planning: replace the mandatory pre-turn gate with an agent-invoked plan tool ...

- Phase 2 (critique) retired; observe/MODE and the top-level DIRECT shortcut
  removed (sub-agents keep DIRECT for trivial subtasks)
- replan merged into plan: `reason` (+ updated_goal) packs the re-plan
  context, without a reason it is fresh planning
- both phases call the LLM with think=False — cloud reasoning models leak
  their chain-of-thought into structured output on non-streaming calls —
  and strip the gemma "thought<channel|>" content artifact
- Phase 1 conversation windowed to ~20k chars, newest-first with the
  original task pinned (28.7k-token prompts came back as 1-token output)
- confirmation by COMPLEXITY: the tool result tells the agent to present
  complex plans and wait; sub-agents keep the execute-now injection
- PlanningStatus/PlanReady reach the UI mid-turn via current_event_sink
  (ctx.event_sink is None in the agent loop — events silently never
  reached the WS before)
- agent gate, casual-message detector and adaptive re-plan nudges removed;
  anti_stall keeps only stall detection

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.

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>

Navi Code: stop via Esc + project cwd propagation ...

- TUI: Esc stops active stream cooperatively via POST /sessions/{id}/stop
- TUI: render stream_stopped as status message
- CLI/WebSocket: send shell cwd in client->server message field
- Orchestrator stores cwd in session.session_metadata
- ContextBuilder injects [Working directory] into LLM context
- Agent sets current_working_directory ContextVar per turn
- tools/base: ToolContext gains cwd field
- filesystem/terminal/code_exec resolve relative paths against session cwd
- Add bin/navi-code wrapper for PATH symlink; document in README.md
- Update docs/websocket.md and tests

Full pytest: 544 passed, 1 skipped.

Co-Authored-By: Claude <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: 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>