perf(semantic-search): index from manifest projection (#64)

## Summary

Carries the tool manifest projection into semantic-search scan jobs by
retaining each manifest source revision alongside the fingerprint. This
makes index work traceable to the source catalog version that produced
it without adding schema reads to scan.

## Changes

- Add optional `sourceRevision` to semantic-search index jobs.
- Copy `ToolSchemaManifest.sourceRevision` into both skipped and changed
scan jobs.
- Add regression coverage that manifest source revisions survive scan
materialization.

## Call Stack

```text
ToolSearchIndex.create()
  -> executor.tools.manifest()
  -> write manifest snapshot

ToolSearchIndex.scan()
  -> read manifest projection
  -> compare manifest.indexFingerprint with stored fingerprint
  -> write IndexJob(sourceRevision, fingerprint, path, status)
```

## Tests

- `bun run --cwd packages/plugins/semantic-search test --
src/sdk/tool-search-index.test.ts`
- `bun run --cwd packages/plugins/semantic-search typecheck`
- `bunx oxfmt --check
packages/plugins/semantic-search/src/sdk/collections.ts
packages/plugins/semantic-search/src/sdk/tool-search-index.ts
packages/plugins/semantic-search/src/sdk/tool-search-index.test.ts`
- `bunx oxlint -c .oxlintrc.jsonc --deny-warnings
packages/plugins/semantic-search/src/sdk/collections.ts
packages/plugins/semantic-search/src/sdk/tool-search-index.ts
packages/plugins/semantic-search/src/sdk/tool-search-index.test.ts`

## Stack

Base: #63

<!-- stack:links:start -->
### [Stack](https://github.com/aryasaatvik/stack)

1. #63
2. **#64** 👈 current
3. #65
<!-- stack:links:end -->

Author: aryasaatvik

packages/plugins/semantic-search/src/sdk/collections.ts

@@ -70,6 +70,7 @@ export const IndexJob = Schema.Struct({
   name: Schema.String,
   integration: Schema.String,
   description: Schema.String,
+  sourceRevision: Schema.optional(Schema.String),
   status: IndexJobStatus,
   fingerprint: Schema.optional(Schema.String),
   oldFingerprint: Schema.optional(Schema.String),

packages/plugins/semantic-search/src/sdk/tool-search-index.test.ts

@@ -67,6 +67,7 @@ const makeMemoryCache = (): Executor["cache"] => {
 const manifestForTool = (
   tool: Tool,
   fingerprint = `fingerprint:${String(tool.address)}`,
+  sourceRevision?: string,
 ): ToolSchemaManifest => ({
   address: tool.address,
   path: String(tool.address).replace(/^tools\./, ""),
@@ -82,6 +83,7 @@ const manifestForTool = (
   definitionSetHash: `definitions:${String(tool.address)}`,
   indexFingerprint: fingerprint,
   fingerprintVersion: "tool-schema-manifest/v1",
+  ...(sourceRevision === undefined ? {} : { sourceRevision }),
 });
 
 const makeExecutor = (
@@ -327,6 +329,7 @@ describe("ToolSearchIndex", () => {
       }
 
       expect(scanned).toMatchObject({ processed: 1, changed: 1, skipped: 0 });
+      expect([...jobs.data.values()][0]?.sourceRevision).toBeUndefined();
       expect(chunked.processed).toBe(1);
       expect(chunked.chunks).toBeGreaterThan(0);
       expect(embedded).toMatchObject({ processed: chunked.chunks, chunks: chunked.chunks });
@@ -350,6 +353,84 @@ describe("ToolSearchIndex", () => {
     }),
   );
 
+  it.effect("copies manifest source revisions into scan jobs", () =>
+    Effect.gen(function* () {
+      const tool: Tool = {
+        address: "tools.github.repos.get" as never,
+        name: "repos.get" as never,
+        integration: "github" as never,
+        description: "Get a repository",
+        owner,
+        connection: "default" as never,
+        pluginId: "test",
+      };
+      const executor: Pick<Executor, "tools" | "cache"> = {
+        tools: {
+          list: () => Effect.succeed([tool]),
+          manifest: () => Effect.succeed([manifestForTool(tool, "fp-source", "spec-hash-v1")]),
+          schema: () => Effect.succeed(null),
+        },
+        cache: makeMemoryCache(),
+      };
+      const base = {
+        namespace,
+        executor: executor as Executor,
+        runs: makeCollection<IndexRun>(indexRuns.name),
+        jobs: makeCollection<IndexJob>(indexJobs.name),
+        chunks: makeCollection<IndexChunk>(indexChunks.name),
+        fingerprints: makeCollection<FingerprintRow>(toolFingerprints.name),
+        blobs: makeBlobs(),
+        owner,
+      };
+
+      yield* create({ ...base, runId: "run-source-revision", partitionCount: 1 });
+      const scanned = yield* scan({
+        ...base,
+        runId: "run-source-revision",
+        partition: 0,
+        limit: 10,
+      });
+
+      expect(scanned).toMatchObject({ processed: 1, changed: 1, skipped: 0 });
+      expect([...base.jobs.data.values()][0]).toMatchObject({
+        path: "github.repos.get",
+        fingerprint: "fp-source",
+        sourceRevision: "spec-hash-v1",
+      });
+
+      const skippedBase = {
+        ...base,
+        jobs: makeCollection<IndexJob>(indexJobs.name),
+        fingerprints: makeCollection<FingerprintRow>(toolFingerprints.name),
+      };
+      yield* skippedBase.fingerprints.put({
+        owner,
+        key: "github.repos.get",
+        data: {
+          path: "github.repos.get",
+          integration: "github",
+          fingerprint: "fp-source",
+          chunkIds: [],
+        },
+      });
+
+      yield* create({ ...skippedBase, runId: "run-source-revision-skipped", partitionCount: 1 });
+      const skipped = yield* scan({
+        ...skippedBase,
+        runId: "run-source-revision-skipped",
+        partition: 0,
+        limit: 10,
+      });
+
+      expect(skipped).toMatchObject({ processed: 1, changed: 0, skipped: 1 });
+      expect([...skippedBase.jobs.data.values()][0]).toMatchObject({
+        path: "github.repos.get",
+        fingerprint: "fp-source",
+        sourceRevision: "spec-hash-v1",
+      });
+    }),
+  );
+
   it.effect("marks pending path work failed and reports progress timestamps", () =>
     Effect.gen(function* () {
       const counters = { raw: 0, codegen: 0 };

packages/plugins/semantic-search/src/sdk/tool-search-index.ts

@@ -1092,6 +1092,9 @@ export const scan = (
               name: manifest.name,
               integration: manifest.integration,
               description: manifest.description,
+              ...(manifest.sourceRevision === undefined
+                ? {}
+                : { sourceRevision: manifest.sourceRevision }),
               status: "skipped",
               fingerprint: manifest.indexFingerprint,
               oldFingerprint: storedRow.fingerprint,
@@ -1110,6 +1113,9 @@ export const scan = (
               name: manifest.name,
               integration: manifest.integration,
               description: manifest.description,
+              ...(manifest.sourceRevision === undefined
+                ? {}
+                : { sourceRevision: manifest.sourceRevision }),
               status: "pendingChunk",
               fingerprint: manifest.indexFingerprint,
               oldFingerprint: storedRow?.fingerprint,