tool_manual: a manual the agent cannot reach is not a manual ...

tool_manual asked the filesystem for the exact string the model sent, then
fell back to registry.get(). The executor already tolerated the ways models
mangle MCP names; the tool that documents them did not, so the agent calling
mcp__navi-3d__compile_scad got a schema dump while manuals/compile_scad.md sat
there unread. Resolving a name now happens in one place — resolve_tool moved
out of the executor into navi/core/tool_utils.py — so a name that works when
the tool is *called* also works when it is *asked about*. A miss suggests the
closest names instead of "not found", and a tool that exists but is not enabled
for this profile says exactly that: documenting it is still the useful answer,
but the agent must not go on to call it. params["tool_name"] was also a crash
waiting to happen — KeyError with the key omitted, AttributeError on null or a
number — and now anything that is not a usable string means "no name given",
which returns the index of manuals grouped by source.

The generated manual now renders the whole schema. An array of objects showed
as "(array, optional)" with its item shape invisible, so a model that could not
see the fields guessed them; objects, array items, oneOf/anyOf branches, enums
and defaults are all spelled out now, depth-capped. The header names the source
(native / mcp__<server>__) and says the text is a parameter contract, not a
curated manual — otherwise a thin schema reads as "this tool is simple".

Then the manuals themselves. A manual is filed under the tool's own name, and
five of the sixteen were not: write_tool.md and write_mcp_server.md documented
tools that do not exist anywhere (the tools are reload_tools and
create_mcp_server), model_3d.md documented compile_scad, render_3d.md documented
render_stl, and write_context_provider.md documented no tool at all — it is a
guide, and now lives in manuals/guides/. The prompts pointed at the same wrong
names (tool_developer's system prompt, persona_navi_code, docs/context_providers),
so fixing the files without the callers would have moved the breakage rather
than removed it. On HEAD the probe was blunt: tool_manual("mcp__navi-3d__compile_scad")
returned None and the agent got the schema; now it returns the manual.

Nothing was enforcing any of this, which is how it drifted. tests/unit/tools/
test_manual_drift.py reads the real repository tree: every manuals/*.md must be
named after a tool that exists (built-ins and tools/*.py by their name
assignments, MCP tools by @mcp.tool(name=…) in the server sources and by the
mcp_servers.d groups, whose file name is the server name), every manual must be
reachable by both its bare name and its full MCP spelling, a guide must never
shadow a tool's name, and every manuals/<x>.md or tool_manual("x") cited in a
doc or a prompt must resolve. The next rename fails the suite instead of
quietly wasting a manual.

Finally, manuals for the built-ins the agent uses most — ssh_exec, todo, memory,
plan, filesystem, notify, code_exec — written from the current schemas and the
code paths that produce the errors, so the gotchas are the real ones (todo's
`done` validation is enforced; memory's `list` returns categories, not facts;
filesystem's `delete` removes a tree with no prompt). reload_tools.md absorbs
the file format from the deleted write_tool.md, which is where a self-extension
recipe belongs now.

1556 passed, 1 skipped. ruff delta zero.

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>

refactor: rewrite tool_developer profile for MCP server development ...

Complete migration from old-style user tools (tools/*.py) to MCP servers.

Profile changes:
- Replace write_tool, delete_tool, test_tool with create_mcp_server,
  test_mcp_tool, mcp_status, reload_tools
- Update system_prompt.txt with 10-step MCP workflow
- Rewrite subagent_system_prompt.txt with canonical server format,
  absolute rules, smoke-test procedures
- Remove mcp_servers mapping from config (no longer bound to
  external servers)

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

Clarify knowledge persistence prompts

Allow subagents to use selected profiles

Clean up SQLite references in docs and prompts after removal ...

- docs/index.md: PostgreSQL via asyncpg
- docs/memory.md: drop aiosqlite fallback mention
- docs/sessions.md: replace SqliteSessionStore with PgSessionStore docs
- webclient/docs/architecture.md: PostgreSQL only
- navi/profiles/tool_developer/system_prompt.txt: remove aiosqlite from available imports
- .gitignore: add .codex and *.db
- No remaining sqlite/aiosqlite/db_path references in codebase

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

Remove tool-call-like examples from prompts

Improve prompt resilience and project context use

Fix profile prompt inconsistencies

Agent improvements: mandatory planning, tool cleanup, smart_edit fixes ...

- Planning now mandatory on first message of every session (force_plan)
- RESOURCES, COMMITMENTS, ATOMICITY fields added to planning phase 1
- Todo auto-injected at iteration 0 so model tracks steps immediately
- Execution trigger injected after plan to prevent model treating plan as response
- Split developer profile: tool_developer (Navi tools) vs developer (general code)
- Simplified persona.txt: trimmed redundant content now handled by mechanics
- AIHelper.ask(): 120s timeout via asyncio.wait_for to prevent smart_edit hangs
- filesystem._smart_edit(): atomic write via temp file + os.replace()
- Removed 5 junk user tools (game project artifacts, trivial utilities)
- Removed instagram tools (to be rewritten); cleaned enabled.json

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