config: capture the live server configuration ...

Profiles gain the gntodo / gnexus-book / gnexus-creds scopes for agent and
subagent runs, refreshed model lists, and write access where the live setup
has it. MCP server configs pick up their user_key slots, gnexus-book learns
delete_pending_change, and the hard-panel / synapse / tgclient servers join
the tree.

Merge remote-tracking branch 'origin/master' ...

# Conflicts:
#	webclient/vendor/gnexus-ui-kit/package-lock.json

synapse reactions W3: reaction runner, notify tool, gateway hookup ...

- navi/synapse/reactions.py: fire-and-forget reaction run — per-user
  reactions_enabled gate, one-shot dispatcher meta-pass (visible profiles
  only, hidden dispatcher, secretary fallback), special=True session
  headed by the resolved profile, headless agent run via the orchestrator
  run registry, finalise: app push per completion_notify +
  low-level reaction.finished/failed event to Synapse
- navi/synapse/outbound.py: source-side emit (syn_* key from env,
  silent when not configured)
- navi/tools/notify.py: notify tool — message + level (info/warning/
  intervention), both legs per push_target, honest delivered/skipped result
- push/service.py: notify_custom without cooldown
- gateway: verified + non-duplicate delivery schedules the reaction
- profiles: notify added to native tools (7 profiles)

synapse reactions W2: hidden dispatcher profile + synapse_instructions tool

Merge remote-tracking branch 'origin/master'

e2e fixes: tasks tool in profiles, bg timeout lift, stepIcon fix, queue semantics docs ...

E2E findings addressed:
- tasks tool was registered but not in any profile's tools.agent.native —
  added to all six profiles (agent could not check/wait/cancel bg tasks)
- detached terminal/code_exec/ssh_exec runs without explicit timeout are
  lifted to 300s: foreground defaults (20/30/60s) marked long commands
  'completed' with partial output while the process still ran
- ToolCard.vue: define stepIcon(status) — template referenced it but the
  function was missing (render crash on task_update step)
- message_queued reachability documented: WS read loop is sequential, the
  queue path is only reachable from a second socket/headless recall

Merge branch 'master' of https://git.gnexus.space/git/root/navi-1

.

swarm stage 2: peer-to-peer channel — /peer endpoints + peer tool ...

Server side (navi/api/routes/peer.py, port 8099):
- GET /peer/hello — open discovery ping (name, uuid prefix, version)
- GET /peer/status — PSK; identity, uptime, machine facts, hive view
- POST /peer/ask — PSK; one-shot agent run under PEER_ASK_PROFILE
  (default server_admin) answers, one concurrent ask at a time
- loop guard: answering agent runs without the peer tool (deterministic
  recursion cut) + own-uuid asks refused with 409
- verify_swarm_key in navi/swarm.py accepts .swarm-key.previous
  (rotation window, constant-time)

Client side (navi/tools/peer.py):
- peer tool: list (hive book, stale cache fallback marked), status,
  ask by swarm name; asks go direct peer-to-peer, hive never on the
  message path
- audit events on both sides (peer.ask_sent/received/answered/failed)

peer tool added to server_admin, navi_code, developer profiles.

.

profiles: retire gate flags and retrain prompts for the plan tool ...

- drop planning_enabled / planning_mandatory / planning_phase2_enabled /
  observe_skips_plan_enabled / adaptive_replan_enabled from AgentProfile,
  the loader and admin serialization
- add `plan` to native tools of developer, navi_code, tool_developer,
  secretary, server_admin, modeler_3d — without the gate they would
  otherwise lose planning entirely
- system prompts: call plan for non-trivial multi-step work before
  execution; complex plans get presented for confirmation; stuck or goal
  changed -> plan with a reason

permissions: remove broken client-side gate; add backend design doc ...

The terminal-TUI permission gate was a race: _execute_tools_with_sink
emits ToolStarted and starts the tool on the backend immediately, so by
the time the client dialog appeared the destructive action had already
run -- 'deny' could only stop the session, not un-execute the tool. It
also existed only in the terminal TUI (webclient/android had nothing),
and the system-prompt 'Strict Confirmation' nudge was an unreliable
duplicate.

Remove the broken machinery for a clean slate and plan the real
replacement from zero:

- delete clients/terminal/tui/permissions.py, screens/permission_dialog.py
  and their tests
- strip tui_app.py (engine, _deny_tool, _show_permission_dialog,
  _confirm_shell_command, _stop_session_worker, on_permission_request,
  tool_started gate) and the PermissionRequest TUI event; !cmd now runs
  directly (user-typed, no agent gate)
- drop the 'Strict Confirmation' prompt rule from navi_code/developer/
  tool_developer
- add docs/permissions.md: authoritative backend gate design (engine +
  registry + event + endpoint + agent gate + postgres policy + global
  rules config, sub-agents gated) -- design only, not yet implemented
- update docs/index.md, navi_code_cli.md, profiles.md, testing.md

Until Phase 1 lands there is no destructive-action confirmation -- a
conscious period without the false security of the old race-gate.

replan: integrated mid-task re-planning tool ...

Add a replan tool that re-runs the planner over the live session context
+ todo + scratchpad when the plan's structure is stale due to discoveries
(NOT failed steps -- that stays [Adaptive re-plan]). Integrated approach:
PlanningEngine.run gains is_replan/replan_context (suppresses DIRECT
shortcut and observe-skip, frames Phase 1 as a revision); ReplanRunner
packs reason/goal/todo/findings/errors and captures PlanReady; the tool
is exposed to navi_code/developer/tool_developer via a
current_replan_runner ContextVar set per-iteration in run_stream (correct
after switch_profile). New plan replaces the todo. Lazy events import
breaks the navi.tools -> navi.core -> navi.tools cycle.

profiles: port context-org/planning instructions to developer & tool_developer ...

Port the context-organization and planning-machinery framing accumulated
in navi_code to the developer and tool_developer profiles, adapted per
profile:

- Working state & memory (todo/scratchpad/context_transfer/schedule_recall/
  reflect/memory) replaces the stale "Context drift recovery" section.
- System signals subsection names the runtime-injected messages each profile
  actually receives: [Goal anchor], [Anti-stall warning], [Adaptive re-plan]
  (adaptive_replan is on for both), [Iteration N/M]. [Scope boundary] is
  omitted — scope_boundary_enabled is off on these profiles.
- Reading & searching, Editing policy (tool_developer), Safety Rules, Git
  discipline, and Project environments (isolated venv) added.
- developer: Workflow rewritten planner-aware with an observe carve-out
  (observe_skips_plan now on); Project knowledge replaced by docs-first
  Documentation; sub-agent briefing gains context_transfer + restricted-toolset
  bullets.
- tool_developer: keeps its MCP-specific 10-step workflow and prerequisites;
  sub-agent briefing gains context_transfer + restricted-toolset bullets
  (sub-agent cannot reload_tools/test_mcp_tool/mcp_status — run those inline).
- config: observe_skips_plan_enabled=true on both, so observe requests skip
  phase3 (no plan/todo for read/explain/inspect) — enables the Workflow
  observe carve-out and saves an LLM call on info requests.

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

filesystem: make edit/edit_lines the default, smart_edit a last-resort fallback ...

Agent overused smart_edit (whole-file LLM call, weak context). Rewrite the
FilesystemTool description decision tree so edit (exact text) is the default and
edit_lines (by line numbers) is the deterministic option; smart_edit is reserved
for genuinely semantic changes that cannot be expressed as exact text or line
numbers. Strengthen the old_not_unique hint to steer back to edit/edit_lines
before smart_edit. Add an "Editing policy" section to the navi_code and
developer profile prompts reinforcing the same priority.

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

profiles: add gemma4:12b-it-qat-128k as top-priority model ...

New local QAT model added at the head of the model priority list across
all profiles, so it is preferred first with cloud fallback.

Fix MCP names and profile API format consistency ...

- Replace stale mcp__navi_web__* / mcp__navi_3d__* names with canonical
  mcp__navi-web__* / mcp__navi-3d__* across prompts and key_tools.
- Update /agents/profiles and /admin/profiles endpoints to expose
  tools.agent / tools.subagent instead of deprecated enabled_tools fields.
- Update docs/mechanics.md to reference the new tools structure.
- Archive stale docs/visual.html.

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

Clarify terminal description param and profile prompts ...

- terminal.py: stronger description for the 'description' field so
  the model knows it is REQUIRED for action=open and what to write
- server_admin and developer system prompts: add a short section
  explaining persistent terminal usage (open/close/list/status/send_input)

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

Prioritise gemma4 and add MCP tools to subagent scopes ...

- modeler_3d: gemma4:31b-cloud first (vision-capable), drop glm-5.1
- modeler_3d subagent: add navi-3d + navi-web MCP tools
- Adjust subagent tool scopes across profiles for explicit MCP access

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

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>

cleanup: remove deprecated tools and orphaned memory tools ...

Removed (no profile used them, no cross-dependencies):
- write_tool.py, delete_tool.py, test_tool.py
- memory_save.py, memory_search.py, memory_forget.py

Updated:
- navi/core/registry.py — removed imports and registrations
- navi/tools/__init__.py — removed imports
- docs/tools.md — removed references, updated self-extension section to MCP
- navi/tools/tool_manual.py — updated example to create_mcp_server

Profile fixes:
- developer: +tool_manual, +ssh_exec
- discuss: +list_profiles
- tool_developer: +mcp_servers navi-web

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>

Clarify knowledge persistence prompts