docs: update docs for tools.agent/tools.subagent and Navi Code TUI ...

- profiles.md: document tools.agent/tools.subagent structure, deprecate enabled_tools
- tools.md: move web tools to MCP section, fix mcp__navi-web__* names, add create_mcp_server/test_mcp_tool/mcp_status/recall tools
- api.md: update /agents/profiles and /admin/profiles/{id} response schemas, fix MCP examples
- navi_code.md: correct navi_code tool list (MCP disabled)
- navi_code_cli.md: add /thinking, /compact, correct TUI layout
- index.md: add navi_code, terminal client, pydantic-settings
- testing.md: refresh test directory layout, replace stale coverage roadmap
- agent.md: mention tools.agent/tools.subagent in loop

Co-Authored-By: Claude <noreply@anthropic.com>

Fix review issues: KV-store NULL, SVG messages, filesystem tests + docs ...

Bugs fixed:
- filesystem.py: add missing `import re` (grep was broken in production)
- image_view.py: consistent SVG rejection message for URL and file paths
- store/__init__.py: normalize user_id None→'' to prevent duplicate rows
  in unique constraint for anonymous sessions; add DDL migration for
  existing NULL values

Tests:
- Add 10 unit tests for filesystem copy, grep, diff operations

Documentation:
- agent.md: document streaming guard wrapper, system prompt caching,
  ContextVar restoration in subagents
- tools.md: document middleware hooks
- websocket.md: document image upload limits and concurrent run guard
- store.md: document user_id normalization
- mechanics.md: mark newly-documented mechanics as documented

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Audit and fix docs/ for accuracy against current codebase ...

Package A (API + WebSocket + Sessions):
- api.md: add missing endpoints (health/embed, auth/status, agents/prompts,
  agents/mcp_servers, sessions/content, 7 admin endpoints). Fix response
  schemas, auth requirements, query params. Update path formats.
- websocket.md: fix planning_status.phase type (int 1|2|3), add metadata
  to tool_call, message_index to stream_end, context_tokens/max_context_tokens
  to context_compressed.
- sessions.md: fix context_compression_threshold default (0.80→0.70),
  add list_page method, add metadata to Message flags.

Package B (Config + Profiles + Tools + Agent + Memory):
- config.md: remove stale ANTHROPIC_API_KEY description, add 12 missing
  env vars (embedding, web search, terminal_user_allowed_commands,
  context_providers_dir, gnauth fields, output_reserve_tokens).
  Fix OPENAI_BASE_URL type.
- profiles.md: fix max_iterations default (20→10), add top_k/top_p/num_thread,
  is_admin_only, context_providers, mcp_servers, subagent_think_enabled.
  Clarify subagent_tools fallback and step_validation_enabled.
- tools.md: replace 3 separate memory tools with unified `memory`, add
  `mcp_status`.
- agent.md: fix run_ephemeral return type (str→tuple), clarify DB reads.
- memory.md: fix search_facts/get_all_facts param order, fix MemoryStore
  init description.

236 tests passing.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Allow subagents to use selected profiles

Add structured planning review and adaptive depth

Add NAVI.md navigation hub and update core docs ...

NAVI.md: lightweight project entry point for Navi — server command,
key paths, doc map with query instructions, tool manual index.
All profiles read this; detailed content stays in docs/.

docs/agent.md: rewrite to cover 3-phase planning, all 10 thinking
mechanics flags, adaptive replan, anti-stall, goal anchoring.

docs/profiles.md: update AgentProfile fields (all flags), correct
profile list (secretary/server_admin/developer), JSON config format,
auto-discovery instead of manual registration.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Add backend documentation ...

10 markdown files covering all backend subsystems: architecture,
agent loop, tool system, sessions, WebSocket protocol, profiles,
memory, config, and API reference. Structured for AI readability
with a single entry point (docs/index.md) and cross-references.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>