Greptile Summary

This PR suppresses the noisy "duplicate plugin id detected" warning that fired on every gateway startup when a user had explicitly npm-installed a global plugin that shared an id with a bundled plugin. The fix inserts an isIntentionalOverride check in loadPluginManifestRegistry that, when one candidate is a verified installed global and the other is bundled, silently replaces the bundled registry record with the higher-precedence global record instead of pushing both and emitting a warning.

Key changes:

• src/plugins/manifest-registry.ts: New isIntentionalOverride guard added between the same-physical-path dedup block and the duplicate-warning push. Calls the existing matchesInstalledPluginRecord / resolveDuplicatePrecedenceRank helpers; the installed global always wins (rank 1 vs bundled rank 2), so the newRank === existingRank edge case cannot arise.
• src/plugins/manifest-registry.test.ts: The replaced test previously asserted that the old noisy diagnostic was present; it now correctly asserts zero duplicate warnings and exactly one origin: "global" record.

Minor concern: The updated test only covers one candidate ordering (bundled first, npm-installed global second). The symmetric ordering (global first, bundled second), which exercises the existingIsInstalled && candidate.origin === "bundled" branch, is not explicitly tested. The logic is sound for both orderings, but a complementary test case would strengthen regression coverage.

Confidence Score: 4/5

• Safe to merge; the logic is correct for all cases and the only gap is a missing test for the reverse candidate ordering.
• The implementation correctly handles both candidate orderings, the precedence ranks guarantee no ambiguous tie-breaking within the intentional-override path, and seenIds stays consistent in all branches. The removed test assertion was deliberately replaced with stricter, behaviour-matching assertions. The only shortcoming is the lack of a test for the symmetric existingIsInstalled && candidate.origin === "bundled" ordering.
• No files require special attention, though src/plugins/manifest-registry.test.ts would benefit from an additional test covering the reverse candidate ordering.

This is a comment left during a code review.
Path: src/plugins/manifest-registry.test.ts
Line: 162-199

Comment:
**Only one candidate ordering is tested**

The test places the bundled candidate first and the npm-installed global second, which exercises the `candidateIsInstalled && existing.candidate.origin === "bundled"` branch of `isIntentionalOverride`. The symmetric branch — `existingIsInstalled && candidate.origin === "bundled"` (global arrives first, bundled second) — is never exercised by any test in the file.

While tracing through the code confirms the reverse ordering is handled correctly (the installed global wins at rank 1 vs bundled at rank 2, so `newRank >= existingRank` causes a silent `continue`), a complementary test would make the invariant explicit and guard against future regressions:

```typescript
it("suppresses duplicate warning for npm-installed plugin overriding bundled (global candidate first)", () => {
  const bundledDir = makeTempDir();
  const globalDir = makeTempDir();
  const manifest = { id: "zalouser", configSchema: { type: "object" } };
  writeManifest(bundledDir, manifest);
  writeManifest(globalDir, manifest);

  const registry = loadPluginManifestRegistry({
    cache: false,
    config: {
      plugins: {
        installs: {
          zalouser: { source: "npm", installPath: globalDir },
        },
      },
    },
    candidates: [
      createPluginCandidate({ idHint: "zalouser", rootDir: globalDir, origin: "global" }),
      createPluginCandidate({ idHint: "zalouser", rootDir: bundledDir, origin: "bundled" }),
    ],
  });

  expect(countDuplicateWarnings(registry)).toBe(0);
  expect(registry.plugins.filter((p) => p.id === "zalouser")).toHaveLength(1);
  expect(registry.plugins.find((p) => p.id === "zalouser")?.origin).toBe("global");
});
```

How can I resolve this? If you propose a fix, please make it concise.

_{Last reviewed commit: 9dd9965}

Closing this as carried forward by a maintainer patch on main.

Landed fix: 713cc74 (fix: quiet installed plugin override warnings).

What landed:

• src/plugins/manifest-registry.ts now suppresses duplicate-plugin warnings only for the intentional case where a tracked npm-installed global plugin from plugins.installs overrides the bundled plugin with the same id.
• The effective registry still keeps one winner by precedence, and unrelated duplicate risks still warn: untracked globals, workspace duplicates, and config-path overrides.
• src/plugins/manifest-registry.test.ts covers both candidate orderings: bundled first and installed global first.

Verification:

• Local pnpm test src/plugins/manifest-registry.test.ts: 43 passed.
• Local pnpm check:changed: passed.
• Blacksmith Testbox tbx_01kq7k5snak04ea9zn88q6prnb: pnpm test src/plugins/manifest-registry.test.ts && pnpm check:changed passed.

Thanks @abdushsk for the focused fix and test shape.