tui: show the changed step's text in the todo update call card ...

The todo update call card (→ todo · #3 → done) now shows the text of the
step being changed, plus the validation when present. The LLM's update args
carry only the index, not the task text, so the text is read from the
current plan row before the tool runs and attached to ToolStarted.metadata
(client-rendering only, backward-compatible).

Backend:
- events.ToolStarted gains a metadata dict (mirrors ToolEvent) → to_wire.
- navi/tools/todo: step_text_for_update(index, ctx) resolves the step text
  via _sid/_uid (so sub-agent isolation holds), started_metadata_for_call
  wraps it for both emit sites.
- agent.py (parent) and subagent_runner.py (sub-agent) enrich ToolStarted
  via the shared helper before emitting.

Renderer:
- TodoStartedRenderer update card reads msg.metadata.step_text → shows the
  step text + validation; falls back to 'no validation' on history replay.
- Removed the step-text line from the result card (it now lives in the call
  card) — result card is back to the compact 'plan · X/N done' summary.

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

Isolate sub-agent todo + render live todo in TUI side panel ...

Phase 1 — sub-agent todo isolation (backend):
- Add current_todo_session_id ContextVar; subagent_runner scopes it to the
  sub-agent's ephemeral run id so its auto-populated plan and todo updates
  land in an isolated KV row instead of clobbering the parent session's todo
  (which the parent's goal-anchoring reads every iteration).
- todo._sid() and planning.set_tasks prefer current_todo_session_id; the
  parent run leaves it unset, so all existing todo consumers (anti-stall,
  goal anchor, get_progress_message) behave exactly as before.

Phase 2 — live todo in the TUI right column:
- TodoUpdated event + emit it from the agent loop after planning auto-populate
  and after each tool-execution turn.
- GET /sessions/{id}/todos reads the parent session's todo KV row (explicit
  user_id/session_id, optional injected kv).
- api.get_todos + TodoList/TodoPanel widgets: status-coloured markers
  (pending dim, in_progress accent+bold, done success, failed error, skipped
  dim), progress header, scrollable panel below the auto-height info block.
- Hybrid delivery: REST seeds the panel on attach/switch, todo_updated WS
  events update it live.

Sub-agent todos as nested sub-lists is deferred to a later phase.

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

compressor: structured summaries, profile-aware compression, adaptive keep_recent ...

- Replace free-form summary with strict Markdown template (Goal, Active Files,
  Decisions, Completed Work, Pending Work/Todo, Errors, Key Values).
- Keep filesystem/code_exec/terminal tool results and messages with
  is_compression_critical=True verbatim during compression instead of 300-char truncation.
- Make compression profile-aware: AgentProfile gains compression_keep_recent,
  compression_max_tokens, compression_prompt_file. navi_code uses dedicated
  compression prompt and larger keep_recent/max_tokens.
- Adaptive partition_messages(): important turns (user corrections, errors,
  critical tools) survive longer; filler/social turns compress sooner.
- Increase default context_summary_max_tokens from 3000 to 4000.
- Propagate active profile changes to ContextCompressor and SubAgentRunner.

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

Add subagent progress report on failure ...

When a subagent stops (timeout, max iterations, thinking stall, user stop),
it now returns a structured progress report built from its local message
context, so the parent agent knows what tools were called and what was
accomplished before the stop.

- Add _build_progress_report() to SubAgentRunner
- Report includes: turn number, assistant text, tool calls with results
- Prepended to result_text for every stop reason (completed also gets it)
- Updated test_run_ephemeral_complete to expect the report prefix

Co-Authored-By: Claude Opus 4.7 <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>

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>

Fix stop button responsiveness and shutdown CancelledError ...

Agent loop (_execute_tools_with_sink):
- Poll stop_event every 1s while draining the event sink via asyncio.wait_for
- When stopped, cancel the tool task, yield a synthetic ToolEvent failure,
  append a cancellation message to session, yield StreamStopped, and return
- Pass stop_event into _execute_tools_with_sink call site

Subagent runner:
- Check stop_event at the start of each tool in turn_tool_calls loop
- Returns early with ("", False) when stopped mid-batch

McpManager.disconnect_all():
- Disconnect clients sequentially instead of asyncio.gather
- Handle asyncio.CancelledError per-client to avoid shutdown traceback

AppContainer.shutdown():
- Catch BaseException instead of Exception for MCP and DB cleanup

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

Fix token counting: show only completion tokens, not cumulative prompt+completion ...

The token_count displayed next to assistant messages was summing
prompt_tokens + completion_tokens across ALL tool-calling iterations,
giving hundreds of thousands of tokens for multi-turn conversations.

Now:
- token_count (coins icon) = only completion tokens generated by the model
- context_tokens (ContextBar) = only prompt tokens (context size sent to LLM)

This gives users a realistic measure of how much the model actually generated.

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>

SubAgentRunner: filter mcp_servers against subagent_tools whitelist ...

When a profile defines subagent_tools (strict whitelist for sub-agents),
MCP servers were still expanded unconditionally, granting sub-agents access
to MCP tools not listed in the whitelist.  Now:

- If subagent_tools contains mcp:xxx entries, only those specific MCP tools
  are passed to build_tool_list.
- If subagent_tools is non-empty but contains no mcp: entries, mcp_servers
  is set to None — sub-agents get no MCP tools at all.
- If subagent_tools is empty (fallback to enabled_tools), full mcp_servers
  is kept for backward compatibility.

400 passed, 1 skipped

McpTool: auto-inject session_id + normalize navi-3d paths ...

- McpTool.execute() now forces the real session_id from current_session_id
  ContextVar, preventing LLM hallucinations of wrong UUIDs (ghost-session bug).
- For navi-3d MCP server, source_path/output_path are normalized to basename
  to prevent double path nesting when the LLM passes full relative paths.
- Updated MCP tool descriptions to ask for filenames only.
- Added system prompt instructions in context_builder and subagent_runner
  reminding the model to pass bare filenames to navi-3d tools.

396 passed, 1 skipped

Step 4: Extract SubAgentRunner from run_ephemeral() ...

- Create navi/core/subagent_runner.py with full sub-agent loop logic
- Move _iter_stream_guarded to navi/core/stream_guard.py
- Move _check_context_size to ContextCompressor.check_context_size()
- Extract build_tool_list() and load_user_enabled_tools() to tool_utils.py
- Agent.run_ephemeral() becomes a thin wrapper delegating to SubAgentRunner
- Remove ~310 lines from agent.py
- All existing run_ephemeral tests pass unchanged

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