McpTool: auto-inject session_id + normalize navi-3d paths ...

- McpTool.execute() now forces the real session_id from current_session_id
  ContextVar, preventing LLM hallucinations of wrong UUIDs (ghost-session bug).
- For navi-3d MCP server, source_path/output_path are normalized to basename
  to prevent double path nesting when the LLM passes full relative paths.
- Updated MCP tool descriptions to ask for filenames only.
- Added system prompt instructions in context_builder and subagent_runner
  reminding the model to pass bare filenames to navi-3d tools.

396 passed, 1 skipped

Enhance native toolset and add persistent KV store ...

- Add PostgreSQL-backed KvStore (navi/store/) for session-scoped data.
- Migrate todo and scratchpad from in-memory dicts to KvStore.
- Filesystem: add copy, grep, diff actions; compress description.
- CodeExec: remove language param, expose working_dir in schema.
- ImageView: resize to 1024px JPEG + Content-Type guard for URLs.
- Memory list: return distinct categories instead of all facts.
- SSH: add scp action with upload/download support.
- Update CLAUDE.md (Postgres-only), docs/tools.md, add docs/store.md.
- Fix agent/planning/context_builder async signatures for todo helpers.

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

Refactor: move tool helper modules into _internal subpackage ...

Moves non-tool infrastructure out of navi/tools/ root so that only
actual tool classes live there:

  base.py           → _internal/base.py
  loader.py         → _internal/loader.py
  middleware.py     → _internal/middleware.py
  logging_middleware.py → _internal/logging_middleware.py
  _time_parser.py   → _internal/time_parser.py

All imports updated across core/, api/, mcp/, tools/, and tests/.
No proxy files remain in navi/tools/ root.

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

refactor: migrate MCP config to directory-based mcp_servers.d ...

Replaces monolithic mcp_servers.json with per-server files in
mcp_servers.d/<name>.json. Filename stem becomes the server name.

- load_mcp_servers() reads directory globs, auto-migrates legacy file
- save_mcp_servers() writes per-server files, cleans up stale ones
- Update docstrings in manager.py and context_builder.py

Auto-migration: existing servers (gnexus-book, navi-3d, navi-web) plus
new ones (project_health, time_toolkit) now live in mcp_servers.d/.

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

Clarify knowledge persistence prompts

Auto-inject relevant memory facts into LLM context on every user turn. ...

Semantic search against the vector memory store runs in parallel with
context provider collection. Number of injected facts scales with
message length (1–3) to reduce noise on short queries. Guardrails:
min length gate, per-turn deduplication, and structured logging at
info level for observability.

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

Inject MCP server instructions into system prompt ...

- McpClient: collect instructions from MCP initialize handshake
- McpServerConfig: add 'instructions' field for Navi-side overlay
- McpManager.get_instructions(): merge server + config instructions
- ContextBuilder: new _mcp_context_msg() injects MCP server
  descriptions into every LLM context as a system message
- Agent passes mcp_manager to ContextBuilder
- mcp_servers.json: add overlay instructions for gnexus-book

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

Propagate user profile to LLM context via current_user_info ContextVar ...

- Extend User model: username, first_name, last_name, phone, birth_date,
  country, city, locale (all from gnexus-auth profile)
- navi_users DDL: add new profile columns
- auth/deps + auth/callback: populate new fields on upsert
- /auth/me: return all profile fields
- Add current_user_info ContextVar for full user profile propagation
- websocket + messages: set current_user_info before agent.run()
- run_ephemeral: inherit and restore current_user_info
- ContextBuilder: _user_context_msg() injects [User context] with name,
  email, location, locale, role into LLM system messages
- _security_policy_msg: reads user_id/role from ContextVar directly

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

Add multi-user sandbox: filesystem, terminal, code_exec, security policy ...

- filesystem, share_file: sandbox non-admin users to user_data/<user_id>/
- terminal: working_dir sandbox + allowlist + dangerous pattern block for users
- code_exec: sandbox CWD and temp files to user_data/<user_id>/ for users
- context_builder: inject dynamic security policy into LLM context (user/admin)
- config: terminal_user_allowed_commands setting
- agent: wire user_id/user_role through ContextBuilder.build()
- base: add current_user_role ContextVar; run_ephemeral inherits role

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

Multi-user auth via gnexus-auth OAuth + hybrid role/permission model ...

- Integrate gnexus-auth-client-py (GAuthClient) for OAuth flow, token refresh,
  and webhook parsing
- Add navi/auth/ package: User model, Fernet encryptor, client singleton,
  deps (get_current_user, require_admin, require_permission)
- New tables: navi_users, user_auth_sessions (auto-created on startup)
- Session/memory isolation by user_id with legacy NULL support
- Cookie-based auth proxy: /auth/login, /callback, /logout, /me
- Webhook receiver /webhooks/gnexus-auth handling user events, global logout,
  session revocation, role/permission changes
- Admin endpoints (/admin/*) gated by role + permissions
- Webclient auth store with isAdmin/hasPermission guards
- Admin-only profile filtering in /agents/profiles
- 200/200 tests passing

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

Improve 3D modeling validation prompts

Fix 3D modeling feedback: session context, CORS, and PNG workflow ...

- Embed session_id into the main system prompt so the model reliably
  sees the correct session files directory instead of hallucinating one.
- Add global CORS middleware to fix STL viewer iframe fetch errors.
- Switch modeler_3d PNG previews from content_publish to image_view
  so renders are debug-only for Navi, not user-facing cards.
- Remove literal {session_id} template from persona.txt.

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

Improve content publishing UX

Bootstrap test suite — Phase 1 unit tests ...

- docs/testing.md: testing strategy, mock strategy, phase breakdown
- tests/conftest.py: autouse fixture to reset navi.config.settings per test
- tests/conftest_factory.py: FakeLLMBackend, FakeTool, make_profile, make_registry helpers
- tests/unit/core/test_events.py: wire serialization for all 15 event dataclasses
- tests/unit/core/test_compressor.py: should_compress, partition_messages, format_for_summary, compress_context
- tests/unit/core/test_registry.py: ToolRegistry, ProfileRegistry, BackendRegistry
- tests/unit/core/test_context_builder.py: system prompt caching, persona injection, goal anchor, iteration budget
- tests/unit/profiles/test_base.py: Pydantic model coercion, defaults, extra fields
- navi/core/context_builder.py: use module-level `import navi.config` instead of `from navi.config import settings` so tests can swap the singleton

59 tests passing.

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

Extract PlanningEngine, ContextBuilder, ToolExecutor from agent.py ...

- navi/core/planning.py: new 3-phase planning pipeline (~390 lines)
- navi/core/context_builder.py: system prompt caching, memory/context injection, goal anchoring (~160 lines)
- navi/core/tool_executor.py: tool execution with middleware chain (~150 lines)
- navi/core/agent.py: reduced from ~1420 to ~770 lines; delegates to extracted classes

All compilation verified.

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