Persist uploaded files in messages, live file tree updates, and UI polish ...

Backend:
- Add `files` field to `Message` model so uploaded file metadata survives page refresh
- Pass `files` through websocket handler → `agent.run_stream` / `agent.run`
- `list_tools`: make `profile_id` required; return error instead of all-tools fallback

Webclient:
- Call `fetchFiles()` after successful file upload for immediate Files tab update
- Live refresh file tree on filesystem (write/edit/append/mkdir/rm/cp/mv), terminal, and code_exec tool calls
- Add manual refresh button (desktop) and pull-to-refresh (mobile) to Files tab
- Fix live link updates: move regex creation inside per-message loop to avoid lastIndex state leak
- Restore full profile name text next to avatar in ChatHeader; hide avatar in header
- Fix mobile ArtifactsPanel: collapse tab text labels so close button fits with 3 tabs

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

Fix agent.py _tool_list to use colon-delimited MCP names ...

The main registry and API routes were migrated, but Agent._tool_list
still built names with the old underscore format. This meant MCP tools
were silently dropped from the tool list passed to the LLM, causing
"tool not found" when the model correctly called mcp:server:tool names.

Also updates stale docstring in McpTools.

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>

Fix ollama_backends / FallbackOllamaBackend issues ...

- registry.py: always use FallbackOllamaBackend (unified backend).
  Enables model priority lists in all deployments, not just multi-server.
- agent.py: add missing think=profile.think_enabled to run() (REST endpoint).
- compressor.py: fix model param type (str → list[str] | str | None).
- fallback.py: harden load_servers_from_file against missing/bad JSON files
  and entries without host. Add clear_blacklists() for manual reset.
- admin.py: add POST /admin/ollama/clear-blacklists endpoint.
- tech_debt_review: document dead stream() methods.
- tests: add tests for single-server fallback, bad file handling,
  missing host skipping, and blacklist clearing.

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

Add deterministic line-based file editing (edit_lines), rating UI fix, and session refresh ...

- filesystem.py: add edit_lines action (deterministic line ops via operations array)
           + numbered param for read (1-based line numbers in output)
           + clarify four editing modes in tool description
- chat.js: fix rating IDs for streaming messages (assign h_ ID on stream_end)
- SessionList.vue: mobile pull-to-refresh with PTR_THRESHOLD=80
- AppSidebar.vue: desktop refresh button next to Conversations header
- planning.py: knowledge source assessment in Phase 1
- debug panel: MCP servers tab + resolved tools per profile
- NAVI.md: reposition as neutral quick-reference

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>

Refactor MCP integration: server groups in profiles ...

- mcp_servers.json: add 'groups' (read/write/admin) for gnexus-book
- AgentProfile: new 'mcp_servers' field (server_name -> group list)
- Profile loader: parse and persist 'mcp_servers' in config.json
- Agent._tool_list(): expands mcp_servers into concrete tool names
  via McpManager.resolve_group(), wildcard '*' supported
- /agents/profiles API: includes 'mcp_servers' in response
- Profiles no longer list individual mcp_ tools in 'enabled_tools'
- discuss: gnexus-book read group
- server_admin: gnexus-book read+write+admin groups

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>

Add per-user filesystem sandbox via current_user_id ContextVar ...

- tools/base.py: add current_user_id ContextVar (set by Agent before
  every tool call, cleared after)
- core/agent.py: set current_user_id in run_stream from session.user_id
  and in run_ephemeral from parent_session.user_id; restore in finally
- tools/filesystem.py: _check_path resolves all paths inside
  user_data/<user_id>/ when current_user_id is present; legacy mode
  (no user_id) falls back to FS_ALLOWED_PATHS
- tools/share_file.py: validate source path is inside user sandbox

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

Fix NameError in run_ephemeral: session was undefined ...

run_ephemeral doesn't have a session variable. Pass user_id from the
parent session (looked up via parent_session_id) instead of referencing
non-existent session variable.

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>

Refine 3D modeler workflow

Simplify 3D SCAD subagent prompt

Disable thinking stalls for 3D subagents

Improve content publishing UX

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>

Architecture extensibility — event bus, middleware, auto-discovery, Pydantic profiles ...

- EventBus: async pub/sub for AgentEvents, WebSocket subscribes instead of direct yield
- Declarative serialization: AgentEvent.to_wire() on all event types
- Auto-discovery for LLM backends (_discover_backends) and workers (scan navi/workers/*.py)
- AgentProfile: Pydantic BaseModel with extra='allow', @field_validator for model coercion
- Tool middleware chain: pre/post execute hooks via ToolRegistry.add_middleware()
- LoggingMiddleware: built-in, logs every tool call
- Fix pg_trgm DDL: conditional GIN indexes via DO $$ block, no CREATE EXTENSION
- New files: event_bus.py, middleware.py, logging_middleware.py

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

Architecture fixes batch — NaN validation, ILIKE indexes, prompt cache, N+1 batching ...

- _vector_to_str: reject NaN/Inf via math.isfinite() to avoid invalid pgvector syntax
- memory DDL: add pg_trgm + GIN trigram indexes on category/key/value for fast ILIKE fallback
- _build_system_prompt: cache per-profile to avoid rebuilding every iteration
- backfill_embeddings: batch UPDATEs via executemany instead of N+1 loop

No new Python deps; pg_trgm is a PostgreSQL extension auto-created on startup.

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

Architecture cleanup: old_webclient, SSH shutdown, todo decoupling, ContextVar reset ...

- Remove old_webclient directory and /static mount from main.py
- Add shutdown handler in main.py to close all SSH pooled connections
- Decouple agent.py from todo module internals:
  - Add public API to navi/tools/todo.py: get_task_snapshot, get_failed_steps,
    get_progress_message, set_tasks, render_todo_lines
  - Replace all direct _plans/_STATUS_ICON/_Task imports in agent.py with API calls
- Wrap run_ephemeral in try/finally to restore _sid_var and _model_var after subagent

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

Stability fixes batch — tech debt review 2026-04-29 ...

Critical:
- Concurrent WS run race guard (#1)
- Tool task cancellation on generator teardown (#2)
- StopAsyncIteration kills fallback chain (#3)
- Session loading race with _lastLoadId guard (#4)
- ContentCard .match() crash on non-string result (#5)
- Image data type guard in buildMessageList (#6)

High:
- Cap WS replay buffer at 500 events (#7)
- Deduplicate memory extraction task with asyncio.Lock (#9)
- TTL-based fallback blacklisting (5 min) (#10)
- Subagent tool exception isolation (#11)
- Inline image size/count validation on WS (#12)
- Clean up orphaned file on DB insert failure (#13)
- Deep watch streamingMsg for auto-scroll (#14)
- WS_SCHEME wss:// support for HTTPS (#15)
- Sending guard against duplicate message sends (#16)
- Global unhandledrejection listener in API layer (#17)

Medium:
- Cap planning_logs at 20 entries (#22)
- Store cleanup_loop task reference (#23)
- BaseException → Exception in _run_with_sentinel (#24)
- Propagate SystemExit in agent loop (#25)
- Configurable output_reserve_tokens (#26)
- Always reloadSession on session_sync (#30)
- FIFO queue for confirm dialogs (#31)
- Reset body.overflow on ImageLightbox unmount (#32)
- try/finally in fallback copy (#33)
- _isConnecting guard in WS send() (#34)

Low:
- Lazy-init deps.py singletons (#36)
- Replace __import__ with direct imports (#38)
- Preserve token count 0 in ollama.py (#39)
- Clear orphaned streamingMsg on reconnect reload (#43)
- Escape single quote in UserMessage (#44)
- Polyfill-free findLast replacement (#48)
- Match <table> tags with attributes in markdown (#49)
- Attach copy buttons only when msg.done (#50)
- Fix hasMeta falsy-0 bug (#53)

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

Fix system prompt leakage into chat history; polish content cards ...

Backend:
- websocket.py + agent.py: separate user-visible display_message from
  LLM user_message. System hints (image/file attachments) no longer leak
  into session.messages and appear after page reload.
- main.py: add ensure_tables() on startup so session_content table is
  created before first publish.
- profiles: add kimi-k2.6:cloud to all model lists as fallback.

Frontend:
- ContentCard.vue: remove border-radius, add scrollbar styles, fix
  metadata fallback parsing so cards survive page reload.
- content-viewers/*.html: add matching scrollbar styles.

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

Add content hosting system with inline viewers ...

Backend:
- Add navi/content/ directory for published files
- Add content_store.py with publish/list/delete/cleanup functions
- Add content_publish tool for publishing files as viewable content
- Add /content static file mount in main.py
- Add /content-viewers mount for viewer pages
- Extend ToolEvent with metadata field
- Forward metadata through websocket tool_call events
- Update Agent to include metadata in ToolEvent

Frontend:
- Add ContentCard.vue component for displaying published content
- Add viewer pages: stl.html (Three.js), svg.html, html.html, pdf.html
- Update AssistantMessage.vue to render ContentCard for content_publish
- Update chat store to preserve metadata in tool cards
- Update websocket protocol docs with metadata field

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

changed llm & new ollama param

Strengthen todo progress discipline

Add structured planning review and adaptive depth

Add context providers: dynamic system message injection per LLM call ...

- navi/context_providers/ registry + built-in public_url provider (global, always injected)
- context_providers/ user directory, hot-reloaded via reload_tools
- AgentProfile.context_providers field for per-profile opt-in providers
- Agent._collect_context_injections() called before every tool-calling loop
- reload_tools now reloads both user tools and user context providers
- manuals/write_context_provider.md for Navi, docs/context_providers.md reference

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

Set temperature=1.0, top_k=64, top_p=0.95 for all profiles (Google recommended for gemma4) ...

Also fixes discuss profile memory tools: use combined "memory" tool name, not nonexistent split variants.

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

Add per-phase planning flags and planning_mandatory ...

- planning_mandatory: disables DIRECT shortcut, forces all phases to run
- planning_phase1_enabled / phase2_enabled / phase3_enabled: per-phase toggles
- planning_phase2_enabled replaces planning_reflect_enabled (migrated in loader with backward compat)
- Migrate all profile configs; rewrite docs/profiles.md as full config reference

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