subagents, secrets: an honest result contract, and two leaks closed ...

A pass over the sub-agent system, plus the two findings from the previous one.

Leaks:

- `redact_args` / `is_sensitive_key` (navi/tools/_internal/redact.py) mask
  credential-shaped keys at every log site that prints tool arguments — by key
  name, for all tools, so a future MCP tool is covered without declaring
  anything. ssh_exec passwords were sitting in the prod journal in plaintext.
- `mcp_servers.d/*.json` are tracked in git and carried the scaffolding
  machine's absolute paths, so navi-3d/navi-web silently vanished from the
  toolset off that machine. They now hold project-relative paths, resolved in
  `McpClient.open_transport` — not at load time, because create_mcp_server
  round-trips every config file through save_mcp_servers.

Sub-agent result contract:

- `run_ephemeral` returns a `SubAgentOutcome` (text + status: ok, timeout,
  max_iterations, thinking_stall, user_stop, context_overflow) instead of
  `(text, bool)`. Every exit routes through `SubAgentRunner._finish`, so token
  accounting is never dropped and a partial run always carries a progress
  report — the stop-after-stream path used to return a bare string.
- `spawn_agent` renders its header from the status. Before this, every short
  run reached the parent as "hit iteration limit", and the parent repeats that
  diagnosis to the user — a timeout was reported as an iteration limit.
- `ContextTooLargeError` no longer kills a sub-agent: the parent compresses its
  own context, a sub-agent has no session to compress into, so it stops with
  `context_overflow` and hands back what it did rather than surfacing as
  "Sub-agent failed: …" with the whole run discarded.
- The result is capped at 8000 chars (head and tail kept) so a long run cannot
  flood the parent's context, and tool arguments in the progress report go
  through `redact_args`.
- The navi-3d calling convention left the runner for the server's own tool
  schemas — a generic runner should not know one MCP server's path shapes.
- Validation moved inside spawn_agent's try: a bad argument is a clean
  ToolResult the model can read, not an exception in the parent's loop.

Tests: 1636 passed, 1 skipped. New: SubAgentOutcome paths and headers, result
truncation, context overflow, clean argument failures.

tools, mcp: a description is a hook, not a manual ...

With 24 tools in a profile the schemas are the largest fixed block of every
request, and they are paid for whether or not the tool is called. Eleven of
them carried a manual's worth of prose in their `description` — examples,
error tables, "common mistakes", the mechanics of the file areas. Reading
them against the manuals first, the manuals already held all of it, and
richer: this was duplication sitting in the one place the model cannot avoid
reading, not knowledge that had nowhere else to live. So the descriptions
became selection hooks — what the tool is for, when to pick it over its
neighbour, and the one rule that cannot wait — and the detail moved to
tool_manual("<tool>"), which costs nothing until the tool is actually in
play.

filesystem, spawn_agent, schedule_recall, manage_recall, scratchpad, plan,
share_file, content_publish, reflect, todo and peer. Descriptions drop from
18.4 KB to 11.5 KB, those tools' schemas from 25.5 KB to 16.8 KB, and a
profile's whole native toolset from 38.3 KB to 29.6 KB (server_admin,
developer; secretary 33.7 → 25.0, navi_code 32.9 → 25.9, tool_developer
37.9 → 29.2, modeler_3d 33.4 → 24.8). Stated as a budget rather than a byte
count: roughly 4k tokens of the model's window per request, back.

Two things were deliberately not shortened. The filesystem edit ladder
(`edit` → `edit_lines` → `smart_edit`, last resort, costs an LLM call) and
todo's mandatory `validation` on `done` both exist to prevent an extra
round trip; a shorter description there would trade tokens for turns. What
todo lost is the prose around the rule, not the rule. `enabled.json` was
left alone too: weather, gmail and get_current_datetime are opt-in and the
DB shows 12, 16 and 40 calls, so they are opt-in tools that are actually
used.

peer had no manual at all, which is how this surfaced: its description was
the only documentation the tool had. manuals/peer.md is now written from
the tool and its /peer route — the ask/status/list actions, the fact that
the hive is only a phone book and the question travels peer-to-peer, the
one-concurrent-answer semaphore, the two independent recursion guards, and
the six error codes.

The MCP server instructions leave the system prompt the same way. They were
8 KB of always-present prose per request, most of it workflow detail the
model only needs when it is about to use that server. Each server now
contributes one line — a new optional `summary` field in mcp_servers.d/*.json,
defaulting to the first sentence of its `instructions` — and
tool_manual("<server>") returns the full text plus the tool names the server
declares. server_admin's MCP block goes from 8.3 KB to 1.3 KB, secretary's
from 8.1 to 1.2. tool_manual learned to answer for a server (a tool name
still wins over a server of the same name, and dash/underscore spelling is
tolerated), and the index names the servers alongside the tools.

One judgement call worth recording: gnexus-book's and navi-web's
instructions end in an absolute "NEVER bypass these tools with filesystem,
terminal or code_exec" rule. Moving that on demand would have been a
behavioural regression dressed as a token saving, so those two `summary`
fields carry the prohibition verbatim alongside the hook, and it stays
always visible.

docs/tools.md gains a section on the split (a description is paid for every
request, a manual only when the tool is used), which is where the next
person will look before trimming a description back into a manual.

Full suite green (1577 passed, 1 skipped). No frontend change and no new
dependency, so the deploy is a pull and a restart.

mcp keys W1: user_key config slot, encrypted keystore, /mcp-keys REST

Add MCP streamable_http transport, integrate gnexus-creds, and document headless nodes ...

- navi/mcp/client.py: add streamable_http transport via httpx + mcp.client.streamable_http
- navi/mcp/config.py: add "streamable_http" to transport literal and is_streamable_http property
- mcp_servers.d/gnexus-creds.json: new MCP server config with overlay instructions for secret workflow
- docs/future_headless_nodes.md: architecture exploration for headless Navi node swarm

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

refactor: migrate MCP config to directory-based mcp_servers.d ...

Replaces monolithic mcp_servers.json with per-server files in
mcp_servers.d/<name>.json. Filename stem becomes the server name.

- load_mcp_servers() reads directory globs, auto-migrates legacy file
- save_mcp_servers() writes per-server files, cleans up stale ones
- Update docstrings in manager.py and context_builder.py

Auto-migration: existing servers (gnexus-book, navi-3d, navi-web) plus
new ones (project_health, time_toolkit) now live in mcp_servers.d/.

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

Add MCP admin endpoints for config, reconnect, status, test, and profile group management ...

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

Inject MCP server instructions into system prompt ...

- McpClient: collect instructions from MCP initialize handshake
- McpServerConfig: add 'instructions' field for Navi-side overlay
- McpManager.get_instructions(): merge server + config instructions
- ContextBuilder: new _mcp_context_msg() injects MCP server
  descriptions into every LLM context as a system message
- Agent passes mcp_manager to ContextBuilder
- mcp_servers.json: add overlay instructions for gnexus-book

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

Refactor MCP integration: server groups in profiles ...

- mcp_servers.json: add 'groups' (read/write/admin) for gnexus-book
- AgentProfile: new 'mcp_servers' field (server_name -> group list)
- Profile loader: parse and persist 'mcp_servers' in config.json
- Agent._tool_list(): expands mcp_servers into concrete tool names
  via McpManager.resolve_group(), wildcard '*' supported
- /agents/profiles API: includes 'mcp_servers' in response
- Profiles no longer list individual mcp_ tools in 'enabled_tools'
- discuss: gnexus-book read group
- server_admin: gnexus-book read+write+admin groups

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

Add MCP server support and fix memory tools user isolation ...

MCP integration:
- New navi/mcp/ package: client, manager, config, tools
- ToolRegistry learns register_external() for MCP tools
- reload_tools reconnects MCP servers on hot reload
- New built-in mcp_status tool
- Startup/shutdown wiring for MCP connections
- 12 new tests (unit + integration with real stdio server)

Memory tools fix:
- memory, memory_save, memory_search, memory_forget now read
  current_user_id from tool context and pass it to MemoryStore
- Fixes invisible facts for authenticated users

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