Refactor attestation engine and synchronize project documentation

- Refine session and storage lifecycle handling
- Improve VM extension architecture across server, shared, and WASM runtimes
- Enhance synthetic gene mutation engine integration and parity guarantees
- Align deterministic state progression between server and browser execution paths
- Update configuration examples and deployment guidance
- Expand architecture, API, threat model, privacy, and WASM build documentation
- Refresh README with comprehensive project overview, operational workflows,
  browser integration details, storage backend documentation, and security model
- Document v0.6.0 refactoring outcomes and design rationale
- Improve consistency across documentation, configuration, and implementation

This commit consolidates the v0.6.0 architectural refactoring effort,
strengthening deterministic browser/server parity while improving
maintainability, operational clarity, and project documentation.

docs/chronoseal.example.toml

@@ -1,9 +1,27 @@
 bind = "0.0.0.0:3000"
-# sqlite-in-memory (default), sqlite-in-disk, valkey (v0.6.0 compatibility mode)
+
+# 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"
-# synthetic gene size (1..=65536), default 512
+
+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