config: give server_admin and secretary the synapse MCP tools ...

The synapse server was connecting and registering all 35 of its tools, but
no profile listed it under tools.*.mcp, so build_tool_list never handed a
single one to an agent — the hub was up and unreachable at the same time.

server_admin takes read + write (32 tools: events, deliveries, rules,
sources, targets, routing); secretary takes read only (15). The admin group
— key_issue, key_revoke, settings_put — is deliberately left out of both:
issuing and revoking hub keys stays a manual operation.

config: run every profile on glm-5.3-flash:cloud first ...

Four chains still led with gemma4:31b-cloud, so those sessions were resolved
onto gemma4 even though glm-5.3-flash:cloud is the instance default. glm now
leads every profile.

The rest of each chain stays behind it as a fallback — that is what carried
today's 16:57 run through a ReadTimeout against ollama.com instead of failing
it. developer, navi_code, discuss and modeler_3d already led with glm and are
untouched.

config: capture the live server configuration ...

Profiles gain the gntodo / gnexus-book / gnexus-creds scopes for agent and
subagent runs, refreshed model lists, and write access where the live setup
has it. MCP server configs pick up their user_key slots, gnexus-book learns
delete_pending_change, and the hard-panel / synapse / tgclient servers join
the tree.

Merge remote-tracking branch 'origin/master' ...

# Conflicts:
#	webclient/vendor/gnexus-ui-kit/package-lock.json

synapse reactions W3: reaction runner, notify tool, gateway hookup ...

- navi/synapse/reactions.py: fire-and-forget reaction run — per-user
  reactions_enabled gate, one-shot dispatcher meta-pass (visible profiles
  only, hidden dispatcher, secretary fallback), special=True session
  headed by the resolved profile, headless agent run via the orchestrator
  run registry, finalise: app push per completion_notify +
  low-level reaction.finished/failed event to Synapse
- navi/synapse/outbound.py: source-side emit (syn_* key from env,
  silent when not configured)
- navi/tools/notify.py: notify tool — message + level (info/warning/
  intervention), both legs per push_target, honest delivered/skipped result
- push/service.py: notify_custom without cooldown
- gateway: verified + non-duplicate delivery schedules the reaction
- profiles: notify added to native tools (7 profiles)

synapse reactions W2: hidden dispatcher profile + synapse_instructions tool

Merge remote-tracking branch 'origin/master'

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

Merge branch 'master' of https://git.gnexus.space/git/root/navi-1

.

swarm stage 2: peer-to-peer channel — /peer endpoints + peer tool ...

Server side (navi/api/routes/peer.py, port 8099):
- GET /peer/hello — open discovery ping (name, uuid prefix, version)
- GET /peer/status — PSK; identity, uptime, machine facts, hive view
- POST /peer/ask — PSK; one-shot agent run under PEER_ASK_PROFILE
  (default server_admin) answers, one concurrent ask at a time
- loop guard: answering agent runs without the peer tool (deterministic
  recursion cut) + own-uuid asks refused with 409
- verify_swarm_key in navi/swarm.py accepts .swarm-key.previous
  (rotation window, constant-time)

Client side (navi/tools/peer.py):
- peer tool: list (hive book, stale cache fallback marked), status,
  ask by swarm name; asks go direct peer-to-peer, hive never on the
  message path
- audit events on both sides (peer.ask_sent/received/answered/failed)

peer tool added to server_admin, navi_code, developer profiles.

.

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

Merge branch 'master' into feature/navi-code ...

# Conflicts:
#	navi/api/websocket.py
#	navi/config.py
#	navi/core/agent.py
#	navi/core/orchestrator.py
#	navi/main.py

navi_code: add gemma4 31b/26b qat models to the profile fallback chain

navi_code: add web lookup, ssh, and image_view — grow beyond local-only ...

navi_code was strictly local: no web, no remote hosts, no image viewing. That
made it lean on the developer profile whenever a coding task needed a doc
lookup or a remote command. Bring those capabilities in so navi_code covers
full coding work itself, while staying terminal-first and local-by-default.

config: agent gains image_view, ssh_exec, and the navi-web MCP (search/browse/
request); subagent gains image_view + navi-web (no ssh_exec — sub-agents don't
reach remote hosts, matching developer). Description/short_description/
full_description updated to "terminal-first with web and remote access". Also
includes the gemma4:12b-it-qat-128k model in the model list (local 128k-context
option alongside 31b-cloud).

prompt: soften "Local-only, no remote hosts" to "local by default, with web
lookup (docs/APIs) and ssh (remote ops) when the task needs it". Add compact
Web lookup and Remote access sections under Execution environment, and update
the sub-agent toolset briefing to list image_view + web and to exclude ssh_exec.
scope_boundary still applies; ssh destructive/system-wide actions need user
confirmation. Kept additions minimal to avoid bloating the prompt for the 12b
model.

navi_code: stop delegating code work to the developer profile ...

navi_code was systematically spawning sub-agents as `developer` instead of
itself, even though it already covers local code work. Root cause was a
three-channel nudge: the navi_code prompt recommended `developer` for "general
code work" and framed omit (-> navi_code) as the exception; spawn_agent's
description listed `developer` as the coding example and never mentioned
navi_code; the injected Available-profiles list shows developer's broad
"General-purpose software development" blurb. The planner locks profile_id at
plan time on those same signals, so the bias is baked in before execution.

Flip the default in all three places: for code work OMIT profile_id so the
sub-agent runs as the current profile (navi_code); set profile_id only for a
different specialisation (secretary/server_admin/tool_developer). developer is
not removed as a profile — it is just no longer recommended from navi_code.

compress: raise budget 6000 + richer prompt detail + input headroom ...

Increase the compression summary budget and push the prompt toward more
detail and completeness, so the agent keeps more durable facts when old turns
are folded into a summary.

Budget (output):
- context_summary_max_tokens 4000 → 6000 (global default).
- navi_code compression_max_tokens 4000 → 6000 (profile override).

Prompt (base, all profiles):
- New 'Intermediate Findings' section: durable facts from read/grep/log/terminal
  that informed decisions (was forbidden by 'do not preserve intermediate
  reasoning'). Existing sections get richer instructions (Active Files: key
  symbol affected; Decisions: rationale + trigger; Completed: step + file +
  verification outcome; Errors: snippet + what was tried + outcome).
- Loosen 'tight bullet points' → 'specific and complete; prefer listing over
  generalizing — losing a fact costs more than a longer summary'.
- 'Do not write implementation code' → 'preserve short critical code verbatim
  (final signatures, one-line fixes, key config lines); drop long blocks'.

Input headroom (so the summarizer can SEE what it must preserve):
- Non-critical tool result preview 300 → 800 chars.
- _MAX_SUMMARY_INPUT_CHARS 24000 → 32000 (fits 65k–128k windows with 6k output).

Profile prompt (navi_code/compression_prompt.txt): preserve short diagnostic
snippets verbatim (exact error line, failing assertion, one-line fix) instead
of blanket 'do not preserve long output'; keep code signatures + short key
snippets, not just names.

Tests: Intermediate Findings section in base prompt; 'short critical code'
phrasing; non-critical preview keeps 800 chars; meta-summary threshold raised
(2×6000 chars). Fixed flaky test_attach_session_seeds_context_fill (relied on
_startup worker timing after Etap 4 lengthened attach; now explicit attach
like its sibling + mock get_todos to skip a 30s×2 real-network timeout).
Full suite: 1008 passed, 1 skipped.

todo: add op — append steps discovered mid-task (preserve statuses) ...

The todo tool only had set/view/update/clear. Adding a step that surfaced
mid-task meant either 'set' (which replaces the plan and resets every status
to pending) or 'replan' (1–3 LLM calls) — both heavy for a single new step, so
the agent usually skipped recording it. Add a cheap 'add' op:

- navi/tools/todo.py: op 'add' (tasks: list[str]) appends new _Task entries to
  the end of the existing plan in pending status; existing steps and their
  statuses are untouched. Requires an existing plan (points to 'set'
  otherwise). Schema enum + op description + tool description updated.
- system_prompt.txt: tell the agent to record new subtasks with 'todo add'
  right away (not held in head, not a replan); clarify the 'small todo edit'
  line — add via 'todo add', drop/merge/reorder via 'set' (re-apply statuses).
- renderers/todo.py: TodoStartedRenderer renders the add card
  ('→ todo · add (N)') listing the new pending steps, not a JSON dump.

Tests: add appends + preserves statuses / requires existing plan / requires
tasks; renderer add card + empty-tasks. Full suite: 1005 passed, 1 skipped.

Автономность мелких моделей: OUTPUT DISCIPLINE, milestone-todo, перехват финала хода ...

Два последовательных захода над одной проблемой — мелкие модели (12–30B) в navi_code
теряют автономность на трудных шагах: «остановился поболтать» вместо действия и
слишком большое расстояние между пунктами плана.

Заход 1 (З1–З3):
- З1: OUTPUT DISCIPLINE в системном промпте navi_code — «act, don't announce»,
  без few-shot антипримеров. Контракт хода: ответ без tool_calls = конец хода, поэтому
  объявление намерения текстом убивает автономность; правила заставляют вызывать
  инструмент в том же ходе.
- З2: плоский todo + метка группы milestone + декомпозиция. _parse_plan_steps
  возвращает list[tuple[milestone, text]]; milestone — метка группировки (не сущность,
  без статуса), «done» вычисляется при рендеринге; подшаги = больше плоских шагов
  (без вложенности). TUI side-panel группирует по milestone (плоский фолбэк при пустом
  milestone). Plan depth: max 15→20 + правило декомпозиции.
- З3: adaptive re-plan «длинный шаг» — nudge «разбей шаг» при in_progress ≥ порога
  итераций без смены todo (порог 4, раньше общего anti-stall warning на 8).

Заход 2 (шаги 1–3, после cloud-теста 31b vs 12b):
Корневая структурная причина: весь спасательный механизм (anti-stall warning с явным
предложением reflect, adaptive re-plan) живёт только внутри tool-цикла — nudge
инжектируется в pre_turn *следующей* итерации, которой при «остановился поболтать»
нет (ход закрылся по return до post_turn). 31b застревала через «продолжаю
tool-итерации» → дожала до warning → спаслась; 12b — через «замолчала текстом» → мимо
всех nudge.

- Шаг 1: перехват финала хода. Если модель выдала bare-text, но в todo есть открытые
  шаги (pending/in_progress) и лимит не исчерпан — НЕ эмитить StreamEnd, а сохранить
  ассистентский текст в session.context, поставить системный nudge и continue
  (без StreamEnd, без workers — консистентно с multi-iteration tool-турами). Счётчик
  final_interceptions на AgentTurnContext, лимит final_intercept_limit (default 2),
  эскалация жёсткости (мягкий → «second stop»). has_open_steps в todo.py: пустой
  todo → False (защита casual-сообщений), failed/skipped терминальны. Профильные
  флаги final_intercept_enabled/limit в base.py + loader + admin.
- Шаг 2: жёсткий reflect-триггер в промпте — «~3 tool attempts on the same step
  without progress → call reflect IN THIS TURN (tool call, not reasoning aloud)».
- Шаг 3: открыть replan для застревания — «call replan when reflect showed the whole
  approach is dead (not one failed step, but the approach itself)».

Тесты: 874 passed, 1 skipped. Новые — has_open_steps (5), final intercept (5),
milestone-группировка, adaptive long-step nudge, парсер шагов с milestone-маркером.

cloud: navi_code model → gemma4:31b-cloud для тестирования догадки (31b признала
застревание, 12b — нет); .env cloud-host уже gitignored.

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

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>

navi_code: prefer isolated project envs and bootstrap NAVI.md when absent ...

Add a "Project environments" section steering the agent toward the
project's existing isolated env (venv/uv/node_modules/target) — use it,
don't duplicate or bypass it — and only create a project-local one when
deps are needed and none exists; never install system-wide (system-wide
changes still require explicit confirmation). Also nudge the agent to
create NAVI.md when it's absent after real orientation work on a
non-trivial task, seeding the pointer structure so the next session
starts oriented.

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

navi_code: enable planning phase 2 (structured review) ...

phase1 already emits REFLECT: yes|no, but with phase2 off the flag was a
dead-end. Enabling phase2 runs a Critic/Pragmatist/Detailer review pass
before phase3 whenever phase1 flags the task as complex (REFLECT: yes),
feeding "Plan Adjustments" into the execution plan. Skipped for simple
tasks and subagents (gated on `needs_reflect and not is_subagent`), so
the extra LLM call only lands on complex parent-agent work.

Resolves F8 machinery-gap G.

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

navi_code: frame planning machinery in system prompt (F8) ...

Workflow "Plan" no longer duplicates the planner (phase1/3 already build a
structured plan and auto-populate todo); adds an observe/act carve-out so
observe requests don't get pushed to create a todo. New "System signals
you'll see" subsection names the runtime-injected messages ([Goal anchor],
[Scope boundary], [Anti-stall warning], [Iteration N/M]) so the model
recognises them as machinery and responds correctly — and corrects the
factual error that the goal anchor reads scratchpad `goal` (it reads the
original request + live todo). Closing paragraph warns that thinking isn't
re-injected and the plan's per-step executor assignments are lost to
compression, so conclusions/assignments should go in scratchpad.

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

navi_code: give the sub-agent operational wisdom (editing/reading/todo) ...

By default (inherit_system_prompt=False) the sub-agent got only the 17-line
subagent_system_prompt — none of the parent's editing/reading/context
discipline. So a sub-agent with a clean context would still burn it: pulling
whole files into read, over-using smart_edit, not tracking steps. The clean
context is the sub-agent's main advantage — keep it clean.

Expand subagent_system_prompt.txt with a compact operational core:
- Editing: prefer edit/edit_lines (deterministic); smart_edit as last resort
  (extra LLM call, reads the whole file) — the same policy the parent now has.
- Reading: info before read, offset/limit to the region, grep/find/query to
  locate — don't read a file just to search it.
- Track steps with todo and record findings in scratchpad (durable within the
  run; context can be compressed).

inherit_system_prompt stays False: the full parent prompt carries orchestration
and spawn_agent sections that are irrelevant to a sub-agent and references
tools it lacks. The sub-agent keeps its own focused, self-contained prompt.

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

navi_code: brief sub-agent on its restricted toolset + context_transfer ...

The sub-agent briefing section told the model to "give the sub-agent
everything it needs" but never said which tools the sub-agent lacks or how
context actually reaches it — so briefings could ask the sub-agent to use
memory, spawn further agents, or switch profiles, all of which it can't.

- context_transfer: write the context the sub-agent needs (files, snippets,
  how to verify) into the scratchpad `context_transfer` section before
  spawning — it is injected automatically; the sub-agent does not inherit
  short-term memory or conversation history.
- Restricted toolset: the sub-agent has todo/scratchpad/reflect/filesystem/
  code_exec/terminal/list_tools but NOT memory/switch_profile/spawn_agent/
  schedule_recall/manage_recall — brief it to use only what it has (e.g.
  record findings in scratchpad, not memory).

The profile list is not duplicated — spawn_agent's own description carries it.

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

navi_code: leverage context-org/planning tools in system prompt ...

Wire the KV-backed context/planning tools into the profile so the agent
uses them instead of relying on lossy conversation memory under compression.

- Workflow Plan: create a todo for non-trivial tasks.
- Workflow Test & verify: record the verification in the todo `validation`
  field when marking done (structural form of "never claim done without
  verification").
- Replace "Context drift recovery" with "Working state & memory":
  - todo: plan + verification tracking.
  - scratchpad: durable working memory across compression (sections
    goal/findings/errors/artifacts); read before final report.
  - Sub-agent handoff: write context to the scratchpad `context_transfer`
    section before spawn_agent — it is injected into the sub-agent
    automatically (the sub-agent does not inherit short-term memory).
  - schedule_recall: continue after the iteration limit, offload heavy
    work headlessly, poll builds/logs, chain multi-phase work.
  - reflect: selectively, before complex plans or when stuck (3 LLM calls).
  - memory: global cross-project facts, not a scratchpad/docs substitute.
  - Drift recovery folded into a closing paragraph aligned with the
    goal_anchoring machinery.

TUI visualization for schedule_recall is a follow-up task.

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