agent: a profile switch now survives the turn that made it ...

switch_profile repoints the session with one narrow UPDATE, and the run's own
save() — which lands right after every tool batch, the switch's own batch
included — wrote its stale in-memory profile back over it. The post-turn
reload then read the row it had just clobbered, saw no change, and left the
turn bound to the old profile's tools: the agent called exactly the tools
switch_profile had just advertised ("Newly available: ssh_exec, terminal, …")
and got "tool not found" for every one of them. Prod shows both halves — the
session that reported two switches kept the profile it started with, and
agent.profile_reloaded appears zero times in the whole boot.

The reload now compares against the profile the run is bound to
(bound_profile_id), which set_profile cannot move, instead of against
session.profile_id, which the store either rewrites or mutates to the new
value — making the old guard false in both branches by construction. And
save() leaves the profile_id column alone on conflict: set_profile owns it
after creation, the same way name/created_at are owned elsewhere.

A tool the live tool_map does not hold is now logged (tool.not_found, with
profile and live tool count). It previously left no trace at all in the
journal, which is why this took a database dig to find.

Three tests, each verified to fail without its fix: the next LLM call is
offered the new profile's tools, save() does not rewrite profile_id, and a
missing tool is logged.

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

agent parallelism: background tools, bg spawn_agent, parallel tool batches, message queue ...

- backgroundable tools (terminal/ssh_exec/peer/spawn_agent/code_exec) detach
  via TaskManager with per-session/global/spawn caps, rate limit and TTL
- completion delivery both ways: task_update event (out-of-band) + pending
  notes injected into the next turn; tasks tool (list/check/wait/cancel)
- parallel tool-call batches (profile-level gate, off by default) with
  ToolStarted up-front, tagged event mux, call-order results, one save,
  plus dangling tool_call repair on session load
- user message queue instead of busy error: message_queued frame,
  back-to-back drain on the same socket, headless fallback on disconnect
- pin mcp<2 (v2 renames FastMCP with breaking API changes)
- docs: tasks.md (new), websocket/api/agent/config updates, tasks manual,
  spawn_agent background param, persona contract section

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>

Fix MCP tool spinner bug: match tool_started → tool_call by tool_call_id ...

- Add tool_call_id field to ToolStarted and ToolEvent dataclasses
- Pass tc.id as tool_call_id from agent.py, subagent_runner.py, and tool_executor.py
- Update frontend chat.js onToolStarted/onToolCall to match cards by toolCallId
  with fallback to name-matching for backward compatibility

Closes spinner issue where LLM short name ("search_docs") didn't match
resolved MCP name ("mcp__gnexus_book__search_docs").

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

Fix MCP tool registration at startup ...

Root cause: _on_mcp_server_connected was defined and registered AFTER
mcp_manager.load_all(), so startup connections never registered their
tools into the ToolRegistry.

Fix: explicitly iterate connected clients after build_default_registries()
creates tool_registry, and register their MCP tools before starting the
health-check loop. The callback stays for future reconnects.

Also adds diagnostic warning in build_tool_list when tools are missing.

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

Add debug logging to trace MCP tool registration / resolution ...

Logs added to:
- _on_mcp_server_connected: shows how many tools are registered per server
- build_tool_list: lists missing tool names and counts
- _resolve_tool: dumps tool_map keys when a lookup fails

This is diagnostic — will be removed once the root cause is found.

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

Pass explicit ToolContext to tools instead of hidden ContextVars ...

Add ToolContext dataclass (session_id, event_sink, stop_event, model,
user_id, user_role, user_info) and thread it through the execution chain:
Agent._execute_tools_with_sink → ToolExecutor → tool.execute().

All ~25 tools updated to accept ctx parameter. Tools that previously
read ContextVar now prefer ctx when provided, falling back to
ContextVar for backward compatibility.

Tests updated to pass ToolContext explicitly — no more test fixtures
that set current_session_id / current_user_id ContextVars.

ContextVar setters remain as fallback for non-tool consumers
(ai_helper, context_builder, planning) and will be removed in a
follow-up refactor.

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>

DRY: unify tool execution in ToolExecutor._execute_one() ...

Three methods (_run_single_tool, _execute_tool_calls,
_execute_tool_calls_streaming) duplicated identical logic:
resolve → middleware → execute → image extraction → build message.

- Extract canonical _execute_one(tc, tool_map) -> (ToolEvent, Message, image_msg)
- All three public methods now delegate to _execute_one
- Public signatures unchanged — no test or caller changes needed

392 passed, 1 skipped

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>

Fix gnexus-book MCP instructions and add old-format fallback in tool executor ...

- Updated mcp_servers.json gnexus-book instructions to use mcp:gnexus-book:
  prefix instead of the old mcp_gnexus-book_ format.
- Added fallback in tool_executor.py for old underscore format
  (mcp_server_tool → mcp:server:tool) so transitional models still work.
- Added unit test for the old-format fallback.

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>

Handle MCP tool aliases robustly

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>