feat(mcp): add loopover_refresh_repo_focus_manifest tool

[bitfathers94]

feat(mcp): add loopover_refresh_repo_focus_manifest tool

Mirror POST /v1/repos/:owner/:repo/focus-manifest/refresh as an MCP tool, the
refresh counterpart to the read-only loopover_get_repo_focus_manifest. Forces a
live reload of the cached .loopover.yml manifest via loadRepoFocusManifest(...,
{ refresh: true }) + compileFocusManifestPolicy, returning the same
{ repoFullName, manifest, policy } shape the REST route returns.

Uses the write-access boundary (requireRepoManageAccess), matching the route's
requireRepoWriteAccess -- stricter than the read tool's read-only boundary --
and registers under the maintainer category, alongside loopover_refresh_repo_docs.

Closes #9299

Validation

Verified locally on this branch before opening:

• npm run typecheck
• npx turbo run build:tsc build:verify
• npm run test:coverage — patch coverage 100.0% of changed lines

[superagent-security]

Superagent didn't find any vulnerabilities or security issues in this PR.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 75.81%. Comparing base (aad3f93) to head (fe28b60).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #9348      +/-   ##
==========================================
+ Coverage   75.38%   75.81%   +0.43%     
==========================================
  Files         275      276       +1     
  Lines       58023    59211    +1188     
  Branches     6181     6417     +236     
==========================================
+ Hits        43739    44892    +1153     
- Misses      14014    14027      +13     
- Partials      270      292      +22     

Flag	Coverage Δ
backend	97.05% <100.00%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
src/mcp/server.ts	97.05% <100.00%> (ø)

[loopover-orb]

Tip

✅ LoopOver review result - approve/merge recommended

_{Review updated: 2026-07-27 13:45:52 UTC}

2 files · 1 AI reviewer · no blockers · readiness 98/100 · CI green · clean

✅ Suggested Action - Approve/Merge

• safe to merge

Review summary
Adds a write-side MCP tool mirroring POST /v1/repos/:owner/:repo/focus-manifest/refresh, reusing the same loadRepoFocusManifest(refresh:true) + compileFocusManifestPolicy pair as the REST route and returning the identical { repoFullName, manifest, policy } shape. The write-access boundary (requireRepoManageAccess) is correctly stricter than the read tool, and the accompanying test suite exercises registration, the cache-bypass behavior via a live-vs-stale fetch assertion, allowlist denial, and the read-vs-write access distinction. The implementation is a thin, well-scoped mirror consistent with the existing loopover_refresh_repo_docs pattern.

Nits — 3 non-blocking

• The `long-file` flag on src/mcp/server.ts (~3571 lines) is a pre-existing condition this PR adds 29 lines to, not something introduced by the diff — worth a follow-up to split this registration file, but not this PR's job.
• The 88-line test file duplicates a fair amount of connect/setup boilerplate seen in sibling MCP tool test files; consider extracting a shared test helper if this pattern repeats further.
• Consider extracting the repeated `connect()` helper and static-identity fixtures across MCP tool test files into a shared test util if more refresh-style tools are added.

Decision drivers

• ✅ Code review — No blockers (1 reviewer)
• ✅ Gate result — Passing (No configured blocker found.)

Context & advisory signals — never blocks the verdict

Signal	Result	Evidence
Linked issue	✅ Linked	#9299
Related work	✅ No active overlap found	No same-issue or scoped active PR overlap found.
Change scope	✅ 20/20	Low review scope from cached public metadata (1 linked issue).
Validation posture	✅ 25/25	PR body includes validation/test evidence.
Contributor workload	✅ 10/10	Author activity: 65 registered-repo PR(s), 45 merged, 0 issue(s).
Contributor context	✅ Confirmed Gittensor contributor	bitfathers94; Gittensor profile; 65 PR(s), 0 issue(s).
Improvement	✅ Minor	risk: clean · value: minor · LLM: moderate

Linked issue satisfaction

Addressed
The PR adds loopover_refresh_repo_focus_manifest in src/mcp/server.ts registered under MCP_TOOL_CATEGORIES as maintainer, using ownerRepoShape input, requireRepoManageAccess (write-access boundary), and loadRepoFocusManifest(..., { refresh: true }) + compileFocusManifestPolicy returning the same {repoFullName, manifest, policy} shape as the REST route. It also includes unit tests covering the happ

Review context

• Author: bitfathers94
• Role context: outside_contributor
• Public audience mode: oss maintainer
• Lane context: Repository is configured for direct PR review.
• Public profile languages: TypeScript
• Official Gittensor activity: 65 PR(s), 0 issue(s).
• PR-specific overlap: none found.

Contributor next steps

• Keep the PR focused and include validation evidence before maintainer review.

Signal definitions

• Related work = same linked issue, overlapping active PRs, or title/path similarity.
• Change scope = cached public metadata such as size labels, draft state, and review-burden hints.
• Validation posture = whether the PR provides enough public validation/test evidence for maintainer review.
• Contributor workload = public contributor activity and cleanup pressure, not a repo-wide quality failure.
• Contributor context = public GitHub/Gittensor identity context; non-Gittensor status is not a blocker.

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_{🟩 Safe / merged · 🟦 Advisory · 🟨 Held for review · 🟥 Blocked / closed}

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[loopover-orb]

LoopOver approves — the gate is satisfied and CI is green.