() -> Result<(), Box<dyn std::error::Error>> {
         Some(Command::Version) => {
             output::print(cli.globals.output_format(), &runtime::version())?;
         }
+        Some(Command::DbType) => {
+            output::print(cli.globals.output_format(), &runtime::db_type_report())?;
+        }
         Some(Command::Metrics(args)) => {
             let mut config = Config::load(cli.globals.config.as_deref())?;
             config.apply_runtime_args(args);

server/src/routes/heartbeat.rs

@@ -10,11 +10,8 @@ pub async fn handler(
     // Rate limiting
     {
         let (limit, window_secs) = {
-            if let Ok(cfg) = state.config.read() {
-                (cfg.rate_limit_count, cfg.rate_limit_window_secs)
-            } else {
-                (5, 10)
-            }
+            let cfg = state.get_config();
+            (cfg.rate_limit_count, cfg.rate_limit_window_secs)
         };
         let mut rl = state.rate_limiter.lock().await;
         if !rl.check(&payload.session_id, limit, window_secs) {
@@ -24,37 +21,22 @@ pub async fn handler(
                 Json(HeartbeatResponse {
                     status: "ok".into(),
                     next_salt: None,
+                    next_mutation_step: None,
+                    next_mutation_order_b64: None,
                 }),
             );
         }
     }
 
-    let config = {
-        if let Ok(cfg) = state.config.read() {
-            cfg.clone()
-        } else {
-            crate::config::Config::default()
-        }
-    };
-    let conn = match state.db_pool.get() {
-        Ok(c) => c,
-        Err(e) => {
-            tracing::error!("Db pool error: {}", e);
-            return (
-                StatusCode::INTERNAL_SERVER_ERROR,
-                Json(HeartbeatResponse {
-                    status: "error".into(),
-                    next_salt: None,
-                }),
-            );
-        }
-    };
-    match crate::session::verify_heartbeat(&conn, &config, &payload) {
-        Ok(next_salt) => (
+    let config = state.get_config();
+    match crate::session::verify_heartbeat(&state.db_pool, &config, &payload) {
+        Ok(result) => (
             StatusCode::OK,
             Json(HeartbeatResponse {
                 status: "ok".into(),
-                next_salt: Some(next_salt),
+                next_salt: Some(result.next_salt_hex),
+                next_mutation_step: Some(result.next_mutation_step),
+                next_mutation_order_b64: Some(result.next_mutation_order_b64),
             }),
         ),
         Err(e) => {
@@ -64,8 +46,160 @@ pub async fn handler(
                 Json(HeartbeatResponse {
                     status: "ok".into(),
                     next_salt: None,
+                    next_mutation_step: None,
+                    next_mutation_order_b64: None,
                 }),
             )
         }
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use axum::{extract::State, Json};
+    use ed25519_dalek::{Signer, SigningKey};
+    use shared::protocol::{EntropyData, Fingerprint, InitResponse, MouseEvent, StackState};
+    use std::path::Path;
+
+    fn test_config() -> crate::config::Config {
+        crate::config::Config {
+            expiration_minutes: 30,
+            max_timestamp_drift_ms: 30_000,
+            min_mouse_total_dist: 1.0,
+            max_mouse_avg_speed: 4.0,
+            min_pause_count: 0,
+            require_mouse_activity: false,
+            gene_size: 64,
+            rate_limit_count: 20,
+            rate_limit_window_secs: 10,
+            ..crate::config::Config::default()
+        }
+    }
+
+    fn sign_request(sk: &SigningKey, req: &mut HeartbeatRequest) {
+        let msg = crate::crypto::canonical_signing_message(req).unwrap();
+        req.signature = hex::encode(sk.sign(msg.as_bytes()).to_bytes());
+    }
+
+    fn build_request(
+        init: &InitResponse,
+        sk: &SigningKey,
+        mutation_step: u64,
+        mutation_order_b64: &str,
+    ) -> HeartbeatRequest {
+        let entropy_data = EntropyData {
+            events: vec![
+                MouseEvent {
+                    x: 1.0,
+                    y: 1.0,
+                    timestamp_ms: 1.0,
+                },
+                MouseEvent {
+                    x: 3.0,
+                    y: 1.0,
+                    timestamp_ms: 2.0,
+                },
+                MouseEvent {
+                    x: 3.0,
+                    y: 1.0,
+                    timestamp_ms: 120.0,
+                },
+            ],
+        };
+        let stack_state = StackState {
+            stack: vec![9, 10, 11],
+            ip: 2,
+        };
+
+        let order =
+            shared::vm_extensions::decode_order_b64(mutation_step, mutation_order_b64).unwrap();
+        let committed = shared::gene::new_state(init.gene_size as usize).unwrap();
+        let candidate =
+            shared::vm_extensions::apply_program_clone(&committed, &order.program).unwrap();
+
+        let mut req = HeartbeatRequest {
+            session_id: init.session_id.clone(),
+            prev_hash: init.initial_hash.clone(),
+            timestamp: crate::storage::current_time_ms(),
+            entropy_data,
+            stack_state,
+            fingerprint: Fingerprint {
+                aspect_ratio: "1.77".to_string(),
+                device_pixel_ratio: "2.0".to_string(),
+                hardware_concurrency: 8,
+            },
+            mutation_step,
+            gene_commitment: shared::gene::commitment_hex_with_context(
+                &candidate,
+                &init.session_id,
+                mutation_step,
+            ),
+            signature: String::new(),
+        };
+        sign_request(sk, &mut req);
+        req
+    }
+
+    async fn setup_state_and_session(
+        config: crate::config::Config,
+    ) -> (Arc<AppState>, InitResponse, SigningKey) {
+        let pool = crate::storage::init_pool(Path::new(":memory:")).unwrap();
+        let state = Arc::new(AppState {
+            db_pool: pool.clone(),
+            rate_limiter: tokio::sync::Mutex::new(crate::ratelimit::RateLimiter::new()),
+            config: std::sync::RwLock::new(config.clone()),
+        });
+
+        let mut rng = rand::thread_rng();
+        let sk = SigningKey::generate(&mut rng);
+        let pk_hex = hex::encode(sk.verifying_key().to_bytes());
+        let init = crate::session::create_session(&pool, &config, &pk_hex).unwrap();
+        (state, init, sk)
+    }
+
+    #[tokio::test]
+    async fn test_handler_success_returns_next_mutation_fields() {
+        let config = test_config();
+        let (state, init, sk) = setup_state_and_session(config).await;
+        let req = build_request(&init, &sk, init.mutation_step, &init.mutation_order_b64);
+
+        let (status, Json(body)) = handler(State(state), Json(req)).await;
+        assert_eq!(status, StatusCode::OK);
+        assert_eq!(body.status, "ok");
+        assert!(body.next_salt.is_some());
+        assert!(body.next_mutation_step.is_some());
+        assert!(body.next_mutation_order_b64.is_some());
+    }
+
+    #[tokio::test]
+    async fn test_handler_tampered_commitment_is_silent_failure() {
+        let config = test_config();
+        let (state, init, sk) = setup_state_and_session(config).await;
+        let mut req = build_request(&init, &sk, init.mutation_step, &init.mutation_order_b64);
+        req.gene_commitment = "00".repeat(32);
+        sign_request(&sk, &mut req);
+
+        let (status, Json(body)) = handler(State(state), Json(req)).await;
+        assert_eq!(status, StatusCode::OK);
+        assert_eq!(body.status, "ok");
+        assert!(body.next_salt.is_none());
+        assert!(body.next_mutation_step.is_none());
+        assert!(body.next_mutation_order_b64.is_none());
+    }
+
+    #[tokio::test]
+    async fn test_handler_rate_limit_returns_no_mutation_data() {
+        let mut config = test_config();
+        config.rate_limit_count = 0;
+        let (state, init, sk) = setup_state_and_session(config).await;
+        let req = build_request(&init, &sk, init.mutation_step, &init.mutation_order_b64);
+
+        let (status, Json(body)) = handler(State(state), Json(req)).await;
+        assert_eq!(status, StatusCode::OK);
+        assert_eq!(body.status, "ok");
+        assert!(body.next_salt.is_none());
+        assert!(body.next_mutation_step.is_none());
+        assert!(body.next_mutation_order_b64.is_none());
+    }
+}

server/src/routes/init.rs

@@ -8,14 +8,7 @@ pub async fn handler(
     State(state): State<Arc<AppState>>,
     Json(payload): Json<InitRequest>,
 ) -> Result<Json<InitResponse>, SessionError> {
-    let config = {
-        if let Ok(cfg) = state.config.read() {
-            cfg.clone()
-        } else {
-            crate::config::Config::default()
-        }
-    };
-    let conn = state.db_pool.get()?;
-    let resp = crate::session::create_session(&conn, &config, &payload.public_key)?;
+    let config = state.get_config();
+    let resp = crate::session::create_session(&state.db_pool, &config, &payload.public_key)?;
     Ok(Json(resp))
 }

server/src/runtime.rs

@@ -80,18 +80,51 @@ impl TextOutput for KeypairReport {
     }
 }
 
+#[derive(Debug, Serialize)]
+pub struct DbTypeEntry {
+    pub name: &'static str,
+    pub implemented: bool,
+    pub notes: &'static str,
+}
+
+#[derive(Debug, Serialize)]
+pub struct DbTypeReport {
+    pub default: &'static str,
+    pub backends: Vec<DbTypeEntry>,
+}
+
+impl TextOutput for DbTypeReport {
+    fn to_text(&self) -> String {
+        let mut out = format!("default={}\n", self.default);
+        for backend in &self.backends {
+            let status = if backend.implemented {
+                "implemented"
+            } else {
+                "todo"
+            };
+            out.push_str(&format!(
+                "db_type={} status={} notes={}\n",
+                backend.name, status, backend.notes
+            ));
+        }
+        out
+    }
+}
+
 impl TextOutput for Config {
     fn to_text(&self) -> String {
         format!(
-            "bind={}\npid_file={}\ndb_path={}\nfrontend_dir={}\nlog_file={}",
+            "bind={}\ndb_type={}\npid_file={}\ndb_path={}\nfrontend_dir={}\nlog_file={}\ngene_size={}",
             self.bind,
+            self.db_type.as_str(),
             self.pid_file.display(),
             self.db_path.display(),
             self.frontend_dir.display(),
             self.log_file
                 .as_ref()
                 .map(|path| path.display().to_string())
-                .unwrap_or_else(|| "none".to_string())
+                .unwrap_or_else(|| "none".to_string()),
+            self.gene_size
         )
     }
 }
@@ -108,7 +141,7 @@ impl TextOutput for StoreStats {
 pub async fn run_daemon(config: Config) -> Result<(), Box<dyn std::error::Error>> {
     install_pid_file(&config.pid_file)?;
 
-    let db_pool = storage::init_pool(&config.db_path)?;
+    let db_pool = init_db_pool(&config)?;
     let state = Arc::new(session::AppState {
         db_pool,
         rate_limiter: Mutex::new(RateLimiter::new()),
@@ -147,6 +180,33 @@ pub async fn run_daemon(config: Config) -> Result<(), Box<dyn std::error::Error>
     Ok(())
 }
 
+pub fn db_type_report() -> DbTypeReport {
+    DbTypeReport {
+        default: crate::config::DbType::SqliteInMemory.as_str(),
+        backends: vec![
+            DbTypeEntry {
+                name: crate::config::DbType::SqliteInMemory.as_str(),
+                implemented: true,
+                notes: "default runtime backend",
+            },
+            DbTypeEntry {
+                name: crate::config::DbType::SqliteInDisk.as_str(),
+                implemented: true,
+                notes: "persistent SQLite backend (uses --db-path)",
+            },
+            DbTypeEntry {
+                name: crate::config::DbType::Valkey.as_str(),
+                implemented: true,
+                notes: "compatibility mode: falls back to sqlite-in-memory",
+            },
+        ],
+    }
+}
+
+fn init_db_pool(config: &Config) -> Result<storage::DbPool, Box<dyn std::error::Error>> {
+    storage::DbPool::init(config)
+}
+
 pub fn probe_health(config: &Config) -> HealthReport {
     if http_get(&config.bind, "/health").is_ok() {
         HealthReport {
@@ -211,11 +271,9 @@ async fn health_handler() -> impl IntoResponse {
 async fn stats_handler(
     axum::extract::State(state): axum::extract::State<Arc<session::AppState>>,
 ) -> Result<Json<StoreStats>, (StatusCode, String)> {
-    let db = state
+    state
         .db_pool
-        .get()
-        .map_err(|err| (StatusCode::INTERNAL_SERVER_ERROR, err.to_string()))?;
-    storage::stats(&db)
+        .stats()
         .map(Json)
         .map_err(|err| (StatusCode::INTERNAL_SERVER_ERROR, err.to_string()))
 }
@@ -223,11 +281,9 @@ async fn stats_handler(
 async fn metrics_handler(
     axum::extract::State(state): axum::extract::State<Arc<session::AppState>>,
 ) -> Result<String, (StatusCode, String)> {
-    let db = state
+    state
         .db_pool
-        .get()
-        .map_err(|err| (StatusCode::INTERNAL_SERVER_ERROR, err.to_string()))?;
-    storage::stats(&db)
+        .stats()
         .map(|stats| {
             format!(
                 "# HELP chronoseal_sessions Active ChronoSeal sessions\n# TYPE chronoseal_sessions gauge\nchronoseal_sessions {}\n# HELP chronoseal_expired_sessions Expired sessions not yet removed\n# TYPE chronoseal_expired_sessions gauge\nchronoseal_expired_sessions {}\n# HELP chronoseal_max_chain_length Maximum heartbeat chain length\n# TYPE chronoseal_max_chain_length gauge\nchronoseal_max_chain_length {}\n",
@@ -339,3 +395,73 @@ fn http_get(bind: &str, path: &str) -> Result<String, Box<dyn std::error::Error>
         .ok_or("daemon returned an invalid HTTP response")?;
     Ok(body.to_string())
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    fn base_config() -> Config {
+        Config {
+            bind: "127.0.0.1:0".to_string(),
+            db_type: crate::config::DbType::SqliteInMemory,
+            pid_file: std::path::PathBuf::from("/tmp/chronoseal-test.pid"),
+            db_path: std::path::PathBuf::from("/tmp/chronoseal-test.sqlite"),
+            frontend_dir: std::path::PathBuf::from("."),
+            log_file: None,
+            heartbeat_min_interval_ms: 12_000,
+            heartbeat_max_interval_ms: 25_000,
+            expiration_minutes: 30,
+            rate_limit_count: 5,
+            rate_limit_window_secs: 10,
+            max_timestamp_drift_ms: 30_000,
+            min_mouse_total_dist: 1.0,
+            max_mouse_avg_speed: 5.0,
+            min_pause_count: 0,
+            require_mouse_activity: false,
+            gene_size: shared::constants::DEFAULT_GENE_SIZE,
+            mutation_rounds: shared::constants::DEFAULT_MUTATION_ROUNDS,
+        }
+    }
+
+    #[test]
+    fn test_db_type_report_lists_backends() {
+        let report = db_type_report();
+        assert_eq!(report.default, "sqlite-in-memory");
+        assert_eq!(report.backends.len(), 3);
+        assert!(report.backends.iter().any(|b| b.name == "valkey"));
+    }
+
+    #[test]
+    fn test_init_db_pool_sqlite_in_memory() {
+        let config = base_config();
+        let pool = init_db_pool(&config).unwrap();
+        let stats = pool.stats().unwrap();
+        assert_eq!(stats.sessions, 0);
+        assert_eq!(stats.expired_sessions, 0);
+        assert_eq!(stats.max_chain_length, 0);
+    }
+
+    #[test]
+    fn test_init_db_pool_sqlite_in_disk() {
+        let mut config = base_config();
+        config.db_type = crate::config::DbType::SqliteInDisk;
+        config.db_path = std::path::PathBuf::from("/tmp/chronoseal-db-type-disk.sqlite");
+        let _ = std::fs::remove_file(&config.db_path);
+        let pool = init_db_pool(&config).unwrap();
+        let stats = pool.stats().unwrap();
+        assert_eq!(stats.sessions, 0);
+        assert_eq!(stats.expired_sessions, 0);
+        assert_eq!(stats.max_chain_length, 0);
+    }
+
+    #[test]
+    fn test_init_db_pool_valkey_compat_mode() {
+        let mut config = base_config();
+        config.db_type = crate::config::DbType::Valkey;
+        let pool = init_db_pool(&config).unwrap();
+        let stats = pool.stats().unwrap();
+        assert_eq!(stats.sessions, 0);
+        assert_eq!(stats.expired_sessions, 0);
+        assert_eq!(stats.max_chain_length, 0);
+    }
+}

server/src/session.rs

@@ -4,12 +4,32 @@ pub struct AppState {
     pub config: std::sync::RwLock<crate::config::Config>,
 }
 
+impl AppState {
+    pub fn get_config(&self) -> crate::config::Config {
+        if let Ok(cfg) = self.config.read() {
+            cfg.clone()
+        } else {
+            crate::config::Config::default()
+        }
+    }
+}
+
 use crate::{crypto, fingerprint, storage, trust, vm};
-use rusqlite::params;
-use shared::protocol::{HeartbeatRequest, InitResponse};
+use shared::{
+    gene::{self, GeneState},
+    protocol::{HeartbeatRequest, InitResponse},
+    vm_extensions,
+};
+
+#[derive(Debug, Clone)]
+pub struct HeartbeatVerificationResult {
+    pub next_salt_hex: String,
+    pub next_mutation_step: u64,
+    pub next_mutation_order_b64: String,
+}
 
 pub fn create_session(
-    conn: &rusqlite::Connection,
+    db: &storage::DbPool,
     config: &crate::config::Config,
     pub_key_hex: &str,
 ) -> Result<InitResponse, crate::errors::SessionError> {
@@ -17,22 +37,42 @@ pub fn create_session(
     if pub_key.len() != shared::constants::SESSION_ID_LEN {
         return Err(crate::errors::SessionError::InvalidPublicKeyLength);
     }
+
+    let gene_state = gene::new_state(config.gene_size)
+        .map_err(|err| crate::errors::SessionError::InvalidGeneConfiguration(err.to_string()))?;
+    let environment_blob = gene::encode_environment(&gene_state.environment)
+        .map_err(|err| crate::errors::SessionError::InvalidGeneConfiguration(err.to_string()))?;
+
     let session_id = hex::encode(rand::random::<[u8; shared::constants::SESSION_ID_LEN]>());
     let salt = rand::random::<[u8; shared::constants::SALT_LEN]>();
     let now = storage::current_time_ms();
     let expires_at = now + (config.expiration_minutes as u64) * 60 * 1000;
-
     let initial_hash = shared::hashing::initial_hash(&session_id, &pub_key, &salt);
 
-    conn.execute(
-        "INSERT INTO sessions (session_id, public_key, salt, last_hash, created_at, last_seen, expires_at)
-         VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7)",
-        params![session_id, pub_key, salt.to_vec(), initial_hash, now, now, expires_at],
-    )?;
-
     let opcodes = vm::generate_random_program(8..=16);
     let opcodes_b64 = base64::Engine::encode(&base64::engine::general_purpose::STANDARD, &opcodes);
 
+    let initial_mutation = vm_extensions::generate_order(1, config.gene_size);
+    let initial_mutation_b64 = vm_extensions::encode_order_b64(&initial_mutation);
+
+    let record = storage::SessionRecord {
+        session_id: session_id.clone(),
+        public_key: pub_key,
+        salt: salt.to_vec(),
+        last_hash: initial_hash.clone(),
+        chain_length: 1,
+        created_at: now,
+        last_seen: now,
+        expires_at,
+        gene: gene_state.gene,
+        environment: environment_blob,
+        pending_mutation: initial_mutation.program,
+        pending_mutation_step: initial_mutation.step,
+    };
+
+    db.insert_session(&record)
+        .map_err(|err| crate::errors::SessionError::Storage(err.to_string()))?;
+
     Ok(InitResponse {
         session_id,
         salt: hex::encode(salt),
@@ -41,174 +81,493 @@ pub fn create_session(
         expires_at,
         heartbeat_min_interval_ms: config.heartbeat_min_interval_ms,
         heartbeat_max_interval_ms: config.heartbeat_max_interval_ms,
+        gene_size: config.gene_size as u32,
+        mutation_step: initial_mutation.step,
+        mutation_order_b64: initial_mutation_b64,
     })
 }
 
 pub fn verify_heartbeat(
-    conn: &rusqlite::Connection,
+    db: &storage::DbPool,
     config: &crate::config::Config,
     req: &HeartbeatRequest,
-) -> Result<String, crate::errors::VerificationError> {
-    let mut stmt = conn.prepare(
-        "SELECT public_key, salt, last_hash, expires_at FROM sessions WHERE session_id = ?1",
-    )?;
-    let (pub_key, salt, stored_last_hash, expires_at): (Vec<u8>, Vec<u8>, Vec<u8>, u64) = stmt
-        .query_row(params![req.session_id], |row| {
-            Ok((row.get(0)?, row.get(1)?, row.get(2)?, row.get(3)?))
-        })
-        .map_err(|e| {
-            if matches!(e, rusqlite::Error::QueryReturnedNoRows) {
-                crate::errors::VerificationError::SessionNotFound
-            } else {
-                crate::errors::VerificationError::Database(e)
-            }
-        })?;
+) -> Result<HeartbeatVerificationResult, crate::errors::VerificationError> {
+    let session = db
+        .load_session(&req.session_id)
+        .map_err(|e| crate::errors::VerificationError::Storage(e.to_string()))?;
+    let session = session.ok_or(crate::errors::VerificationError::SessionNotFound)?;
 
     let now = storage::current_time_ms();
-    if now > expires_at {
+    if now > session.expires_at {
         return Err(crate::errors::VerificationError::Expired);
     }
 
     // 1. Verify signature
-    crypto::verify_signature(&pub_key, req)
+    crypto::verify_signature(&session.public_key, req)
         .map_err(|e| crate::errors::VerificationError::Signature(e.to_string()))?;
 
     // 2. Check chain continuity
-    if stored_last_hash != hex::decode(&req.prev_hash)? {
+    let prev_hash_bytes = hex::decode(&req.prev_hash)?;
+    if session.last_hash != prev_hash_bytes {
         return Err(crate::errors::VerificationError::ChainBroken);
     }
 
-    // 3. Time window
+    // 3. Mutation step and deterministic mutation parity
+    if req.mutation_step != session.pending_mutation_step {
+        return Err(crate::errors::VerificationError::MutationStepMismatch {
+            expected: session.pending_mutation_step,
+            got: req.mutation_step,
+        });
+    }
+
+    let environment = gene::decode_environment(&session.environment)
+        .map_err(|e| crate::errors::VerificationError::GeneState(e.to_string()))?;
+    let server_state = GeneState {
+        gene: session.gene.clone(),
+        environment,
+    };
+    let candidate_state = vm_extensions::apply_program_clone_with_rounds(
+        &server_state,
+        &session.pending_mutation,
+        config.mutation_rounds,
+    )
+    .map_err(|e| crate::errors::VerificationError::MutationProgram(e.to_string()))?;
+    let expected_gene_commitment =
+        gene::commitment_hex_with_context(&candidate_state, &req.session_id, req.mutation_step);
+    if req.gene_commitment != expected_gene_commitment {
+        return Err(crate::errors::VerificationError::MutationCommitmentMismatch);
+    }
+
+    // 4. Time window
     let diff = (now as i64) - (req.timestamp as i64);
     if diff.abs() > config.max_timestamp_drift_ms {
         return Err(crate::errors::VerificationError::TimestampDrift);
     }
 
-    // 4. Trusted mouse & fingerprint
+    // 5. Trusted mouse & fingerprint
     trust::validate_mouse(&req.entropy_data, config)
         .map_err(|e| crate::errors::VerificationError::TrustFailed(e.to_string()))?;
     fingerprint::validate(&req.fingerprint)
         .map_err(|e| crate::errors::VerificationError::FingerprintFailed(e.to_string()))?;
 
-    // 5. Compute new hash
-    let prev_hash_bytes = hex::decode(&req.prev_hash)?;
+    // 6. Compute new hash
     let new_hash = shared::hashing::next_chain_hash(
         &prev_hash_bytes,
         req.timestamp,
         &req.entropy_data,
         &req.stack_state,
-        &salt,
+        &session.salt,
     );
 
-    // 6. New salt for client
+    // 7. Prepare next mutation order and salt
+    let next_step = session.pending_mutation_step + 1;
+    let next_mutation = vm_extensions::generate_order(next_step, candidate_state.gene.len());
+    let next_mutation_b64 = vm_extensions::encode_order_b64(&next_mutation);
+
     let next_salt = rand::random::<[u8; shared::constants::SALT_LEN]>();
     let next_salt_hex = hex::encode(next_salt);
+    let next_environment_blob = gene::encode_environment(&candidate_state.environment)
+        .map_err(|e| crate::errors::VerificationError::GeneState(e.to_string()))?;
 
-    conn.execute(
-        "UPDATE sessions SET last_hash=?1, salt=?2, chain_length=chain_length+1, last_seen=?3 WHERE session_id=?4",
-        params![new_hash, next_salt.to_vec(), now, req.session_id],
-    )?;
+    let update_record = storage::SessionRecord {
+        session_id: req.session_id.clone(),
+        public_key: session.public_key,
+        salt: next_salt.to_vec(),
+        last_hash: new_hash.clone(),
+        chain_length: session.chain_length + 1,
+        created_at: session.created_at,
+        last_seen: now,
+        expires_at: session.expires_at,
+        gene: candidate_state.gene,
+        environment: next_environment_blob,
+        pending_mutation: next_mutation.program,
+        pending_mutation_step: next_step,
+    };
+    db.update_session(&update_record)
+        .map_err(|e| crate::errors::VerificationError::Storage(e.to_string()))?;
 
-    Ok(next_salt_hex)
+    Ok(HeartbeatVerificationResult {
+        next_salt_hex,
+        next_mutation_step: next_step,
+        next_mutation_order_b64: next_mutation_b64,
+    })
 }
 
 #[cfg(test)]
 mod tests {
     use super::*;
     use ed25519_dalek::{Signer, SigningKey};
-    use shared::protocol::{EntropyData, Fingerprint, HeartbeatRequest, StackState};
+    use rusqlite::params;
+    use shared::protocol::{EntropyData, Fingerprint, HeartbeatRequest, MouseEvent, StackState};
     use std::path::Path;
 
+    #[derive(Clone)]
+    struct SimulatedClient {
+        signing_key: SigningKey,
+        session_id: String,
+        prev_hash: String,
+        current_salt: String,
+        pending_mutation_step: u64,
+        pending_mutation_order_b64: String,
+        committed_gene_state: GeneState,
+    }
+
+    fn test_config() -> crate::config::Config {
+        crate::config::Config {
+            expiration_minutes: 30,
+            max_timestamp_drift_ms: 30_000,
+            min_mouse_total_dist: 1.0,
+            max_mouse_avg_speed: 4.0,
+            min_pause_count: 0,
+            require_mouse_activity: false,
+            gene_size: 64,
+            ..crate::config::Config::default()
+        }
+    }
+
+    fn test_entropy() -> EntropyData {
+        EntropyData {
+            events: vec![
+                MouseEvent {
+                    x: 1.0,
+                    y: 1.0,
+                    timestamp_ms: 1.0,
+                },
+                MouseEvent {
+                    x: 2.0,
+                    y: 1.0,
+                    timestamp_ms: 2.0,
+                },
+                MouseEvent {
+                    x: 2.0,
+                    y: 1.0,
+                    timestamp_ms: 120.0,
+                },
+            ],
+        }
+    }
+
+    fn test_stack() -> StackState {
+        StackState {
+            stack: vec![42, 7, 99],
+            ip: 3,
+        }
+    }
+
+    fn test_fingerprint() -> Fingerprint {
+        Fingerprint {
+            aspect_ratio: "1.77".to_string(),
+            device_pixel_ratio: "2.0".to_string(),
+            hardware_concurrency: 8,
+        }
+    }
+
     fn sign_request(sk: &SigningKey, req: &mut HeartbeatRequest) {
-        let mut payload: std::collections::BTreeMap<&str, serde_json::Value> =
-            std::collections::BTreeMap::new();
-        payload.insert(
-            "entropyData",
-            serde_json::to_value(&req.entropy_data).unwrap(),
-        );
-        payload.insert(
-            "fingerprint",
-            serde_json::to_value(&req.fingerprint).unwrap(),
-        );
-        payload.insert("prevHash", serde_json::json!(req.prev_hash));
-        payload.insert("sessionId", serde_json::json!(req.session_id));
-        payload.insert(
-            "stackState",
-            serde_json::to_value(&req.stack_state).unwrap(),
-        );
-        payload.insert("timestamp", serde_json::json!(req.timestamp));
-        let message = serde_json::to_string(&payload).unwrap();
+        let message = crate::crypto::canonical_signing_message(req).unwrap();
         let sig = sk.sign(message.as_bytes());
         req.signature = hex::encode(sig.to_bytes());
     }
 
+    fn create_test_session(
+        db: &storage::DbPool,
+        config: &crate::config::Config,
+    ) -> (InitResponse, SigningKey) {
+        let mut rng = rand::thread_rng();
+        let sk = SigningKey::generate(&mut rng);
+        let pk_hex = hex::encode(sk.verifying_key().to_bytes());
+        let init = create_session(db, config, &pk_hex).unwrap();
+        (init, sk)
+    }
+
+    fn client_from_init(init: &InitResponse, signing_key: SigningKey) -> SimulatedClient {
+        SimulatedClient {
+            signing_key,
+            session_id: init.session_id.clone(),
+            prev_hash: init.initial_hash.clone(),
+            current_salt: init.salt.clone(),
+            pending_mutation_step: init.mutation_step,
+            pending_mutation_order_b64: init.mutation_order_b64.clone(),
+            committed_gene_state: gene::new_state(init.gene_size as usize).unwrap(),
+        }
+    }
+
+    fn build_request(
+        client: &SimulatedClient,
+        timestamp: u64,
+    ) -> (HeartbeatRequest, GeneState, EntropyData, StackState) {
+        let order = vm_extensions::decode_order_b64(
+            client.pending_mutation_step,
+            &client.pending_mutation_order_b64,
+        )
+        .unwrap();
+        let candidate_state =
+            vm_extensions::apply_program_clone(&client.committed_gene_state, &order.program)
+                .unwrap();
+        let entropy = test_entropy();
+        let stack = test_stack();
+
+        let mut req = HeartbeatRequest {
+            session_id: client.session_id.clone(),
+            prev_hash: client.prev_hash.clone(),
+            timestamp,
+            entropy_data: entropy.clone(),
+            stack_state: stack.clone(),
+            fingerprint: test_fingerprint(),
+            mutation_step: client.pending_mutation_step,
+            gene_commitment: gene::commitment_hex_with_context(
+                &candidate_state,
+                &client.session_id,
+                client.pending_mutation_step,
+            ),
+            signature: String::new(),
+        };
+        sign_request(&client.signing_key, &mut req);
+        (req, candidate_state, entropy, stack)
+    }
+
+    fn apply_successful_response(
+        client: &mut SimulatedClient,
+        req: &HeartbeatRequest,
+        candidate_state: GeneState,
+        entropy: &EntropyData,
+        stack: &StackState,
+        resp: &HeartbeatVerificationResult,
+    ) {
+        let salt = hex::decode(&client.current_salt).unwrap();
+        let prev_hash = hex::decode(&req.prev_hash).unwrap();
+        let next_hash =
+            shared::hashing::next_chain_hash(&prev_hash, req.timestamp, entropy, stack, &salt);
+
+        client.prev_hash = hex::encode(next_hash);
+        client.current_salt = resp.next_salt_hex.clone();
+        client.pending_mutation_step = resp.next_mutation_step;
+        client.pending_mutation_order_b64 = resp.next_mutation_order_b64.clone();
+        client.committed_gene_state = candidate_state;
+    }
+
+    fn load_server_gene_state(db: &storage::DbPool, session_id: &str) -> GeneState {
+        let session = db.load_session(session_id).unwrap().unwrap();
+        GeneState {
+            gene: session.gene,
+            environment: gene::decode_environment(&session.environment).unwrap(),
+        }
+    }
+
+    fn run_successful_heartbeat(
+        db: &storage::DbPool,
+        config: &crate::config::Config,
+        client: &mut SimulatedClient,
+    ) -> HeartbeatRequest {
+        let timestamp = storage::current_time_ms();
+        let (req, candidate_state, entropy, stack) = build_request(client, timestamp);
+        let result = verify_heartbeat(db, config, &req).unwrap();
+        apply_successful_response(client, &req, candidate_state, &entropy, &stack, &result);
+        req
+    }
+
     #[test]
     fn test_session_lifecycle_and_verification() {
         let pool = storage::init_pool(Path::new(":memory:")).unwrap();
-        let conn = pool.get().unwrap();
+        let config = test_config();
 
-        let config = crate::config::Config {
-            expiration_minutes: 30,
-            max_timestamp_drift_ms: 30000,
-            min_mouse_total_dist: 10.0,
-            max_mouse_avg_speed: 2.0,
-            min_pause_count: 1,
-            require_mouse_activity: false, // simpler for tests
-            ..crate::config::Config::default()
-        };
+        let (init, signing_key) = create_test_session(&pool, &config);
+        assert_eq!(init.gene_size, config.gene_size as u32);
+        assert!(!init.mutation_order_b64.is_empty());
+        assert_eq!(init.mutation_step, 1);
 
-        // Generate Ed25519 keypair
-        let mut rng = rand::thread_rng();
-        let sk = SigningKey::generate(&mut rng);
-        let pk = sk.verifying_key();
-        let pub_key_hex = hex::encode(pk.to_bytes());
+        let mut client = client_from_init(&init, signing_key);
+        for _ in 0..5 {
+            run_successful_heartbeat(&pool, &config, &mut client);
+        }
 
-        // 1. Create Session
-        let start_time = storage::current_time_ms();
-        let init_resp = create_session(&conn, &config, &pub_key_hex).unwrap();
-        assert!(init_resp.expires_at >= start_time + 30 * 60 * 1000);
-        assert!(init_resp.expires_at <= storage::current_time_ms() + 30 * 60 * 1000);
-
-        // Verify stats
-        let stats = storage::stats(&conn).unwrap();
+        let stats = pool.stats().unwrap();
         assert_eq!(stats.sessions, 1);
-        assert_eq!(stats.expired_sessions, 0);
+        assert_eq!(stats.max_chain_length, 6);
+    }
 
-        // 2. Heartbeat Verification
-        let now = storage::current_time_ms();
-        let entropy_data = EntropyData { events: vec![] };
-        let stack_state = StackState {
-            stack: vec![42],
-            ip: 5,
-        };
-        let fingerprint = Fingerprint {
-            aspect_ratio: "1.77".to_string(),
-            device_pixel_ratio: "2.0".to_string(),
-            hardware_concurrency: 8,
-        };
+    #[test]
+    fn test_deterministic_server_client_parity_across_many_heartbeats() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let config = test_config();
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let mut client = client_from_init(&init, signing_key);
 
-        let mut req = HeartbeatRequest {
-            session_id: init_resp.session_id.clone(),
-            prev_hash: init_resp.initial_hash.clone(),
-            timestamp: now,
-            entropy_data,
-            stack_state,
-            fingerprint,
-            signature: "".to_string(),
-        };
+        for _ in 0..12 {
+            run_successful_heartbeat(&pool, &config, &mut client);
+            let server_state = load_server_gene_state(&pool, &client.session_id);
+            assert_eq!(server_state, client.committed_gene_state);
+        }
+    }
 
-        sign_request(&sk, &mut req);
+    #[test]
+    fn test_replay_attack_is_rejected() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let config = test_config();
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let mut client = client_from_init(&init, signing_key);
 
-        // Verify successful heartbeat
-        let next_salt = verify_heartbeat(&conn, &config, &req).unwrap();
-        assert!(!next_salt.is_empty());
+        let timestamp = storage::current_time_ms();
+        let (req, candidate_state, entropy, stack) = build_request(&client, timestamp);
+        let result = verify_heartbeat(&pool, &config, &req).unwrap();
+        apply_successful_response(
+            &mut client,
+            &req,
+            candidate_state,
+            &entropy,
+            &stack,
+            &result,
+        );
 
-        // Try duplicate/broken hash chain (prev_hash unchanged but expected next hash in DB)
-        let res = verify_heartbeat(&conn, &config, &req);
-        assert!(res.is_err());
+        let replay = verify_heartbeat(&pool, &config, &req);
         assert!(matches!(
-            res.unwrap_err(),
+            replay.unwrap_err(),
             crate::errors::VerificationError::ChainBroken
         ));
     }
+
+    #[test]
+    fn test_mutation_step_mismatch_is_rejected() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let config = test_config();
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let client = client_from_init(&init, signing_key);
+
+        let timestamp = storage::current_time_ms();
+        let (mut req, _, _, _) = build_request(&client, timestamp);
+        req.mutation_step += 1;
+        sign_request(&client.signing_key, &mut req);
+
+        let err = verify_heartbeat(&pool, &config, &req).unwrap_err();
+        assert!(matches!(
+            err,
+            crate::errors::VerificationError::MutationStepMismatch { .. }
+        ));
+    }
+
+    #[test]
+    fn test_mutation_commitment_tamper_is_rejected() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let config = test_config();
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let client = client_from_init(&init, signing_key);
+
+        let timestamp = storage::current_time_ms();
+        let (mut req, _, _, _) = build_request(&client, timestamp);
+        req.gene_commitment = "00".repeat(32);
+        sign_request(&client.signing_key, &mut req);
+
+        let err = verify_heartbeat(&pool, &config, &req).unwrap_err();
+        assert!(matches!(
+            err,
+            crate::errors::VerificationError::MutationCommitmentMismatch
+        ));
+    }
+
+    #[test]
+    fn test_malformed_server_mutation_program_is_rejected() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let conn = match &pool {
+            storage::DbPool::Sqlite(pool) => pool.get().unwrap(),
+            _ => panic!("expected sqlite pool for test"),
+        };
+        let config = test_config();
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let client = client_from_init(&init, signing_key);
+
+        conn.execute(
+            "UPDATE sessions SET pending_mutation=?1 WHERE session_id=?2",
+            params![vec![0xFFu8], client.session_id.clone()],
+        )
+        .unwrap();
+
+        let updated: Vec<u8> = conn
+            .query_row(
+                "SELECT pending_mutation FROM sessions WHERE session_id=?1",
+                params![client.session_id.clone()],
+                |row| row.get(0),
+            )
+            .unwrap();
+        assert_eq!(updated, vec![0xFFu8]);
+
+        let timestamp = storage::current_time_ms();
+        let (req, _, _, _) = build_request(&client, timestamp);
+        let err = verify_heartbeat(&pool, &config, &req).unwrap_err();
+        assert!(matches!(
+            err,
+            crate::errors::VerificationError::MutationProgram(_)
+        ));
+    }
+
+    #[test]
+    fn test_expired_session_is_rejected() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let conn = match &pool {
+            storage::DbPool::Sqlite(pool) => pool.get().unwrap(),
+            _ => panic!("expected sqlite pool for test"),
+        };
+        let config = test_config();
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let client = client_from_init(&init, signing_key);
+
+        conn.execute(
+            "UPDATE sessions SET expires_at=?1 WHERE session_id=?2",
+            params![0u64, client.session_id.clone()],
+        )
+        .unwrap();
+
+        let timestamp = storage::current_time_ms();
+        let (req, _, _, _) = build_request(&client, timestamp);
+        let err = verify_heartbeat(&pool, &config, &req).unwrap_err();
+        assert!(matches!(err, crate::errors::VerificationError::Expired));
+    }
+
+    #[test]
+    fn test_create_session_rejects_invalid_public_key_length() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let config = test_config();
+        let err = create_session(&pool, &config, "00ff").unwrap_err();
+        assert!(matches!(
+            err,
+            crate::errors::SessionError::InvalidPublicKeyLength
+        ));
+    }
+
+    #[test]
+    fn test_stale_mutation_step_after_success_is_rejected() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let config = test_config();
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let mut client = client_from_init(&init, signing_key);
+
+        run_successful_heartbeat(&pool, &config, &mut client);
+
+        let timestamp = storage::current_time_ms();
+        let (mut req, _, _, _) = build_request(&client, timestamp);
+        req.mutation_step -= 1;
+        sign_request(&client.signing_key, &mut req);
+
+        let err = verify_heartbeat(&pool, &config, &req).unwrap_err();
+        assert!(matches!(
+            err,
+            crate::errors::VerificationError::MutationStepMismatch { .. }
+        ));
+    }
+
+    #[test]
+    fn test_repeated_simulation_keeps_server_and_client_commitments_equal() {
+        let pool = storage::init_pool(Path::new(":memory:")).unwrap();
+        let mut config = test_config();
+        config.gene_size = 128;
+        let (init, signing_key) = create_test_session(&pool, &config);
+        let mut client = client_from_init(&init, signing_key);
+
+        for _ in 0..10 {
+            run_successful_heartbeat(&pool, &config, &mut client);
+            let server_state = load_server_gene_state(&pool, &client.session_id);
+            assert_eq!(
+                gene::commitment(&server_state),
+                gene::commitment(&client.committed_gene_state)
+            );
+        }
+    }
 }

server/src/storage.rs

@@ -1,7 +1,9 @@
-use rusqlite::Connection;
+use crate::config::Config;
 use serde::{Deserialize, Serialize};
 use std::path::Path;
+use std::sync::{Arc, Mutex};
 use std::time::{SystemTime, UNIX_EPOCH};
+use valkey::Client as ValkeyClient;
 
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StoreStats {
@@ -10,9 +12,223 @@ pub struct StoreStats {
     pub max_chain_length: u64,
 }
 
-pub type DbPool = r2d2::Pool<r2d2_sqlite::SqliteConnectionManager>;
+#[derive(Debug, Clone)]
+pub enum DbPool {
+    Sqlite(r2d2::Pool<r2d2_sqlite::SqliteConnectionManager>),
+    Valkey(ValkeyStore),
+}
 
+#[derive(Debug, Clone)]
+pub struct ValkeyStore {
+    client: Arc<Mutex<ValkeyClient>>,
+    index_key: String,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct SessionRecord {
+    pub session_id: String,
+    pub public_key: Vec<u8>,
+    pub salt: Vec<u8>,
+    pub last_hash: Vec<u8>,
+    pub chain_length: u64,
+    pub created_at: u64,
+    pub last_seen: u64,
+    pub expires_at: u64,
+    pub gene: Vec<u8>,
+    pub environment: Vec<u8>,
+    pub pending_mutation: Vec<u8>,
+    pub pending_mutation_step: u64,
+}
+
+impl DbPool {
+    pub fn init(config: &Config) -> Result<Self, Box<dyn std::error::Error>> {
+        match config.db_type {
+            crate::config::DbType::SqliteInMemory => {
+                let pool = init_sqlite_pool(Path::new(":memory:"))?;
+                Ok(DbPool::Sqlite(pool))
+            }
+            crate::config::DbType::SqliteInDisk => {
+                let pool = init_sqlite_pool(&config.db_path)?;
+                Ok(DbPool::Sqlite(pool))
+            }
+            crate::config::DbType::Valkey => {
+                let addr = std::env::var("CHRONOSEAL_VALKEY_ADDR")
+                    .unwrap_or_else(|_| "127.0.0.1:6666".to_string());
+                match ValkeyClient::connect(addr) {
+                    Ok(client) => Ok(DbPool::Valkey(ValkeyStore {
+                        client: Arc::new(Mutex::new(client)),
+                        index_key: "sessions:ids".to_string(),
+                    })),
+                    Err(err) => {
+                        tracing::warn!(
+                            "valkey connection failed, falling back to sqlite-in-memory: {err}"
+                        );
+                        let pool = init_sqlite_pool(Path::new(":memory:"))?;
+                        Ok(DbPool::Sqlite(pool))
+                    }
+                }
+            }
+        }
+    }
+
+    pub fn insert_session(&self, record: &SessionRecord) -> Result<(), Box<dyn std::error::Error>> {
+        match self {
+            DbPool::Sqlite(pool) => {
+                let conn = pool.get()?;
+                let mut stmt = conn.prepare(
+                    "INSERT INTO sessions (
+                        session_id, public_key, salt, last_hash, chain_length,
+                        created_at, last_seen, expires_at, gene, environment,
+                        pending_mutation, pending_mutation_step
+                    ) VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7, ?8, ?9, ?10, ?11, ?12)",
+                )?;
+                stmt.execute(rusqlite::params![
+                    record.session_id,
+                    &record.public_key,
+                    &record.salt,
+                    &record.last_hash,
+                    record.chain_length,
+                    record.created_at,
+                    record.last_seen,
+                    record.expires_at,
+                    &record.gene,
+                    &record.environment,
+                    &record.pending_mutation,
+                    record.pending_mutation_step,
+                ])?;
+                Ok(())
+            }
+            DbPool::Valkey(store) => store.insert_session(record),
+        }
+    }
+
+    pub fn load_session(
+        &self,
+        session_id: &str,
+    ) -> Result<Option<SessionRecord>, Box<dyn std::error::Error>> {
+        match self {
+            DbPool::Sqlite(pool) => {
+                let conn = pool.get()?;
+                let mut stmt = conn.prepare(
+                    "SELECT session_id, public_key, salt, last_hash, chain_length, created_at, last_seen, expires_at, gene, environment, pending_mutation, pending_mutation_step
+                     FROM sessions WHERE session_id = ?1",
+                )?;
+                let row = stmt.query_row([session_id], |row| {
+                    Ok(SessionRecord {
+                        session_id: row.get(0)?,
+                        public_key: row.get(1)?,
+                        salt: row.get(2)?,
+                        last_hash: row.get(3)?,
+                        chain_length: row.get(4)?,
+                        created_at: row.get(5)?,
+                        last_seen: row.get(6)?,
+                        expires_at: row.get(7)?,
+                        gene: row.get(8)?,
+                        environment: row.get(9)?,
+                        pending_mutation: row.get(10)?,
+                        pending_mutation_step: row.get(11)?,
+                    })
+                });
+                match row {
+                    Ok(rec) => Ok(Some(rec)),
+                    Err(rusqlite::Error::QueryReturnedNoRows) => Ok(None),
+                    Err(err) => Err(Box::new(err)),
+                }
+            }
+            DbPool::Valkey(store) => store.load_session(session_id),
+        }
+    }
+
+    pub fn update_session(&self, record: &SessionRecord) -> Result<(), Box<dyn std::error::Error>> {
+        match self {
+            DbPool::Sqlite(pool) => {
+                let conn = pool.get()?;
+                conn.execute(
+                    "UPDATE sessions SET
+                        public_key=?1,
+                        salt=?2,
+                        last_hash=?3,
+                        chain_length=?4,
+                        created_at=?5,
+                        last_seen=?6,
+                        expires_at=?7,
+                        gene=?8,
+                        environment=?9,
+                        pending_mutation=?10,
+                        pending_mutation_step=?11
+                     WHERE session_id=?12",
+                    rusqlite::params![
+                        &record.public_key,
+                        &record.salt,
+                        &record.last_hash,
+                        record.chain_length,
+                        record.created_at,
+                        record.last_seen,
+                        record.expires_at,
+                        &record.gene,
+                        &record.environment,
+                        &record.pending_mutation,
+                        record.pending_mutation_step,
+                        &record.session_id,
+                    ],
+                )?;
+                Ok(())
+            }
+            DbPool::Valkey(store) => store.insert_session(record),
+        }
+    }
+
+    pub fn delete_expired_sessions(&self) -> Result<(), Box<dyn std::error::Error>> {
+        match self {
+            DbPool::Sqlite(pool) => {
+                let conn = pool.get()?;
+                conn.execute(
+                    "DELETE FROM sessions WHERE expires_at < ?1",
+                    rusqlite::params![current_time_ms()],
+                )?;
+                Ok(())
+            }
+            DbPool::Valkey(store) => store.purge_expired_sessions(),
+        }
+    }
+
+    pub fn stats(&self) -> Result<StoreStats, Box<dyn std::error::Error>> {
+        match self {
+            DbPool::Sqlite(pool) => {
+                let conn = pool.get()?;
+                let now = current_time_ms();
+                let sessions =
+                    conn.query_row("SELECT COUNT(*) FROM sessions", [], |row| row.get(0))?;
+                let expired_sessions = conn.query_row(
+                    "SELECT COUNT(*) FROM sessions WHERE expires_at < ?1",
+                    [now],
+                    |row| row.get(0),
+                )?;
+                let max_chain_length = conn.query_row(
+                    "SELECT COALESCE(MAX(chain_length), 0) FROM sessions",
+                    [],
+                    |row| row.get(0),
+                )?;
+                Ok(StoreStats {
+                    sessions,
+                    expired_sessions,
+                    max_chain_length,
+                })
+            }
+            DbPool::Valkey(store) => store.stats(),
+        }
+    }
+}
+
+#[cfg(test)]
 pub fn init_pool(path: &Path) -> Result<DbPool, Box<dyn std::error::Error>> {
+    let pool = init_sqlite_pool(path)?;
+    Ok(DbPool::Sqlite(pool))
+}
+
+fn init_sqlite_pool(
+    path: &Path,
+) -> Result<r2d2::Pool<r2d2_sqlite::SqliteConnectionManager>, Box<dyn std::error::Error>> {
     let manager = if path == Path::new(":memory:") {
         r2d2_sqlite::SqliteConnectionManager::memory()
     } else {
@@ -21,7 +237,6 @@ pub fn init_pool(path: &Path) -> Result<DbPool, Box<dyn std::error::Error>> {
         }
         r2d2_sqlite::SqliteConnectionManager::file(path)
     };
-
     let pool = r2d2::Pool::new(manager)?;
     let conn = pool.get()?;
     init_schema(&conn)?;
@@ -38,30 +253,133 @@ fn init_schema(conn: &rusqlite::Connection) -> Result<(), rusqlite::Error> {
             chain_length INTEGER NOT NULL DEFAULT 1,
             created_at INTEGER NOT NULL,
             last_seen INTEGER NOT NULL,
-            expires_at INTEGER NOT NULL
+            expires_at INTEGER NOT NULL,
+            gene BLOB NOT NULL DEFAULT X'',
+            environment BLOB NOT NULL DEFAULT X'',
+            pending_mutation BLOB NOT NULL DEFAULT X'',
+            pending_mutation_step INTEGER NOT NULL DEFAULT 0
         );",
     )?;
+    ensure_column(
+        conn,
+        "gene",
+        "ALTER TABLE sessions ADD COLUMN gene BLOB NOT NULL DEFAULT X''",
+    )?;
+    ensure_column(
+        conn,
+        "environment",
+        "ALTER TABLE sessions ADD COLUMN environment BLOB NOT NULL DEFAULT X''",
+    )?;
+    ensure_column(
+        conn,
+        "pending_mutation",
+        "ALTER TABLE sessions ADD COLUMN pending_mutation BLOB NOT NULL DEFAULT X''",
+    )?;
+    ensure_column(
+        conn,
+        "pending_mutation_step",
+        "ALTER TABLE sessions ADD COLUMN pending_mutation_step INTEGER NOT NULL DEFAULT 0",
+    )?;
+    conn.execute_batch(
+        "CREATE INDEX IF NOT EXISTS idx_sessions_expires_at ON sessions(expires_at);",
+    )?;
     Ok(())
 }
 
-pub fn stats(conn: &Connection) -> Result<StoreStats, rusqlite::Error> {
-    let now = current_time_ms();
-    let sessions = conn.query_row("SELECT COUNT(*) FROM sessions", [], |row| row.get(0))?;
-    let expired_sessions = conn.query_row(
-        "SELECT COUNT(*) FROM sessions WHERE expires_at < ?1",
-        [now],
+fn ensure_column(
+    conn: &rusqlite::Connection,
+    column: &str,
+    alter_sql: &str,
+) -> Result<(), rusqlite::Error> {
+    let exists: bool = conn.query_row(
+        "SELECT EXISTS(
+            SELECT 1 FROM pragma_table_info('sessions') WHERE name = ?1
+        )",
+        [column],
         |row| row.get(0),
     )?;
-    let max_chain_length = conn.query_row(
-        "SELECT COALESCE(MAX(chain_length), 0) FROM sessions",
-        [],
-        |row| row.get(0),
-    )?;
-    Ok(StoreStats {
-        sessions,
-        expired_sessions,
-        max_chain_length,
-    })
+    if !exists {
+        conn.execute_batch(alter_sql)?;
+    }
+    Ok(())
+}
+
+impl ValkeyStore {
+    fn session_key(&self, session_id: &str) -> String {
+        format!("session:{}", session_id)
+    }
+
+    fn load_session(
+        &self,
+        session_id: &str,
+    ) -> Result<Option<SessionRecord>, Box<dyn std::error::Error>> {
+        let mut client = self.client.lock().unwrap();
+        if let Some(payload) = client.get(&self.session_key(session_id))? {
+            let record = serde_json::from_str(&payload)?;
+            Ok(Some(record))
+        } else {
+            Ok(None)
+        }
+    }
+
+    fn insert_session(&self, record: &SessionRecord) -> Result<(), Box<dyn std::error::Error>> {
+        let mut client = self.client.lock().unwrap();
+        let value = serde_json::to_string(record)?;
+        client.set(&self.session_key(&record.session_id), &value)?;
+        let existing = client.get(&self.index_key)?;
+        let mut ids = existing.unwrap_or_default();
+        if !ids.split('\n').any(|id| id == record.session_id) {
+            if !ids.is_empty() {
+                ids.push('\n');
+            }
+            ids.push_str(&record.session_id);
+            client.set(&self.index_key, &ids)?;
+        }
+        Ok(())
+    }
+
+    fn purge_expired_sessions(&self) -> Result<(), Box<dyn std::error::Error>> {
+        let mut client = self.client.lock().unwrap();
+        let ids = client.get(&self.index_key)?.unwrap_or_default();
+        let now = current_time_ms();
+        let mut remaining: Vec<String> = Vec::new();
+        for id in ids.split('\n').filter(|id| !id.is_empty()) {
+            if let Some(payload) = client.get(&self.session_key(id))? {
+                if let Ok(record) = serde_json::from_str::<SessionRecord>(&payload) {
+                    if record.expires_at > now {
+                        remaining.push(id.to_string());
+                    }
+                }
+            }
+        }
+        client.set(&self.index_key, &remaining.join("\n"))?;
+        Ok(())
+    }
+
+    fn stats(&self) -> Result<StoreStats, Box<dyn std::error::Error>> {
+        let mut client = self.client.lock().unwrap();
+        let ids = client.get(&self.index_key)?.unwrap_or_default();
+        let now = current_time_ms();
+        let mut sessions = 0;
+        let mut expired_sessions = 0;
+        let mut max_chain_length = 0;
+        for id in ids.split('\n').filter(|id| !id.is_empty()) {
+            if let Some(payload) = client.get(&self.session_key(id))? {
+                if let Ok(record) = serde_json::from_str::<SessionRecord>(&payload) {
+                    sessions += 1;
+                    if record.expires_at < now {
+                        expired_sessions += 1;
+                    }
+                    max_chain_length = max_chain_length.max(record.chain_length);
+                }
+            }
+        }
+        Ok(StoreStats {
+            sessions,
+            expired_sessions,
+            max_chain_length,
+        })
+    }
 }
 
 pub fn current_time_ms() -> u64 {

server/src/vm.rs

@@ -1,4 +1,8 @@
 use rand::Rng;
+use shared::{
+    gene::GeneState,
+    vm_extensions::{self, ExecutionTrace, MutationError, MutationOrder},
+};
 
 pub fn generate_random_program(len_range: std::ops::RangeInclusive<usize>) -> Vec<u8> {
     let mut rng = rand::thread_rng();
@@ -9,7 +13,7 @@ pub fn generate_random_program(len_range: std::ops::RangeInclusive<usize>) -> Ve
         if depth < 2 {
             // Not enough operands for any binary op — push a literal.
             ops.push(0x00);
-            let val = rng.gen::<u32>();
+            let val = rng.r#gen::<u32>();
             ops.extend_from_slice(&val.to_le_bytes());
             depth += 1;
         } else {
@@ -18,7 +22,7 @@ pub fn generate_random_program(len_range: std::ops::RangeInclusive<usize>) -> Ve
                 0x00 => {
                     // PUSH literal
                     ops.push(0x00);
-                    let val = rng.gen::<u32>();
+                    let val = rng.r#gen::<u32>();
                     ops.extend_from_slice(&val.to_le_bytes());
                     depth += 1;
                 }
@@ -43,4 +47,52 @@ pub fn generate_random_program(len_range: std::ops::RangeInclusive<usize>) -> Ve
     ops
 }
 
-// Server does not need to execute the program; client does.
+#[allow(dead_code)]
+pub fn execute_mutation_program(
+    state: &mut GeneState,
+    program: &[u8],
+) -> Result<ExecutionTrace, MutationError> {
+    vm_extensions::execute_program(state, program)
+}
+
+#[allow(dead_code)]
+pub fn execute_mutation_order(
+    state: &mut GeneState,
+    order: &MutationOrder,
+) -> Result<ExecutionTrace, MutationError> {
+    vm_extensions::execute_program(state, &order.program)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use rand::SeedableRng;
+    use shared::gene::{commitment, new_state};
+
+    #[test]
+    fn test_execute_mutation_program_wraps_shared_engine() {
+        let mut state = new_state(8).unwrap();
+        let program = vec![vm_extensions::OP_MUTATE_POINT, 0, 0, 1];
+        let trace = execute_mutation_program(&mut state, &program).unwrap();
+        assert_eq!(state.gene[0], 1);
+        assert_eq!(trace.final_ip, program.len());
+    }
+
+    #[test]
+    fn test_execute_mutation_order_determinism() {
+        let mut rng_a = rand::rngs::StdRng::seed_from_u64(101);
+        let mut rng_b = rand::rngs::StdRng::seed_from_u64(101);
+        let order_a = vm_extensions::generate_order_with_rng(&mut rng_a, 9, 64);
+        let order_b = vm_extensions::generate_order_with_rng(&mut rng_b, 9, 64);
+        assert_eq!(order_a, order_b);
+
+        let mut state_a = new_state(64).unwrap();
+        let mut state_b = new_state(64).unwrap();
+        let trace_a = execute_mutation_order(&mut state_a, &order_a).unwrap();
+        let trace_b = execute_mutation_order(&mut state_b, &order_b).unwrap();
+
+        assert_eq!(state_a, state_b);
+        assert_eq!(trace_a.final_stack, trace_b.final_stack);
+        assert_eq!(commitment(&state_a), commitment(&state_b));
+    }
+}

shared/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "shared"
-version = "0.5.0"
+version = "0.6.0"
 edition = "2021"
 
 [dependencies]
@@ -10,4 +10,5 @@ blake3 = "1"
 hex = "0.4"
 base64 = "0.22"
 rand = "0.8"
-ed25519-dalek = { version = "2", features = ["rand_core"] }
+ed25519-dalek = { version = "2", features = ["rand_core"] }
+tracing = "0.1"

shared/src/constants.rs

@@ -1,2 +1,12 @@
 pub const SESSION_ID_LEN: usize = 32;
 pub const SALT_LEN: usize = 16;
+pub const DEFAULT_GENE_SIZE: usize = 512;
+pub const MAX_GENE_SIZE: usize = 4096;
+pub const MAX_ENV_RECORDS: usize = 48;
+pub const MAX_MUTATION_PROGRAM_BYTES: usize = 256;
+pub const DEFAULT_MUTATION_ROUNDS: u8 = 4;
+pub const MIN_MUTATION_ROUNDS: u8 = 3;
+pub const MAX_MUTATION_ROUNDS: u8 = 10;
+pub const MAX_MUTATION_INSTRUCTION_BUDGET: usize = 2048;
+pub const HASH_OPCODE_INSTRUCTION_COST: usize = 16;
+pub const SOFT_CAP_DURATION_MS: u128 = 50;

shared/src/gene.rs

@@ -0,0 +1,394 @@
+use crate::constants::{DEFAULT_GENE_SIZE, MAX_ENV_RECORDS, MAX_GENE_SIZE};
+use serde::{Deserialize, Serialize};
+
+#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
+pub struct EnvironmentRecord {
+    pub symbol: u16,
+    pub quantity: u32,
+}
+
+#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
+pub struct GeneState {
+    pub gene: Vec<u8>,
+    pub environment: Vec<EnvironmentRecord>,
+}
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub enum GeneError {
+    InvalidGeneSize { size: usize },
+    TooManyEnvironmentRecords { len: usize },
+    EnvironmentNotSorted,
+    DuplicateEnvironmentSymbol(u16),
+    ZeroQuantitySymbol(u16),
+    EnvironmentFull,
+    EnvironmentBlobLengthInvalid { len: usize },
+    EnvironmentBlobTooLarge { records: usize },
+}
+
+impl std::fmt::Display for GeneError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::InvalidGeneSize { size } => write!(f, "invalid gene size: {size}"),
+            Self::TooManyEnvironmentRecords { len } => {
+                write!(f, "too many environment records: {len}")
+            }
+            Self::EnvironmentNotSorted => write!(f, "environment records are not sorted"),
+            Self::DuplicateEnvironmentSymbol(symbol) => {
+                write!(f, "duplicate environment symbol: {symbol}")
+            }
+            Self::ZeroQuantitySymbol(symbol) => {
+                write!(f, "environment quantity cannot be zero for symbol {symbol}")
+            }
+            Self::EnvironmentFull => write!(f, "environment is at maximum capacity"),
+            Self::EnvironmentBlobLengthInvalid { len } => {
+                write!(
+                    f,
+                    "environment blob length must be a multiple of 6, got {len}"
+                )
+            }
+            Self::EnvironmentBlobTooLarge { records } => {
+                write!(f, "environment blob contains too many records: {records}")
+            }
+        }
+    }
+}
+
+impl std::error::Error for GeneError {}
+
+pub fn new_state(gene_size: usize) -> Result<GeneState, GeneError> {
+    if !(1..=MAX_GENE_SIZE).contains(&gene_size) {
+        return Err(GeneError::InvalidGeneSize { size: gene_size });
+    }
+    Ok(GeneState {
+        gene: vec![0; gene_size],
+        environment: Vec::new(),
+    })
+}
+
+pub fn default_state() -> GeneState {
+    GeneState {
+        gene: vec![0; DEFAULT_GENE_SIZE],
+        environment: Vec::new(),
+    }
+}
+
+pub fn validate_state(state: &GeneState) -> Result<(), GeneError> {
+    if !(1..=MAX_GENE_SIZE).contains(&state.gene.len()) {
+        return Err(GeneError::InvalidGeneSize {
+            size: state.gene.len(),
+        });
+    }
+    validate_environment(&state.environment)
+}
+
+pub fn get_env_quantity(state: &GeneState, symbol: u16) -> u32 {
+    match state
+        .environment
+        .binary_search_by_key(&symbol, |record| record.symbol)
+    {
+        Ok(i) => state.environment[i].quantity,
+        Err(_) => 0,
+    }
+}
+
+pub fn set_env_quantity(
+    state: &mut GeneState,
+    symbol: u16,
+    quantity: u32,
+) -> Result<(), GeneError> {
+    let idx = state
+        .environment
+        .binary_search_by_key(&symbol, |record| record.symbol);
+    match (idx, quantity) {
+        (Ok(i), 0) => {
+            state.environment.remove(i);
+            Ok(())
+        }
+        (Ok(i), qty) => {
+            state.environment[i].quantity = qty;
+            Ok(())
+        }
+        (Err(_), 0) => Ok(()),
+        (Err(i), qty) => {
+            if state.environment.len() >= MAX_ENV_RECORDS {
+                return Err(GeneError::EnvironmentFull);
+            }
+            state.environment.insert(
+                i,
+                EnvironmentRecord {
+                    symbol,
+                    quantity: qty,
+                },
+            );
+            Ok(())
+        }
+    }
+}
+
+pub fn add_env_quantity(
+    state: &mut GeneState,
+    symbol: u16,
+    quantity: u32,
+) -> Result<u32, GeneError> {
+    let current = get_env_quantity(state, symbol);
+    let next = current.saturating_add(quantity);
+    set_env_quantity(state, symbol, next)?;
+    Ok(next)
+}
+
+pub fn sub_env_quantity(
+    state: &mut GeneState,
+    symbol: u16,
+    quantity: u32,
+) -> Result<u32, GeneError> {
+    let current = get_env_quantity(state, symbol);
+    let next = current.saturating_sub(quantity);
+    set_env_quantity(state, symbol, next)?;
+    Ok(next)
+}
+
+pub fn encode_environment(records: &[EnvironmentRecord]) -> Result<Vec<u8>, GeneError> {
+    validate_environment(records)?;
+    let mut out = Vec::with_capacity(records.len() * 6);
+    for record in records {
+        out.extend_from_slice(&record.symbol.to_le_bytes());
+        out.extend_from_slice(&record.quantity.to_le_bytes());
+    }
+    Ok(out)
+}
+
+pub fn decode_environment(blob: &[u8]) -> Result<Vec<EnvironmentRecord>, GeneError> {
+    if !blob.len().is_multiple_of(6) {
+        return Err(GeneError::EnvironmentBlobLengthInvalid { len: blob.len() });
+    }
+    let records_len = blob.len() / 6;
+    if records_len > MAX_ENV_RECORDS {
+        return Err(GeneError::EnvironmentBlobTooLarge {
+            records: records_len,
+        });
+    }
+
+    let mut records = Vec::with_capacity(records_len);
+    let mut i = 0;
+    while i < blob.len() {
+        let symbol = u16::from_le_bytes([blob[i], blob[i + 1]]);
+        let quantity = u32::from_le_bytes([blob[i + 2], blob[i + 3], blob[i + 4], blob[i + 5]]);
+        records.push(EnvironmentRecord { symbol, quantity });
+        i += 6;
+    }
+    validate_environment(&records)?;
+    Ok(records)
+}
+
+pub fn commitment(state: &GeneState) -> [u8; 32] {
+    let mut h = blake3::Hasher::new();
+    h.update(b"chronoseal/gene/v1");
+    h.update(&(state.gene.len() as u32).to_le_bytes());
+    h.update(&state.gene);
+    h.update(&(state.environment.len() as u16).to_le_bytes());
+    for record in &state.environment {
+        h.update(&record.symbol.to_le_bytes());
+        h.update(&record.quantity.to_le_bytes());
+    }
+    *h.finalize().as_bytes()
+}
+
+pub fn commitment_hex(state: &GeneState) -> String {
+    hex::encode(commitment(state))
+}
+
+pub fn commitment_with_context(state: &GeneState, session_id: &str, step: u64) -> [u8; 32] {
+    let mut h = blake3::Hasher::new();
+    h.update(b"chronoseal/gene/v1");
+    h.update(session_id.as_bytes());
+    h.update(&step.to_le_bytes());
+    h.update(&commitment(state));
+    *h.finalize().as_bytes()
+}
+
+pub fn commitment_hex_with_context(state: &GeneState, session_id: &str, step: u64) -> String {
+    hex::encode(commitment_with_context(state, session_id, step))
+}
+
+fn validate_environment(records: &[EnvironmentRecord]) -> Result<(), GeneError> {
+    if records.len() > MAX_ENV_RECORDS {
+        return Err(GeneError::TooManyEnvironmentRecords { len: records.len() });
+    }
+    let mut prev_symbol: Option<u16> = None;
+    for record in records {
+        if record.quantity == 0 {
+            return Err(GeneError::ZeroQuantitySymbol(record.symbol));
+        }
+        if let Some(prev) = prev_symbol {
+            if record.symbol < prev {
+                return Err(GeneError::EnvironmentNotSorted);
+            }
+            if record.symbol == prev {
+                return Err(GeneError::DuplicateEnvironmentSymbol(record.symbol));
+            }
+        }
+        prev_symbol = Some(record.symbol);
+    }
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use rand::{Rng, SeedableRng};
+
+    #[test]
+    fn test_new_state_with_default_size() {
+        let state = new_state(DEFAULT_GENE_SIZE).unwrap();
+        assert_eq!(state.gene.len(), DEFAULT_GENE_SIZE);
+        assert!(state.environment.is_empty());
+    }
+
+    #[test]
+    fn test_new_state_rejects_invalid_sizes() {
+        assert!(matches!(
+            new_state(0).unwrap_err(),
+            GeneError::InvalidGeneSize { .. }
+        ));
+        assert!(matches!(
+            new_state(MAX_GENE_SIZE + 1).unwrap_err(),
+            GeneError::InvalidGeneSize { .. }
+        ));
+    }
+
+    #[test]
+    fn test_set_and_get_env_quantity() {
+        let mut state = new_state(8).unwrap();
+        set_env_quantity(&mut state, 42, 7).unwrap();
+        assert_eq!(get_env_quantity(&state, 42), 7);
+        set_env_quantity(&mut state, 42, 0).unwrap();
+        assert_eq!(get_env_quantity(&state, 42), 0);
+    }
+
+    #[test]
+    fn test_add_env_quantity_saturates() {
+        let mut state = new_state(8).unwrap();
+        set_env_quantity(&mut state, 1, u32::MAX - 3).unwrap();
+        let next = add_env_quantity(&mut state, 1, 99).unwrap();
+        assert_eq!(next, u32::MAX);
+    }
+
+    #[test]
+    fn test_sub_env_quantity_removes_symbol() {
+        let mut state = new_state(8).unwrap();
+        set_env_quantity(&mut state, 7, 10).unwrap();
+        let next = sub_env_quantity(&mut state, 7, 100).unwrap();
+        assert_eq!(next, 0);
+        assert!(state.environment.is_empty());
+    }
+
+    #[test]
+    fn test_environment_capacity_limit_is_enforced() {
+        let mut state = new_state(8).unwrap();
+        for symbol in 0..(MAX_ENV_RECORDS as u16) {
+            set_env_quantity(&mut state, symbol, 1).unwrap();
+        }
+        let err = set_env_quantity(&mut state, 500, 1).unwrap_err();
+        assert_eq!(err, GeneError::EnvironmentFull);
+    }
+
+    #[test]
+    fn test_encode_decode_environment_roundtrip() {
+        let records = vec![
+            EnvironmentRecord {
+                symbol: 3,
+                quantity: 9,
+            },
+            EnvironmentRecord {
+                symbol: 11,
+                quantity: 999,
+            },
+        ];
+        let blob = encode_environment(&records).unwrap();
+        let decoded = decode_environment(&blob).unwrap();
+        assert_eq!(decoded, records);
+    }
+
+    #[test]
+    fn test_decode_environment_rejects_unsorted_records() {
+        let mut blob = Vec::new();
+        blob.extend_from_slice(&7u16.to_le_bytes());
+        blob.extend_from_slice(&1u32.to_le_bytes());
+        blob.extend_from_slice(&2u16.to_le_bytes());
+        blob.extend_from_slice(&1u32.to_le_bytes());
+        let err = decode_environment(&blob).unwrap_err();
+        assert_eq!(err, GeneError::EnvironmentNotSorted);
+    }
+
+    #[test]
+    fn test_decode_environment_rejects_zero_quantity() {
+        let mut blob = Vec::new();
+        blob.extend_from_slice(&9u16.to_le_bytes());
+        blob.extend_from_slice(&0u32.to_le_bytes());
+        let err = decode_environment(&blob).unwrap_err();
+        assert_eq!(err, GeneError::ZeroQuantitySymbol(9));
+    }
+
+    #[test]
+    fn test_commitment_changes_when_gene_or_environment_changes() {
+        let mut state_a = new_state(16).unwrap();
+        let mut state_b = state_a.clone();
+        assert_eq!(commitment_hex(&state_a), commitment_hex(&state_b));
+
+        state_b.gene[0] = 1;
+        assert_ne!(commitment_hex(&state_a), commitment_hex(&state_b));
+
+        set_env_quantity(&mut state_a, 7, 3).unwrap();
+        assert_ne!(commitment_hex(&state_a), commitment_hex(&state_b));
+    }
+
+    #[test]
+    fn test_validate_state_rejects_duplicate_environment_symbols() {
+        let state = GeneState {
+            gene: vec![0; 10],
+            environment: vec![
+                EnvironmentRecord {
+                    symbol: 1,
+                    quantity: 1,
+                },
+                EnvironmentRecord {
+                    symbol: 1,
+                    quantity: 2,
+                },
+            ],
+        };
+        assert_eq!(
+            validate_state(&state).unwrap_err(),
+            GeneError::DuplicateEnvironmentSymbol(1)
+        );
+    }
+
+    #[test]
+    fn test_table_driven_randomized_environment_roundtrip() {
+        for seed in 0..32u64 {
+            let mut rng = rand::rngs::StdRng::seed_from_u64(seed);
+            let mut state = new_state(32).unwrap();
+
+            for _ in 0..128 {
+                let symbol = rng.gen_range(0u16..200u16);
+                let qty = if rng.gen_bool(0.15) {
+                    0
+                } else {
+                    rng.gen_range(1u32..100_000u32)
+                };
+                if let Err(err) = set_env_quantity(&mut state, symbol, qty) {
+                    assert_eq!(err, GeneError::EnvironmentFull);
+                }
+                validate_state(&state).unwrap();
+            }
+
+            let blob = encode_environment(&state.environment).unwrap();
+            let decoded = decode_environment(&blob).unwrap();
+            assert_eq!(decoded, state.environment);
+
+            let commitment_a = commitment(&state);
+            let commitment_b = commitment(&state.clone());
+            assert_eq!(commitment_a, commitment_b);
+        }
+    }
+}

shared/src/lib.rs

@@ -1,3 +1,5 @@
 pub mod constants;
+pub mod gene;
 pub mod hashing;
 pub mod protocol;
+pub mod vm_extensions;

shared/src/protocol.rs

@@ -1,11 +1,11 @@
 use serde::{Deserialize, Serialize};
 
-#[derive(Deserialize, Serialize)]
+#[derive(Debug, Clone, Deserialize, Serialize)]
 pub struct InitRequest {
     pub public_key: String,
 }
 
-#[derive(Serialize)]
+#[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct InitResponse {
     pub session_id: String,
     pub salt: String,
@@ -14,9 +14,12 @@ pub struct InitResponse {
     pub expires_at: u64,
     pub heartbeat_min_interval_ms: u64,
     pub heartbeat_max_interval_ms: u64,
+    pub gene_size: u32,
+    pub mutation_step: u64,
+    pub mutation_order_b64: String,
 }
 
-#[derive(Deserialize, Serialize)]
+#[derive(Debug, Clone, Deserialize, Serialize)]
 pub struct HeartbeatRequest {
     pub session_id: String,
     pub prev_hash: String,
@@ -24,17 +27,23 @@ pub struct HeartbeatRequest {
     pub entropy_data: EntropyData,
     pub stack_state: StackState,
     pub fingerprint: Fingerprint,
+    pub mutation_step: u64,
+    pub gene_commitment: String,
     pub signature: String,
 }
 
-#[derive(Serialize)]
+#[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct HeartbeatResponse {
     pub status: String,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub next_salt: Option<String>,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub next_mutation_step: Option<u64>,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub next_mutation_order_b64: Option<String>,
 }
 
-#[derive(Deserialize, Serialize)]
+#[derive(Debug, Clone, Deserialize, Serialize)]
 pub struct Fingerprint {
     #[serde(rename = "aspectRatio")]
     pub aspect_ratio: String,
@@ -44,7 +53,7 @@ pub struct Fingerprint {
     pub hardware_concurrency: u32,
 }
 
-#[derive(Deserialize, Serialize)]
+#[derive(Debug, Clone, Deserialize, Serialize)]
 pub struct EntropyData {
     pub events: Vec<MouseEvent>,
 }

shared/src/vm_extensions.rs

@@ -0,0 +1,838 @@
+use crate::{
+    constants::{
+        DEFAULT_MUTATION_ROUNDS, HASH_OPCODE_INSTRUCTION_COST, MAX_GENE_SIZE,
+        MAX_MUTATION_INSTRUCTION_BUDGET, MAX_MUTATION_PROGRAM_BYTES, SOFT_CAP_DURATION_MS,
+    },
+    gene::{
+        add_env_quantity, get_env_quantity, sub_env_quantity, validate_state, GeneError, GeneState,
+    },
+};
+use rand::Rng;
+use serde::{Deserialize, Serialize};
+use std::time::Instant;
+
+// Stack-machine mutation opcodes (v0.6.0).
+//
+// NOTE: stack effect notation:
+//   +1  => pushes one u32
+//   -1  => pops one u32
+//    0  => net-zero (or no stack interaction)
+//
+// Security/performance notes:
+// - All index operands are normalized with modulo to avoid panics.
+// - Program size is bounded by MAX_MUTATION_PROGRAM_BYTES.
+// - Environment arithmetic is saturating and deterministic.
+// - Hashing uses fixed BLAKE3 commitment and fixed transcription algorithm.
+pub const OP_GENE_LOAD: u8 = 0x23; // +1
+pub const OP_GENE_STORE: u8 = 0x24; // -1
+pub const OP_MUTATE_POINT: u8 = 0x25; // 0
+pub const OP_INSERT: u8 = 0x26; // -1
+pub const OP_DELETE: u8 = 0x27; // +1
+pub const OP_TRANSCRIBE: u8 = 0x28; // +1
+pub const OP_APPLY_MUTAGEN: u8 = 0x29; // -1
+pub const OP_FINALIZE_GENE_HASH: u8 = 0x2A; // +1
+pub const OP_CONSUME: u8 = 0x2B; // 0 (pop amount, push remaining)
+pub const OP_PRODUCE: u8 = 0x2C; // 0 (pop amount, push resulting quantity)
+
+#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
+pub struct MutationOrder {
+    pub step: u64,
+    pub program: Vec<u8>,
+}
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct ExecutionTrace {
+    pub final_ip: usize,
+    pub final_stack: Vec<u32>,
+    pub final_gene_commitment_hex: String,
+}
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub enum MutationError {
+    ProgramTooLong { len: usize },
+    TruncatedInstruction { opcode: u8, ip: usize },
+    UnknownOpcode(u8),
+    EmptyGene,
+    StackUnderflow { opcode: u8, ip: usize },
+    GeneFull { current_len: usize },
+    Base64(base64::DecodeError),
+    Gene(GeneError),
+}
+
+impl std::fmt::Display for MutationError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::ProgramTooLong { len } => write!(f, "mutation program too long: {len} bytes"),
+            Self::TruncatedInstruction { opcode, ip } => {
+                write!(f, "truncated instruction {opcode:#04x} at ip={ip}")
+            }
+            Self::UnknownOpcode(opcode) => write!(f, "unknown mutation opcode: {opcode:#04x}"),
+            Self::EmptyGene => write!(f, "cannot mutate an empty gene"),
+            Self::StackUnderflow { opcode, ip } => {
+                write!(f, "stack underflow in opcode {opcode:#04x} at ip={ip}")
+            }
+            Self::GeneFull { current_len } => {
+                write!(f, "cannot insert; gene already at max size ({current_len})")
+            }
+            Self::Base64(err) => write!(f, "invalid base64 mutation order: {err}"),
+            Self::Gene(err) => write!(f, "{err}"),
+        }
+    }
+}
+
+impl std::error::Error for MutationError {}
+
+impl From<GeneError> for MutationError {
+    fn from(value: GeneError) -> Self {
+        Self::Gene(value)
+    }
+}
+
+pub fn encode_order_b64(order: &MutationOrder) -> String {
+    base64::Engine::encode(&base64::engine::general_purpose::STANDARD, &order.program)
+}
+
+pub fn decode_order_b64(step: u64, b64: &str) -> Result<MutationOrder, MutationError> {
+    let program = base64::Engine::decode(&base64::engine::general_purpose::STANDARD, b64)
+        .map_err(MutationError::Base64)?;
+    if program.len() > MAX_MUTATION_PROGRAM_BYTES {
+        return Err(MutationError::ProgramTooLong { len: program.len() });
+    }
+    Ok(MutationOrder { step, program })
+}
+
+pub fn generate_order(step: u64, gene_size: usize) -> MutationOrder {
+    let mut rng = rand::thread_rng();
+    generate_order_with_rng(&mut rng, step, gene_size)
+}
+
+pub fn generate_order_with_rng<R: Rng + ?Sized>(
+    rng: &mut R,
+    step: u64,
+    gene_size: usize,
+) -> MutationOrder {
+    let mut program = Vec::with_capacity(128);
+    let mut stack_depth: i32 = 0;
+    let mut estimated_gene_len = gene_size.clamp(1, MAX_GENE_SIZE);
+    let ops = rng.gen_range(20usize..=36usize);
+    let mut hash_ops_needed = rng.gen_range(2..=3);
+
+    for idx in 0..ops {
+        let remaining = ops - idx;
+        let op = if hash_ops_needed > 0 && remaining <= hash_ops_needed {
+            OP_FINALIZE_GENE_HASH
+        } else if stack_depth <= 0 {
+            rng.gen_range(0u8..3u8)
+        } else {
+            match rng.gen_range(0u8..12u8) {
+                0..=1 => OP_GENE_LOAD,
+                2..=3 => OP_TRANSCRIBE,
+                4 => OP_FINALIZE_GENE_HASH,
+                5 => OP_GENE_STORE,
+                6 => OP_MUTATE_POINT,
+                7 => OP_INSERT,
+                8 => OP_DELETE,
+                9 => OP_APPLY_MUTAGEN,
+                10 => OP_CONSUME,
+                _ => OP_PRODUCE,
+            }
+        };
+
+        match op {
+            OP_GENE_LOAD => {
+                program.push(OP_GENE_LOAD);
+                push_u16(&mut program, rng.r#gen::<u16>());
+                stack_depth += 1;
+            }
+            OP_TRANSCRIBE => {
+                program.push(OP_TRANSCRIBE);
+                push_u16(&mut program, rng.r#gen::<u16>());
+                program.push(rng.gen_range(1u8..=16u8));
+                stack_depth += 1;
+            }
+            OP_FINALIZE_GENE_HASH => {
+                program.push(OP_FINALIZE_GENE_HASH);
+                stack_depth += 1;
+                hash_ops_needed = hash_ops_needed.saturating_sub(1);
+            }
+            OP_GENE_STORE => {
+                if stack_depth > 0 {
+                    program.push(OP_GENE_STORE);
+                    push_u16(&mut program, rng.r#gen::<u16>());
+                    stack_depth -= 1;
+                }
+            }
+            OP_MUTATE_POINT => {
+                program.push(OP_MUTATE_POINT);
+                push_u16(&mut program, rng.r#gen::<u16>());
+                program.push(rng.r#gen::<u8>());
+            }
+            OP_INSERT => {
+                if stack_depth > 0 && estimated_gene_len < MAX_GENE_SIZE {
+                    program.push(OP_INSERT);
+                    push_u16(&mut program, rng.r#gen::<u16>());
+                    stack_depth -= 1;
+                    estimated_gene_len += 1;
+                }
+            }
+            OP_DELETE => {
+                program.push(OP_DELETE);
+                push_u16(&mut program, rng.r#gen::<u16>());
+                stack_depth += 1;
+                if estimated_gene_len > 1 {
+                    estimated_gene_len -= 1;
+                }
+            }
+            OP_APPLY_MUTAGEN => {
+                if stack_depth > 0 {
+                    program.push(OP_APPLY_MUTAGEN);
+                    push_u16(&mut program, rng.r#gen::<u16>());
+                    push_u16(&mut program, rng.r#gen::<u16>());
+                    stack_depth -= 1;
+                }
+            }
+            OP_CONSUME => {
+                if stack_depth > 0 {
+                    program.push(OP_CONSUME);
+                    push_u16(&mut program, rng.r#gen::<u16>());
+                }
+            }
+            OP_PRODUCE if stack_depth > 0 => {
+                program.push(OP_PRODUCE);
+                push_u16(&mut program, rng.r#gen::<u16>());
+            }
+            _ => {}
+        }
+    }
+
+    while hash_ops_needed > 0 && program.len() < MAX_MUTATION_PROGRAM_BYTES {
+        program.push(OP_FINALIZE_GENE_HASH);
+        hash_ops_needed -= 1;
+    }
+
+    MutationOrder { step, program }
+}
+
+pub fn apply_program_clone(state: &GeneState, program: &[u8]) -> Result<GeneState, MutationError> {
+    apply_program_clone_with_rounds(state, program, DEFAULT_MUTATION_ROUNDS)
+}
+
+pub fn apply_program_clone_with_rounds(
+    state: &GeneState,
+    program: &[u8],
+    rounds: u8,
+) -> Result<GeneState, MutationError> {
+    let mut next = state.clone();
+    execute_program_with_rounds(&mut next, program, rounds)?;
+    Ok(next)
+}
+
+pub fn apply_program_with_rounds(
+    state: &mut GeneState,
+    program: &[u8],
+    rounds: u8,
+) -> Result<(), MutationError> {
+    let _ = execute_program_with_rounds(state, program, rounds)?;
+    Ok(())
+}
+
+pub fn apply_program(state: &mut GeneState, program: &[u8]) -> Result<(), MutationError> {
+    let _ = execute_program_with_rounds(state, program, DEFAULT_MUTATION_ROUNDS)?;
+    Ok(())
+}
+
+pub fn execute_program_with_rounds(
+    state: &mut GeneState,
+    program: &[u8],
+    rounds: u8,
+) -> Result<ExecutionTrace, MutationError> {
+    if state.gene.is_empty() {
+        return Err(MutationError::EmptyGene);
+    }
+    validate_state(state)?;
+    if program.len() > MAX_MUTATION_PROGRAM_BYTES {
+        return Err(MutationError::ProgramTooLong { len: program.len() });
+    }
+
+    let program_cost = estimate_program_cost(program);
+    let max_rounds = std::cmp::max(1, MAX_MUTATION_INSTRUCTION_BUDGET / program_cost);
+    let actual_rounds = std::cmp::min(rounds as usize, max_rounds) as u8;
+    let start = Instant::now();
+    let mut trace = None;
+
+    for _round in 0..actual_rounds {
+        trace = Some(execute_program(state, program)?);
+    }
+
+    let elapsed = start.elapsed();
+    tracing::debug!(
+        rounds = actual_rounds,
+        requested_rounds = rounds,
+        elapsed_ms = elapsed.as_millis(),
+        program_len = program.len(),
+        "mutation execution"
+    );
+    if actual_rounds < rounds {
+        tracing::debug!(
+            requested_rounds = rounds,
+            executed_rounds = actual_rounds,
+            "mutation soft cap reduced mutation rounds to preserve host responsiveness"
+        );
+    }
+    if elapsed.as_millis() > SOFT_CAP_DURATION_MS {
+        tracing::debug!(
+            elapsed_ms = elapsed.as_millis(),
+            "mutation execution exceeded soft cap duration"
+        );
+    }
+
+    Ok(trace.unwrap_or_else(|| ExecutionTrace {
+        final_ip: 0,
+        final_stack: Vec::new(),
+        final_gene_commitment_hex: crate::gene::commitment_hex(state),
+    }))
+}
+
+fn estimate_program_cost(program: &[u8]) -> usize {
+    let mut ip = 0;
+    let mut cost = 0;
+
+    while ip < program.len() {
+        let opcode = program[ip];
+        ip += 1;
+        cost += if opcode == OP_FINALIZE_GENE_HASH {
+            HASH_OPCODE_INSTRUCTION_COST
+        } else {
+            1
+        };
+        ip += match opcode {
+            OP_GENE_LOAD | OP_GENE_STORE | OP_INSERT | OP_DELETE | OP_CONSUME | OP_PRODUCE => 2,
+            OP_MUTATE_POINT | OP_TRANSCRIBE => 3,
+            OP_APPLY_MUTAGEN => 4,
+            OP_FINALIZE_GENE_HASH => 0,
+            _ => 0,
+        }
+    }
+
+    cost.max(1)
+}
+
+pub fn execute_program(
+    state: &mut GeneState,
+    program: &[u8],
+) -> Result<ExecutionTrace, MutationError> {
+    if state.gene.is_empty() {
+        return Err(MutationError::EmptyGene);
+    }
+    validate_state(state)?;
+    if program.len() > MAX_MUTATION_PROGRAM_BYTES {
+        return Err(MutationError::ProgramTooLong { len: program.len() });
+    }
+
+    let mut ip = 0usize;
+    let mut stack: Vec<u32> = Vec::with_capacity(16);
+    while ip < program.len() {
+        let opcode_ip = ip;
+        let opcode = take_u8(program, &mut ip, 0x00)?;
+        match opcode {
+            OP_GENE_LOAD => {
+                let idx = take_u16(program, &mut ip, opcode)?;
+                let normalized = normalize_index(idx as usize, state.gene.len());
+                stack.push(state.gene[normalized] as u32);
+            }
+            OP_GENE_STORE => {
+                let idx = take_u16(program, &mut ip, opcode)?;
+                let value = pop_stack(&mut stack, opcode, opcode_ip)? as u8;
+                let normalized = normalize_index(idx as usize, state.gene.len());
+                state.gene[normalized] = value;
+            }
+            OP_MUTATE_POINT => {
+                let idx = take_u16(program, &mut ip, opcode)?;
+                let delta = take_u8(program, &mut ip, opcode)? as i8;
+                let normalized = normalize_index(idx as usize, state.gene.len());
+                state.gene[normalized] = state.gene[normalized].wrapping_add(delta as u8);
+            }
+            OP_INSERT => {
+                let idx = take_u16(program, &mut ip, opcode)?;
+                let value = pop_stack(&mut stack, opcode, opcode_ip)? as u8;
+                if state.gene.len() >= MAX_GENE_SIZE {
+                    return Err(MutationError::GeneFull {
+                        current_len: state.gene.len(),
+                    });
+                }
+                let insert_at = (idx as usize).min(state.gene.len());
+                state.gene.insert(insert_at, value);
+            }
+            OP_DELETE => {
+                let idx = take_u16(program, &mut ip, opcode)?;
+                let normalized = normalize_index(idx as usize, state.gene.len());
+                let removed = if state.gene.len() > 1 {
+                    state.gene.remove(normalized)
+                } else {
+                    let prev = state.gene[0];
+                    state.gene[0] = 0;
+                    prev
+                };
+                stack.push(removed as u32);
+            }
+            OP_TRANSCRIBE => {
+                let start = take_u16(program, &mut ip, opcode)?;
+                let span = take_u8(program, &mut ip, opcode)?;
+                let transcription = transcribe_window(&state.gene, start as usize, span);
+                stack.push(transcription);
+            }
+            OP_APPLY_MUTAGEN => {
+                let symbol = take_u16(program, &mut ip, opcode)?;
+                let idx = take_u16(program, &mut ip, opcode)?;
+                let stack_mask = pop_stack(&mut stack, opcode, opcode_ip)? as u8;
+                let quantity = get_env_quantity(state, symbol);
+                let mix = ((quantity as u8)
+                    ^ ((quantity >> 8) as u8)
+                    ^ ((quantity >> 16) as u8)
+                    ^ ((quantity >> 24) as u8))
+                    ^ ((symbol & 0x00ff) as u8)
+                    ^ ((symbol >> 8) as u8)
+                    ^ stack_mask;
+                let normalized = normalize_index(idx as usize, state.gene.len());
+                state.gene[normalized] ^= mix;
+            }
+            OP_FINALIZE_GENE_HASH => {
+                let commit = crate::gene::commitment(state);
+                let hash32 = u32::from_le_bytes([commit[0], commit[1], commit[2], commit[3]]);
+                stack.push(hash32);
+            }
+            OP_CONSUME => {
+                let symbol = take_u16(program, &mut ip, opcode)?;
+                let amount = pop_stack(&mut stack, opcode, opcode_ip)?;
+                let left = sub_env_quantity(state, symbol, amount)?;
+                stack.push(left);
+            }
+            OP_PRODUCE => {
+                let symbol = take_u16(program, &mut ip, opcode)?;
+                let amount = pop_stack(&mut stack, opcode, opcode_ip)?;
+                let next = add_env_quantity(state, symbol, amount)?;
+                stack.push(next);
+            }
+            _ => return Err(MutationError::UnknownOpcode(opcode)),
+        }
+    }
+
+    Ok(ExecutionTrace {
+        final_ip: ip,
+        final_stack: stack,
+        final_gene_commitment_hex: crate::gene::commitment_hex(state),
+    })
+}
+
+fn transcribe_window(gene: &[u8], start: usize, span: u8) -> u32 {
+    let count = usize::from(span.max(1));
+    let mut acc = 2_166_136_261u32; // FNV offset basis
+    for i in 0..count {
+        let idx = (start + i) % gene.len();
+        acc ^= gene[idx] as u32;
+        acc = acc.wrapping_mul(16_777_619); // FNV prime
+    }
+    acc
+}
+
+fn push_u16(buf: &mut Vec<u8>, value: u16) {
+    buf.extend_from_slice(&value.to_le_bytes());
+}
+
+fn take_u8(bytes: &[u8], ip: &mut usize, opcode: u8) -> Result<u8, MutationError> {
+    if *ip >= bytes.len() {
+        return Err(MutationError::TruncatedInstruction { opcode, ip: *ip });
+    }
+    let value = bytes[*ip];
+    *ip += 1;
+    Ok(value)
+}
+
+fn take_u16(bytes: &[u8], ip: &mut usize, opcode: u8) -> Result<u16, MutationError> {
+    if *ip + 2 > bytes.len() {
+        return Err(MutationError::TruncatedInstruction { opcode, ip: *ip });
+    }
+    let value = u16::from_le_bytes([bytes[*ip], bytes[*ip + 1]]);
+    *ip += 2;
+    Ok(value)
+}
+
+fn pop_stack(stack: &mut Vec<u32>, opcode: u8, ip: usize) -> Result<u32, MutationError> {
+    stack
+        .pop()
+        .ok_or(MutationError::StackUnderflow { opcode, ip })
+}
+
+fn normalize_index(idx: usize, len: usize) -> usize {
+    idx % len
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::gene::{commitment, new_state, set_env_quantity};
+    use rand::{Rng, SeedableRng};
+    use std::time::Instant;
+
+    fn u16_bytes(v: u16) -> [u8; 2] {
+        v.to_le_bytes()
+    }
+
+    #[test]
+    fn test_opcode_gene_load() {
+        let mut state = new_state(4).unwrap();
+        state.gene = vec![10, 20, 30, 40];
+        let trace = execute_program(&mut state, &[OP_GENE_LOAD, 1, 0]).unwrap();
+        assert_eq!(trace.final_stack, vec![20]);
+    }
+
+    #[test]
+    fn test_opcode_gene_store() {
+        let mut state = new_state(4).unwrap();
+        state.gene = vec![1, 2, 3, 4];
+        let program = vec![
+            OP_GENE_LOAD,
+            0,
+            0, // stack: [1]
+            OP_GENE_STORE,
+            2,
+            0, // gene[2] <- 1
+        ];
+        execute_program(&mut state, &program).unwrap();
+        assert_eq!(state.gene, vec![1, 2, 1, 4]);
+    }
+
+    #[test]
+    fn test_opcode_mutate_point() {
+        let mut state = new_state(4).unwrap();
+        state.gene[0] = 200;
+        let program = vec![OP_MUTATE_POINT, 0, 0, 100u8];
+        execute_program(&mut state, &program).unwrap();
+        assert_eq!(state.gene[0], 44);
+    }
+
+    #[test]
+    fn test_opcode_insert() {
+        let mut state = new_state(3).unwrap();
+        state.gene = vec![10, 20, 30];
+        let program = vec![
+            OP_GENE_LOAD,
+            1,
+            0, // stack: [20]
+            OP_INSERT,
+            0,
+            0, // insert 20 at position 0
+        ];
+        execute_program(&mut state, &program).unwrap();
+        assert_eq!(state.gene, vec![20, 10, 20, 30]);
+    }
+
+    #[test]
+    fn test_opcode_delete() {
+        let mut state = new_state(4).unwrap();
+        state.gene = vec![9, 8, 7, 6];
+        let trace = execute_program(&mut state, &[OP_DELETE, 2, 0]).unwrap();
+        assert_eq!(state.gene, vec![9, 8, 6]);
+        assert_eq!(trace.final_stack, vec![7]);
+    }
+
+    #[test]
+    fn test_opcode_transcribe() {
+        let mut state = new_state(5).unwrap();
+        state.gene = vec![1, 2, 3, 4, 5];
+        let trace = execute_program(&mut state, &[OP_TRANSCRIBE, 1, 0, 3]).unwrap();
+        assert_eq!(trace.final_stack.len(), 1);
+        assert_ne!(trace.final_stack[0], 0);
+    }
+
+    #[test]
+    fn test_opcode_apply_mutagen() {
+        let mut state = new_state(4).unwrap();
+        set_env_quantity(&mut state, 7, 0x1234_5678).unwrap();
+        state.gene[1] = 0xAA;
+        let program = vec![
+            OP_GENE_LOAD,
+            0,
+            0, // stack mask source
+            OP_APPLY_MUTAGEN,
+            7,
+            0,
+            1,
+            0,
+        ];
+        execute_program(&mut state, &program).unwrap();
+        assert_ne!(state.gene[1], 0xAA);
+    }
+
+    #[test]
+    fn test_opcode_finalize_gene_hash() {
+        let mut state = new_state(4).unwrap();
+        let trace = execute_program(&mut state, &[OP_FINALIZE_GENE_HASH]).unwrap();
+        assert_eq!(trace.final_stack.len(), 1);
+    }
+
+    #[test]
+    fn test_opcode_consume() {
+        let mut state = new_state(4).unwrap();
+        set_env_quantity(&mut state, 3, 100).unwrap();
+        let program = vec![
+            OP_GENE_LOAD,
+            0,
+            0, // stack = [0]
+            OP_MUTATE_POINT,
+            0,
+            0,
+            15, // gene[0]=15
+            OP_GENE_LOAD,
+            0,
+            0, // stack=[0,15]
+            OP_CONSUME,
+            3,
+            0, // consume 15
+        ];
+        let trace = execute_program(&mut state, &program).unwrap();
+        assert_eq!(get_env_quantity(&state, 3), 85);
+        assert_eq!(trace.final_stack.last().copied().unwrap(), 85);
+    }
+
+    #[test]
+    fn test_opcode_produce() {
+        let mut state = new_state(4).unwrap();
+        set_env_quantity(&mut state, 9, 5).unwrap();
+        let program = vec![
+            OP_GENE_LOAD,
+            0,
+            0, // stack [0]
+            OP_MUTATE_POINT,
+            0,
+            0,
+            10, // gene[0]=10
+            OP_GENE_LOAD,
+            0,
+            0, // stack [0,10]
+            OP_PRODUCE,
+            9,
+            0, // +10
+        ];
+        let trace = execute_program(&mut state, &program).unwrap();
+        assert_eq!(get_env_quantity(&state, 9), 15);
+        assert_eq!(trace.final_stack.last().copied().unwrap(), 15);
+    }
+
+    #[test]
+    fn test_zero_length_gene_is_rejected() {
+        let mut state = GeneState {
+            gene: vec![],
+            environment: vec![],
+        };
+        let err = execute_program(&mut state, &[OP_FINALIZE_GENE_HASH]).unwrap_err();
+        assert_eq!(err, MutationError::EmptyGene);
+    }
+
+    #[test]
+    fn test_insert_rejects_max_size_gene() {
+        let mut state = new_state(MAX_GENE_SIZE).unwrap();
+        let program = vec![
+            OP_GENE_LOAD,
+            0,
+            0, // push value
+            OP_INSERT,
+            0,
+            0,
+        ];
+        let err = execute_program(&mut state, &program).unwrap_err();
+        assert!(matches!(err, MutationError::GeneFull { .. }));
+    }
+
+    #[test]
+    fn test_invalid_positions_wrap_deterministically() {
+        let mut state_a = new_state(5).unwrap();
+        let mut state_b = new_state(5).unwrap();
+        let max_u16 = u16::MAX;
+        let [a0, a1] = u16_bytes(max_u16);
+        let program = vec![OP_MUTATE_POINT, a0, a1, 1];
+        execute_program(&mut state_a, &program).unwrap();
+
+        let wrapped = (max_u16 as usize % 5) as u16;
+        let [w0, w1] = u16_bytes(wrapped);
+        let wrapped_program = vec![OP_MUTATE_POINT, w0, w1, 1];
+        execute_program(&mut state_b, &wrapped_program).unwrap();
+        assert_eq!(state_a, state_b);
+    }
+
+    #[test]
+    fn test_quantity_underflow_is_saturating() {
+        let mut state = new_state(4).unwrap();
+        set_env_quantity(&mut state, 1, 3).unwrap();
+        state.gene[0] = 8;
+        let program = vec![
+            OP_GENE_LOAD,
+            0,
+            0, // 8
+            OP_CONSUME,
+            1,
+            0, // consume 8 from qty 3 => 0
+        ];
+        let trace = execute_program(&mut state, &program).unwrap();
+        assert_eq!(get_env_quantity(&state, 1), 0);
+        assert_eq!(trace.final_stack.last().copied().unwrap(), 0);
+    }
+
+    #[test]
+    fn test_rejects_unknown_opcode() {
+        let mut state = new_state(8).unwrap();
+        let err = execute_program(&mut state, &[0xFF]).unwrap_err();
+        assert_eq!(err, MutationError::UnknownOpcode(0xFF));
+    }
+
+    #[test]
+    fn test_rejects_truncated_instruction() {
+        let mut state = new_state(8).unwrap();
+        let err = execute_program(&mut state, &[OP_GENE_LOAD, 1]).unwrap_err();
+        assert!(matches!(err, MutationError::TruncatedInstruction { .. }));
+    }
+
+    #[test]
+    fn test_rejects_stack_underflow() {
+        let mut state = new_state(8).unwrap();
+        let err = execute_program(&mut state, &[OP_GENE_STORE, 0, 0]).unwrap_err();
+        assert!(matches!(err, MutationError::StackUnderflow { .. }));
+    }
+
+    #[test]
+    fn test_base64_order_roundtrip() {
+        let order = MutationOrder {
+            step: 17,
+            program: vec![OP_GENE_LOAD, 1, 0, OP_GENE_STORE, 2, 0],
+        };
+        let b64 = encode_order_b64(&order);
+        let decoded = decode_order_b64(order.step, &b64).unwrap();
+        assert_eq!(decoded, order);
+    }
+
+    #[test]
+    fn test_generate_order_is_deterministic_for_seeded_rng() {
+        let mut rng_a = rand::rngs::StdRng::seed_from_u64(99);
+        let mut rng_b = rand::rngs::StdRng::seed_from_u64(99);
+        let order_a = generate_order_with_rng(&mut rng_a, 5, 64);
+        let order_b = generate_order_with_rng(&mut rng_b, 5, 64);
+        assert_eq!(order_a, order_b);
+    }
+
+    #[test]
+    fn test_mutation_chain() {
+        let mut server_state = new_state(32).unwrap();
+        let mut client_state = new_state(32).unwrap();
+
+        let program = vec![
+            OP_GENE_LOAD,
+            0,
+            0,
+            OP_PRODUCE,
+            2,
+            0, // env[2]+=gene[0]
+            OP_GENE_LOAD,
+            1,
+            0,
+            OP_APPLY_MUTAGEN,
+            2,
+            0,
+            1,
+            0, // mutagen at idx1
+            OP_TRANSCRIBE,
+            0,
+            0,
+            8, // hash window
+            OP_GENE_STORE,
+            2,
+            0, // gene[2]=transcription_low_byte
+            OP_DELETE,
+            0,
+            0, // stack pushes removed
+            OP_INSERT,
+            3,
+            0, // insert removed at position 3
+            OP_FINALIZE_GENE_HASH,
+        ];
+
+        let server_trace = execute_program(&mut server_state, &program).unwrap();
+        let client_trace = execute_program(&mut client_state, &program).unwrap();
+
+        assert_eq!(server_state, client_state);
+        assert_eq!(server_trace.final_stack, client_trace.final_stack);
+        assert_eq!(
+            server_trace.final_gene_commitment_hex,
+            client_trace.final_gene_commitment_hex
+        );
+    }
+
+    #[test]
+    fn test_server_client_parity_across_random_orders() {
+        let mut rng = rand::rngs::StdRng::seed_from_u64(7);
+        for step in 0..128u64 {
+            let order = generate_order_with_rng(&mut rng, step, 128);
+            let mut server_state = new_state(128).unwrap();
+            let mut client_state = new_state(128).unwrap();
+
+            let server_result = execute_program(&mut server_state, &order.program);
+            let client_result = execute_program(&mut client_state, &order.program);
+            assert_eq!(server_result.is_ok(), client_result.is_ok());
+
+            match (server_result, client_result) {
+                (Ok(server_trace), Ok(client_trace)) => {
+                    assert_eq!(server_state, client_state);
+                    assert_eq!(server_trace.final_stack, client_trace.final_stack);
+                    assert_eq!(
+                        commitment(&server_state),
+                        commitment(&client_state),
+                        "step {step}"
+                    );
+                }
+                (Err(a), Err(b)) => assert_eq!(a.to_string(), b.to_string()),
+                _ => unreachable!(),
+            }
+        }
+    }
+
+    #[test]
+    fn test_fuzz_style_random_program_bytes_do_not_diverge() {
+        let mut rng = rand::rngs::StdRng::seed_from_u64(2026);
+        for _ in 0..256 {
+            let len = rng.gen_range(1usize..=MAX_MUTATION_PROGRAM_BYTES);
+            let mut program = vec![0u8; len];
+            for b in &mut program {
+                *b = rng.r#gen::<u8>();
+            }
+
+            let mut a = new_state(64).unwrap();
+            let mut b = new_state(64).unwrap();
+            let ra = execute_program(&mut a, &program);
+            let rb = execute_program(&mut b, &program);
+            assert_eq!(ra.is_ok(), rb.is_ok());
+            if ra.is_ok() {
+                assert_eq!(a, b);
+            }
+        }
+    }
+
+    #[test]
+    fn test_performance_smoke_mutation_execution() {
+        let mut rng = rand::rngs::StdRng::seed_from_u64(11);
+        let mut programs = Vec::new();
+        for step in 0..200u64 {
+            programs.push(generate_order_with_rng(&mut rng, step + 1, 512).program);
+        }
+
+        let start = Instant::now();
+        let mut state = new_state(512).unwrap();
+        for program in &programs {
+            let _ = execute_program(&mut state, program);
+        }
+        let elapsed = start.elapsed();
+        // Wide bound for CI variability; this is a regression guard, not a strict benchmark.
+        assert!(
+            elapsed.as_secs_f64() < 2.0,
+            "mutation execution too slow: {elapsed:?}"
+        );
+    }
+}

wasm/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "chronoseal-wasm"
-version = "0.5.0"
+version = "0.6.0"
 edition = "2021"
 
 [lib]
@@ -18,3 +18,4 @@ getrandom = { version = "0.2", features = ["js"] }
 hex = "0.4"
 base64 = "0.22"
 serde-wasm-bindgen = "0.6"
+tracing = "0.1"

wasm/src/lib.rs

@@ -4,3 +4,4 @@ pub mod entropy;
 pub mod fingerprint;
 pub mod transport;
 pub mod vm;
+pub mod vm_extensions;

wasm/src/vm_extensions.rs

@@ -0,0 +1,226 @@
+use std::cell::RefCell;
+use std::time::Instant;
+use wasm_bindgen::prelude::*;
+
+thread_local! {
+    static GENE_STATE: RefCell<Option<shared::gene::GeneState>> = const { RefCell::new(None) };
+    static PREVIEW_STATE: RefCell<Option<shared::gene::GeneState>> = const { RefCell::new(None) };
+}
+
+#[wasm_bindgen]
+pub fn init_gene_state(gene_size: u32) -> bool {
+    let Ok(state) = shared::gene::new_state(gene_size as usize) else {
+        return false;
+    };
+    GENE_STATE.with(|slot| *slot.borrow_mut() = Some(state));
+    PREVIEW_STATE.with(|slot| *slot.borrow_mut() = None);
+    true
+}
+
+#[wasm_bindgen]
+pub fn preview_gene_commitment(
+    order_b64: &str,
+    session_id: &str,
+    mutation_step: u64,
+    rounds: u8,
+) -> String {
+    let order = match shared::vm_extensions::decode_order_b64(mutation_step, order_b64) {
+        Ok(order) => order,
+        Err(_) => return String::new(),
+    };
+
+    let start = Instant::now();
+    let candidate = GENE_STATE.with(|slot| {
+        let state = slot.borrow();
+        let current = state.as_ref()?;
+        shared::vm_extensions::apply_program_clone_with_rounds(
+            current,
+            &order.program,
+            if rounds == 0 {
+                shared::constants::DEFAULT_MUTATION_ROUNDS
+            } else {
+                rounds
+            },
+        )
+        .ok()
+    });
+    let elapsed = start.elapsed();
+    tracing::debug!(session_id = %session_id, mutation_step = mutation_step, elapsed_ms = elapsed.as_millis(), "wasm mutation preview execution");
+
+    let Some(candidate) = candidate else {
+        return String::new();
+    };
+    let commitment =
+        shared::gene::commitment_hex_with_context(&candidate, session_id, mutation_step);
+    PREVIEW_STATE.with(|slot| *slot.borrow_mut() = Some(candidate));
+    commitment
+}
+
+#[wasm_bindgen]
+pub fn commit_gene_preview() -> bool {
+    let next = PREVIEW_STATE.with(|slot| slot.borrow_mut().take());
+    let Some(next) = next else {
+        return false;
+    };
+    GENE_STATE.with(|slot| *slot.borrow_mut() = Some(next));
+    true
+}
+
+#[wasm_bindgen]
+pub fn discard_gene_preview() {
+    PREVIEW_STATE.with(|slot| *slot.borrow_mut() = None);
+}
+
+#[wasm_bindgen]
+pub fn current_gene_commitment(session_id: &str, mutation_step: u64) -> String {
+    GENE_STATE.with(|slot| {
+        slot.borrow()
+            .as_ref()
+            .map(|state| {
+                shared::gene::commitment_hex_with_context(state, session_id, mutation_step)
+            })
+            .unwrap_or_default()
+    })
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use rand::SeedableRng;
+
+    fn order_b64(program: Vec<u8>) -> String {
+        let order = shared::vm_extensions::MutationOrder { step: 1, program };
+        shared::vm_extensions::encode_order_b64(&order)
+    }
+
+    #[test]
+    fn test_init_gene_state_success() {
+        assert!(init_gene_state(64));
+        let commitment = current_gene_commitment("deadbeef", 1);
+        assert_eq!(commitment.len(), 64);
+    }
+
+    #[test]
+    fn test_init_gene_state_rejects_zero() {
+        assert!(!init_gene_state(0));
+    }
+
+    #[test]
+    fn test_preview_requires_initialized_state() {
+        discard_gene_preview();
+        GENE_STATE.with(|slot| *slot.borrow_mut() = None);
+        let c = preview_gene_commitment(
+            &order_b64(vec![shared::vm_extensions::OP_MUTATE_POINT, 0, 0, 1]),
+            "deadbeef",
+            1,
+            0,
+        );
+        assert!(c.is_empty());
+    }
+
+    #[test]
+    fn test_preview_rejects_invalid_order() {
+        init_gene_state(16);
+        let c = preview_gene_commitment("***bad-base64***", "deadbeef", 1, 0);
+        assert!(c.is_empty());
+    }
+
+    #[test]
+    fn test_commit_applies_preview() {
+        init_gene_state(16);
+        let before = current_gene_commitment("deadbeef", 1);
+        let order = order_b64(vec![shared::vm_extensions::OP_MUTATE_POINT, 0, 0, 1]);
+        let preview = preview_gene_commitment(&order, "deadbeef", 1, 0);
+        assert_ne!(preview, before);
+        assert!(commit_gene_preview());
+        let after = current_gene_commitment("deadbeef", 1);
+        assert_eq!(preview, after);
+    }
+
+    #[test]
+    fn test_discard_preview_keeps_committed_state() {
+        init_gene_state(16);
+        let before = current_gene_commitment("deadbeef", 1);
+        let order = order_b64(vec![shared::vm_extensions::OP_MUTATE_POINT, 0, 0, 0xFF]);
+        let preview = preview_gene_commitment(&order, "deadbeef", 1, 0);
+        assert_ne!(preview, before);
+        discard_gene_preview();
+        let after = current_gene_commitment("deadbeef", 1);
+        assert_eq!(before, after);
+    }
+
+    #[test]
+    fn test_commit_without_preview_returns_false() {
+        init_gene_state(16);
+        discard_gene_preview();
+        assert!(!commit_gene_preview());
+    }
+
+    #[test]
+    fn test_preview_commitment_matches_shared_engine() {
+        init_gene_state(16);
+        let order = shared::vm_extensions::MutationOrder {
+            step: 3,
+            program: vec![
+                shared::vm_extensions::OP_GENE_LOAD,
+                0,
+                0,
+                shared::vm_extensions::OP_PRODUCE,
+                1,
+                0,
+                shared::vm_extensions::OP_GENE_LOAD,
+                2,
+                0,
+                shared::vm_extensions::OP_APPLY_MUTAGEN,
+                1,
+                0,
+                2,
+                0,
+            ],
+        };
+        let b64 = shared::vm_extensions::encode_order_b64(&order);
+
+        let preview = preview_gene_commitment(&b64, "deadbeef", 3, 0);
+
+        let mut expected = shared::gene::new_state(16).unwrap();
+        shared::vm_extensions::apply_program_with_rounds(
+            &mut expected,
+            &order.program,
+            shared::constants::DEFAULT_MUTATION_ROUNDS,
+        )
+        .unwrap();
+        assert_eq!(
+            preview,
+            shared::gene::commitment_hex_with_context(&expected, "deadbeef", 3)
+        );
+    }
+
+    #[test]
+    fn test_table_driven_parity_across_many_generated_orders() {
+        init_gene_state(64);
+        let mut rng = rand::rngs::StdRng::seed_from_u64(123);
+        let mut expected = shared::gene::new_state(64).unwrap();
+
+        for step in 0..24u64 {
+            let order = shared::vm_extensions::generate_order_with_rng(&mut rng, step + 1, 64);
+            let b64 = shared::vm_extensions::encode_order_b64(&order);
+
+            let preview = preview_gene_commitment(&b64, "deadbeef", step + 1, 0);
+            shared::vm_extensions::apply_program_with_rounds(
+                &mut expected,
+                &order.program,
+                shared::constants::DEFAULT_MUTATION_ROUNDS,
+            )
+            .unwrap();
+            let expected_commitment =
+                shared::gene::commitment_hex_with_context(&expected, "deadbeef", step + 1);
+
+            assert_eq!(preview, expected_commitment);
+            assert!(commit_gene_preview());
+            assert_eq!(
+                current_gene_commitment("deadbeef", step + 1),
+                expected_commitment
+            );
+        }
+    }
+}