tools: list_tools tells the truth and costs a tenth of the context ...

The tool read the profile config, not the registry: a tool the config declares
but nothing registered — mcp__navi_ui__render_component, whose server never
connects — was advertised as callable, and the agent walked into "tool not
found" (28 such warnings on prod). It now resolves every name against the live
registry and reports the rest separately as "Not registered", so a phantom
entry reads as a broken server, not as a tool to try.

It also returned every description it could find. For server_admin that was
125 tools and 35 316 bytes per call — ~9k tokens to answer "do I have anything
for ssh". Names are now grouped by source (native, then one section per MCP
server) with descriptions behind verbose, and query filters by substring over
names and descriptions: the ssh question costs 88 bytes instead of 35 KB, and
a plain listing drops to 3.7 KB (9.5x smaller).

Tests cover the phantom-tool case, query matching by name and by description,
and the size property that makes names-only the default.

reload: pick up the new code, and drop MCP tools that are gone ...

reload_tools reported success while three separate things kept it from
doing what it says.

The bytecode cache is keyed on (mtime in whole seconds, file size), so a
tool edited to the same length inside the same second as its previous
load re-ran the OLD code — the reload was real, the new version was not
live. The loader now compiles the source itself instead of consulting
__pycache__ (importlib.invalidate_caches() does not help here).

MCP registrations only ever grew: register_mcp_tools called
register_external, and unregister_external was used in one place, so a
server removed from the config or a tool a server stopped exposing
stayed in the registry and failed only when the model called it. Reload
now clears external tools and rebuilds them.

enabled.json naming a tool that failed to load (the gmail/html2text case)
was visible only as a log line. It is now part of the report.

The reload itself moves to navi/core/reload.py, one implementation shared
by the tool and the admin route, so the two cannot leave different
toolsets behind. list_tools.py also read enabled.json through its own
cwd-relative path, which made it disagree with the real toolset, and the
class-based loader rejected execute(self, params, ctx=None) — the shape
every built-in uses.

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>

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>

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>

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>

Add profile_id support to list_tools ...

ListToolsTool now accepts an optional `profile_id` parameter. When
provided, it returns only the tools enabled for that specific profile
(enabled_tools + user tools + resolved MCP tools). This helps the agent
preview what a profile can do before switching.

- Updated ListToolsTool.execute() with profile-aware filtering
- Patched _profile_registry in build_default_registries
- Patched _mcp_manager in main.py startup loop

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

Add self-extension tool system: write_tool, list_tools, tool_manual ...

- loader.py: module-level format (name/description/parameters/execute)
  preferred, class-based as fallback; isolated errors per file
- write_tool: validates + writes tools/name.py, reloads registry,
  adds to tools/enabled.json in one call
- list_tools: live tool list from registry (prevents hallucination)
- tool_manual: serves manuals/*.md or auto-generates from schema
- reload_tools: hot-reload without server restart
- registry: registry injection pattern for tools that need it;
  _builtin_names set to guard against reload overwriting builtins

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