docs: fix 40+ discrepancies between documentation and codebase (#5818)

Comprehensive audit of all ~100 doc pages against the actual code, fixing:

Reference docs:
- HERMES_API_TIMEOUT default 900 -> 1800 (env-vars)
- TERMINAL_DOCKER_IMAGE default python:3.11 -> nikolaik/python-nodejs (env-vars)
- compression.summary_model default shown as gemini -> actually empty string (env-vars)
- Add missing GOOGLE_API_KEY, GEMINI_API_KEY, GEMINI_BASE_URL env vars (env-vars)
- Add missing /branch (/fork) slash command (slash-commands)
- Fix hermes-cli tool count 39 -> 38 (toolsets-reference)
- Fix hermes-api-server drop list to include text_to_speech (toolsets-reference)
- Fix total tool count 47 -> 48, standalone 14 -> 15 (tools-reference)

User guide:
- web_extract.timeout default 30 -> 360 (configuration)
- Remove display.theme_mode (not implemented in code) (configuration)
- Remove display.background_process_notifications (not in defaults) (configuration)
- Browser inactivity timeout 300/5min -> 120/2min (browser)
- Screenshot path browser_screenshots -> cache/screenshots (browser)
- batch_runner default model claude-sonnet-4-20250514 -> claude-sonnet-4.6
- Add minimax to TTS provider list (voice-mode)
- Remove credential_pool_strategies from auth.json example (credential-pools)
- Fix Slack token path platforms/slack/ -> root ~/.hermes/ (slack)
- Fix Matrix store path for new installs (matrix)
- Fix WhatsApp session path for new installs (whatsapp)
- Fix HomeAssistant config from gateway.json to config.yaml (homeassistant)
- Fix WeCom gateway start command (wecom)

Developer guide:
- Fix tool/toolset counts in architecture overview
- Update line counts: main.py ~5500, setup.py ~3100, run.py ~7500, mcp_tool ~2200
- Replace nonexistent agent/memory_store.py with memory_manager.py + memory_provider.py
- Update _discover_tools() list: remove honcho_tools, add skill_manager_tool
- Add session_search and delegate_task to intercepted tools list (agent-loop)
- Fix budget warning: two-tier system (70% caution, 90% warning) (agent-loop)
- Fix gateway auth order (per-platform first, global last) (gateway-internals)
- Fix email_adapter.py -> email.py, add webhook.py + api_server.py (gateway-internals)
- Add 7 missing providers to provider-runtime list

Other:
- Add Docker --cap-add entries to security doc
- Fix Python version 3.10+ -> 3.11+ (contributing)
- Fix AGENTS.md discovery claim (not hierarchical walk) (tips)
- Fix cron 'add' -> canonical 'create' (cron-internals)
- Add pre_api_request/post_api_request hooks to plugin guide
- Add Google/Gemini provider to providers page
- Clarify OPENAI_BASE_URL deprecation (providers)

website/docs/user-guide/messaging/matrix.md

@@ -265,13 +265,13 @@ MATRIX_ENCRYPTION=true
 
 When E2EE is enabled, Hermes:
 
-- Stores encryption keys in `~/.hermes/matrix/store/`
+- Stores encryption keys in `~/.hermes/platforms/matrix/store/` (legacy installs: `~/.hermes/matrix/store/`)
 - Uploads device keys on first connection
 - Decrypts incoming messages and encrypts outgoing messages automatically
 - Auto-joins encrypted rooms when invited
 
 :::warning
-If you delete the `~/.hermes/matrix/store/` directory, the bot loses its encryption keys. You'll need to verify the device again in your Matrix client. Back up this directory if you want to preserve encrypted sessions.
+If you delete the `~/.hermes/platforms/matrix/store/` directory, the bot loses its encryption keys. You'll need to verify the device again in your Matrix client. Back up this directory if you want to preserve encrypted sessions.
 :::
 
 :::info