Refactor profile tool config to explicit agent/subagent structure ...

Replaces the confusing mix of enabled_tools + mcp_servers + subagent_tools
with a single explicit structure:

    tools: {
      agent:   {native: [...], mcp: {server: [groups]}},
      subagent:{native: [...], mcp: {server: [groups]}}
    }

Why:
- Old fields mixed native and MCP names (mcp__server__tool) in one list,
  making it impossible to tell at a glance what a subagent actually gets.
- subagent_runner.py had 25 lines of runtime MCP filtering logic that
  was hard to follow and error-prone.

Changes:
- AgentProfile: add ToolConfig / ToolScopeConfig pydantic models,
  keep old fields (enabled_tools, mcp_servers, subagent_tools) for
  auto-migration via _migrate_tools validator.
- loader.py: read new "tools" key, auto-migrate legacy configs.
- agent.py: _tool_list now accepts ToolScopeConfig.
- subagent_runner.py: simplified — profile.get_subagent_tools() returns
  the exact scope, no runtime filtering needed.
- context_builder.py, list_tools.py, spawn_agent.py: updated to use
  profile.get_agent_tools() / get_subagent_tools().
- All 6 profile config.json files migrated to new schema.
- Secretary subagent now explicitly gets navi-web MCP tools for web search.

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

Migrate MCP tool naming from mcp:server:tool to mcp__server__tool ...

The colon separator (mcp:server:tool) confuses many LLMs during
tool-calling because colons appear in schemas and URLs. Switch to
double-underscore separator (mcp__server__tool) for robust parsing.

Key changes:
- navi/mcp/tools.py: add build_mcp_name(), parse_mcp_name(), is_mcp_tool()
- navi/core/tool_executor.py: update _resolve_tool() with new helpers
  and legacy colon fallback for old sessions
- navi/core/tool_utils.py, subagent_runner.py: use build_mcp_name()
- navi/api/routes/{admin,agents}.py: prefix via build_mcp_name()
- navi/tools/{list_tools,reload_tools}.py: migrated
- All profile configs + system_prompt.txt: replace mcp: with mcp__
- manuals/{model_3d,lint_scad,render_3d,spawn_agent}.md: updated
- mcp_servers.d/gnexus-book.json: instructions updated
- docs/{api,profiles,tools,mechanics,visual.html}: updated
- tests: test_tool_executor.py and test_mcp.py aligned

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

Add self-recall (scheduled callback) system ...

Core features:
- schedule_recall tool: once/recurring/immediate callbacks
- manage_recall tool: cancel/skip/list scheduled recalls
- Natural-language time parser (ISO, relative, "tomorrow at 09:00")
- PostgreSQL-backed RecallScheduler with lazy pool init
- Background recall_scheduler_loop with asyncio.Semaphore(3)
- _busy_sessions guard prevents user messages during headless runs
- Agent.run() preserves thinking field for session history visibility
- API endpoints: GET/DELETE/POST for session recall, admin list
- Frontend: recall badge, filter, cancel/skip in sidebar and chat header
- Tests: parser, scheduler CRUD, tools, API, scheduler loop (53 tests)
- Manuals: schedule_recall.md and manage_recall.md

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

Fix profile MCP server groups to use group names instead of tool names ...

Profile configs were listing individual tool names (web_view, http_request)
in mcp_servers.navi-web instead of group names (browse, request). This caused
resolve_group() to return empty results, so MCP tools never appeared in the
profile's resolved tool list.

Also fixes modeler_3d stale tool references in system_prompt.txt.

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

Rename MCP tools to mcp:server:tool format and restore human-readable names ...

- Core naming: mcp_server_tool → mcp:server:tool (colon-delimited)
- navi-web tools: search/view/request → web_search/web_view/http_request
- navi-3d tools: compile_scad/render_stl/lint_scad (unchanged names)
- Updated all profile configs, system prompts, docs, manuals, tests
- Added new lint_scad.md manual
- Fixed modeler_3d prompt stale references (scad_lint, model_3d, render_3d)
- All 240 tests pass

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

Clean up remaining web_search / web_view / http_request references ...

- Deleted stale source files: navi/tools/web_search.py, web_view.py,
  http_request.py (no longer imported or registered).
- Updated system_prompt.txt in all profiles (secretary, server_admin,
  discuss, modeler_3d subagent) to reference mcp_navi-web_* tool names.
- Updated key_tools in developer, secretary, server_admin config.json.
- Updated docs (tools.md, profiles.md, api.md) to reflect MCP migration.

Tests: 240 passed.

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

Rename navi-web MCP tools and compact search output ...

- web_search → search, web_view → view, http_request → request
  This removes the redundant 'web' prefix from tool names in the
  navi-web MCP server, making them cleaner: mcp_navi-web_search etc.

- Compact search output: output string now contains only
  [Source] + [N] Title — URL, without duplicating the body snippet.
  Full results with body/description remain in metadata for
  programmatic use.

- Updated mcp_servers.json groups and all profile configs.

Tests: 240 passed.

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

Migrate web tools (web_search, web_view, http_request) to navi-web MCP server ...

New MCP server: mcp-servers/navi-web/
- app/search.py    — SearXNG primary, DDG fallback, Brave tertiary
- app/browse.py    — Playwright headless browser page extraction
- app/request.py   — httpx raw HTTP requests
- app/mcp_server.py — FastMCP entry point with stdio transport
- pyproject.toml   — deps: mcp, httpx, ddgs, playwright, pydantic

Changes:
- Added "navi-web" block to mcp_servers.json (stdio transport)
- Removed web_search, web_view, http_request from built-in registry
- Removed them from navi/tools/__init__.py
- Removed them from enabled_tools / subagent_tools in all profiles
- Added "navi-web": ["search", "browse", "request"] to mcp_servers
  in all profiles (developer, secretary, server_admin, tool_developer,
  modeler_3d, discuss)

Tests: 240 passed.

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

Increase max_iterations across all profiles ...

- developer: 45 → 100
- discuss: 12 → 30
- modeler_3d: 50 → 70
- secretary: 35 → 70
- server_admin: 40 → 100
- tool_developer: 35 → 100

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>

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>

Connect gnexus-book MCP server and enable in profiles ...

- mcp_servers.json: SSE transport to 192.168.1.170:8001
- server_admin profile: all 16 gnexus-book tools
- discuss profile: read-only gnexus-book tools (docs + inventory)

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

Improve content publishing UX

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>

changed llm

changed llm & new ollama param

changed model

Add structured planning review and adaptive depth

Tune profile sampling configs

temp -

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>

Add Ollama multi-server fallback with in-memory blacklisting ...

- New FallbackOllamaBackend (navi/llm/fallback.py): tries servers and
  models in priority order; on LLMConnectionError blacklists the server
  for the process lifetime, on LLMModelNotFoundError blacklists the
  (server, model) pair — eliminates latency from repeated failed probes
- OllamaBackend now raises typed LLMConnectionError / LLMModelNotFoundError
  instead of bare LLMBackendError; accepts list[str] | str | None for model
- AgentProfile.model changed from str to list[str] (str auto-normalised);
  all profiles updated to ["gemma4:31b-cloud", "gemma4:26b-a4b-it-q4_K_M"]
- New config field OLLAMA_BACKENDS_FILE: path to [{host, api_key?}] JSON;
  when set, registry creates FallbackOllamaBackend instead of OllamaBackend
- ollama_backends.json template added (gitignored — contains API key)
- current_model ContextVar type widened to list[str] | str | None

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

Use gemma4 cloud model by default

Support Ollama Cloud API key

Autonomous reasoning improvements: budget, anchoring, anti-stall, validation ...

- AgentProfile: per-profile thinking mechanics flags (think_enabled,
  iteration_budget_enabled, goal_anchoring, anti_stall, step_validation,
  planning_reflect, adaptive_replan) — all profiles updated in config.json
- Iteration budget: inject remaining iterations into context so model knows
  when to wrap up; urgency levels at ≤7 and ≤3 remaining
- Goal anchoring: inject original goal + todo state every N iterations to
  prevent drift on long tasks
- Anti-stall: two signals — no todo progress for N iterations, or identical
  tool calls repeated N times; warning injected into context
- Todo step validation: marking done requires a validation field describing
  how result was verified; failed gets a soft nudge with tip for re-planning
- stream_complete: add think param to base class, ollama and openai backends
- Summarizer: raise max_tokens 1024→3000, expand system prompt with
  user-preferences section and verbatim-value instructions
- Compression card: persist to session.messages (is_compression flag on
  Message), show expandable summary in webclient with markdown body
- ToolResult.to_message_content: always include output on failure so
  tracebacks and error details reach the model (fixes silent Error: None)
- Developer profile: fix subagent profile secretary→developer, add write_tool
  to subagent_tools, clarify write_tool vs filesystem in system prompt

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

Fix spawn_agent: restore briefing, fix status leakage, enable subagent planning ...

spawn_agent:
- Restore briefing param (task = goal, briefing = context — good separation)
- Add system_prompt as third param for role specialisation per task
- Remove [STATUS: ...] prefix that was leaking into Navi's responses and
  causing hallucination — replaced with natural-language headers that are
  less likely to be regurgitated verbatim
- completed → neutral header; limit_reached → explicit warning about incompleteness

Profiles:
- subagent_planning_enabled: false → true in all three profiles
  (planning is on by default, disable per-profile if needed)

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

Improve subagent system: isolated tools, custom prompts, context transfer, timeout ...

AgentProfile:
- New fields: subagent_tools, subagent_planning_enabled, subagent_system_prompt
- loader.py: loads subagent_tools/subagent_planning_enabled from config.json,
  reads optional subagent_system_prompt.txt per profile

Profiles:
- Each profile now has a dedicated subagent_tools list (focused subset, no admin tools)
- subagent_planning_enabled: false (configurable per profile)
- New subagent_system_prompt.txt per profile with executor-focused instructions

run_ephemeral:
- Uses profile.subagent_tools instead of enabled_tools
- Builds subagent context without persona or profiles block (focused executor)
- Injects subagent_system_prompt after profile.system_prompt
- Accepts context_transfer: priming exchange injected before task message
- Wall-clock timeout (default 5 min) checked per iteration
- Returns (result_text, completed: bool) instead of bare string
- Optionally runs planning phase if profile.subagent_planning_enabled

spawn_agent:
- Removed briefing param; task is now fully self-contained
- Added system_prompt param: custom injected prompt for this specific task
- Auto-reads parent scratchpad context_transfer section via get_section()
- Result prefixed with [STATUS: completed|limit_reached]
- Timeout 300s

scratchpad:
- Added get_section(session_id, section) helper for cross-session reads

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

Planning phases, context compression, and tool improvements ...

Agent:
- Planning now a 3-phase async generator: Analysis → Execution plan → AIHelper critic
- Yield PlanningStatus events before each phase (UI progress labels)
- Phase 1 runs with think=True for deeper analysis
- Phase 2 includes available tool list so executor assignments are accurate
- Phase 3: independent critic pass validates and corrects TOOL: names against real tool list
- Planning converted from list return to async generator (fixes token accounting)

Backend:
- Context compression threshold: 80% → 70% to trigger earlier
- Compressor summary prompt: structured sections (goal, work state, key facts, outputs, errors)
- Terminal output capped at 5000 chars to prevent context flooding
- Web search: region=wt-wt for DDG, country=ALL for Brave, language=all for SearxNG
- Scratchpad: mandate writing a 'goal' section at start of multi-step tasks
- secretary max_iterations: 40→25, temperature: 0.7→0.5
- server_admin max_iterations: 40→20

Webclient:
- ThinkingCard strips <thought> XML tags leaked by Ollama
- planning_status WS event wired to chat.onPlanningStatus()

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

Add reflect tool: three parallel expert perspectives ...

ReflectTool runs Critic / Pragmatist / Detailer advisors concurrently
via asyncio.gather() + AIHelper.ask(). Each role has a distinct system
prompt designed to produce genuinely different analysis:
- Critic: challenges assumptions, surfaces risks and logical gaps
- Pragmatist: finds the simplest path, cuts unnecessary complexity
- Detailer: spots missing requirements, edge cases, ambiguities

Parameters: situation (required), assumptions (required list — the key
input that forces Navi to surface implicit beliefs), tried (optional).

Registered as a builtin with AIHelper injection. Added to all three
profiles. Persona updated with guidance on when to use it (complex or
ambiguous tasks before planning, or when stuck mid-execution).

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