fix(agent-server): remove the unreachable /api/credentials/update endpoint (#2008)

[dolho]

Summary

POST /api/credentials/update had no callers. I re-verified the issue's claim across src/, docker/, scripts/, config/, the .claude submodule and the populated src/backend/enterprise submodule: the only hits are the definition itself and the files.py comment pointing at it.

Meanwhile its docstring said "called by the Trinity backend", routers/files.py named it as the sanctioned alternative to raw .mcp.json editing — with both direct-edit blocks resting on that one sentence — and architecture.md listed it as a live endpoint. The documented escape hatch for configuring MCP servers did not exist.

It was also the one path that would substitute a credential value into command: a whole-text str.replace over .mcp.json.template, with no validate_mcp_config anywhere on it. That is the RCE-by-config class #590 closed — inert only because nothing called it, while the security comment above actively invited someone to call it.

Decision: delete

This is the branch the issue anticipated ("if that one is fixed by rendering at creation in the backend, this endpoint should be deleted rather than revived"), reached by a slightly different route: #2007 / PR #2013 puts the .mcp.json.template renderer where the files actually are — in the container at startup, env-only, validated per server, refusing rather than blanking. Reviving this endpoint would mean a second renderer with weaker rules on the same file.

Deleted: the route, and its now-unused CredentialUpdateRequest model — a dangling model is how a deleted route quietly comes back.

References corrected to name paths that exist

File	Was	Now
agent_server/routers/files.py	"the platform-internal /api/credentials/update flow"	the template (#2007) + the validated POST /api/agents/{name}/credentials/inject (#598)
docs/memory/architecture.md	listed as a live agent endpoint	removed
docs/testing/API_TEST_REQUIREMENTS.md	REQ-AS-CRED-001	removed
docs/diagrams/03-agent-container.md	POST /api/credentials/update	/api/credentials/inject
docs/diagrams/09-agent-lifecycle-states.md	claimed inject_assigned_credentials posts there	/api/credentials/inject — which is what credential_encryption.py:375 actually calls
docs/planning/TARGET_ARCHITECTURE.md:297	listed it under "keep"	repointed

Left alone deliberately: docs/archive/**, docs/security-reports/**, and the 2026-06 meta-analysis — point-in-time records that were true when written. TARGET_ARCHITECTURE.md:315 also mentions it, in a historical sentence explaining why #1089 added a different endpoint in June; rewriting that would be rewriting the record rather than fixing a pointer.

Acceptance criteria

AC	Status
Endpoint removed, or reachable and validated	removed
files.py:181-186 describes a path that exists	done
architecture.md:331 matches reality	done
If retained: validated, ${...} in command refused	n/a — not retained
A test that fails if ${VAR} can reach command through this path	expressed as: the path is gone (AST-checked, not substring), its model is gone, the whole-text replace renderer is gone, and no live doc sends anyone back to it

Test plan

• tests/unit/test_2008_dead_credentials_update.py — 7 tests; all 7 fail on dev and pass here (verified by stashing the change)
• Route absence checked by AST, not substring — the corrected files.py comment and the test file itself both still contain the string, so a grep-shaped assertion would be self-defeating
• 661 adjacent tests green (-k "credential or agent_server or reload_token or 1089 or files")

Merge order

⚠️ Merge after #2010 (issue #1999). That PR modifies update_credentials, which this PR deletes. If #2010 lands first, this branch needs a rebase whose conflict resolution is mechanically "keep the deletion" — the function is gone either way. Merging this first would silently drop #2010's sync_process_env wiring on that endpoint, so please keep the order.

Closes #2008

[github-actions]

⚠️ Nightly unit-suite check skipped — merge conflict against dev.

Resolve by running git merge dev locally and pushing the result. The next nightly run will re-test once the conflict is gone.