deploy: MCP servers' own venvs are synced by the deploy, not by memory ...

Each server under mcp-servers/ runs from its own .venv — the interpreter its
config in mcp_servers.d/*.json names — and Navi's venv does not carry those
dependencies. When a server's pyproject.toml gained one (trafilatura, Nov
2026) and the host was only pulled and restarted, the server died at import:
the manager could not connect, its tools silently left every profile's tool
list, and nothing reached the chat. SearXNG was healthy the whole time.

sync-mcp-venvs.sh installs every mcp-servers/*/pyproject.toml into its own
venv, stamped by a sha256 of the pyproject so an unchanged server is skipped
and a re-run is cheap. install.sh calls it as a numbered step; UPDATE.md
runs it unconditionally after a pull and verifies the MCP connection in the
journal; docs/mcp.md no longer reads as "install it yourself by hand".

navi-web: search backends, three-at-a-time batches, and pages read as markdown ...

web_search runs SearXNG first, DuckDuckGo with one retry after a real failure,
and Brave last; measured 0.2-1.4s through SearXNG against 1.7-11.8s on
scraping. Both tools take one item or up to three and run them concurrently —
three pages went from 17.3s to 1.9s, three searches from 3.5s to 0.6s — each
under its own deadline, so one hung backend or page is named in the output
instead of erasing what the others already returned. Text is capped at 20k for
one page and 40k for a batch. A call that opened nothing now raises: a green
journal line carrying "success": false is how a server whose browser could not
launch at all looked like a working one, and how 604 search calls in two weeks
reported no errors.

web_view returns the main content as markdown, not innerText after a tag
kill-list. The old path could not tell navigation from prose (462 of the asyncio
page's 1018 lines were shorter than 40 characters), collapsed tables into one
line per thousand characters — news.ycombinator.com came back as four lines —
marked no headings and dropped every link. trafilatura now picks the content by
density, and its html output keeps the whitespace inside <pre> that its markdown
output throws away, so the fragment is rendered here: # headings, fenced code
with its indentation, table rows joined by |, and up to 40 links lifted into a
"Links on this page" appendix rather than sprinkled through the sentences.
Threads are read again with comments when the extractor keeps less than a
quarter of the visible text; if it still finds nothing, the old visible-text
read answers and metadata.extractor says which one did.

trafilatura goes into the server's own venv, which deploy/install.sh does not
build — docs/mcp.md and deploy/UPDATE.md carry the install line. The tests load
the server by path, so it also joins Navi's dev extra.

mcp: credentials leave the tree, and sub-agents lose the task board ...

Five tracked configs (gnexus-creds, gntodo, hard-panel, synapse, tgclient)
carried live bearer tokens — in git, in every clone, and handed to the admin
client by GET /admin/mcp/config. They now name a variable, and the value lives
in the service .env (chmod 600, untracked).

Substitution happens once, at transport open, next to the project-relative
path resolution: that is the single place a transport is built, so every
stored and serialised config stays placeholder-only and save_mcp_servers —
reached by create_mcp_server and PUT /admin/mcp/config — cannot write a secret
back into a tracked file. A variable that is not set refuses the connection
instead of dropping the header, which would fail open: a server may answer an
unauthenticated request as an anonymous user rather than returning 401.

Sub-agents also drop gntodo, gnexus-creds, tgclient and synapse from their
scopes, and the runner injects a scope anchor unconditionally — a sub-agent
asked to echo one word had picked a project off the task board and researched
it for forty iterations.

Docs: docs/mcp.md#secrets, a migration recipe in deploy/UPDATE.md, the variable
names in .env.example and deploy/env.template, and a regression guard over the
tracked configs.

The old values stay in git history; rotating all five at their sources is the
remediation, not a follow-up.

deploy: runbook for updating a running instance ...

Adds deploy/UPDATE.md: preflight, the branch shapes (master vs the
tracked .env on deploy), what to rebuild before pushing (the frontend
dist is committed and the server never builds it), the verification
commands that prove the new bundle is the one being served, rollback,
and the traps — tracked secrets in mcp_servers.d/, gitignored vendor
kit dist, service-worker cache, Android app needing only a restart.

Linked from deploy/README.md.