fix(MULTIVERSION-0001): prevent version jobs from overwriting repo-wide NULL rules entry

Version jobs now write rules only to the version-specific (repo, versionId)
row. Previously every version job unconditionally wrote to the (repo, NULL)
row as well, causing whichever version indexed last to contaminate the
repo-wide rules that the context API merges into every query response.

Adds a regression test (Bug5b) that indexes the main branch, then indexes a
version with different rules, and asserts the NULL row still holds the
main-branch rules.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

src/lib/server/pipeline/indexing.pipeline.test.ts

@@ -869,15 +869,17 @@ describe('IndexingPipeline', () => {
 
 		await pipeline.run(job as never);
 
-		// Repo-wide row (version_id IS NULL) must exist.
+		// Repo-wide row (version_id IS NULL) must NOT be written by a version job —
+		// writing it here would contaminate the NULL entry with version-specific rules
+		// (Bug 5b regression guard).
 		const repoRow = db
 			.prepare(
 				`SELECT rules FROM repository_configs WHERE repository_id = '/test/repo' AND version_id IS NULL`
 			)
 			.get() as { rules: string } | undefined;
-		expect(repoRow).toBeDefined();
+		expect(repoRow).toBeUndefined();
 
-		// Version-specific row must also exist.
+		// Version-specific row must exist with the correct rules.
 		const versionRow = db
 			.prepare(
 				`SELECT rules FROM repository_configs WHERE repository_id = '/test/repo' AND version_id = ?`
@@ -888,6 +890,69 @@ describe('IndexingPipeline', () => {
 		expect(rules).toEqual(['This is v2. Use the new Builder API.']);
 	});
 
+	it('regression(Bug5b): version job does not overwrite the repo-wide NULL rules entry', async () => {
+		// Arrange: index the main branch first to establish a repo-wide rules entry.
+		const mainBranchRules = ['Always use TypeScript strict mode.'];
+		const mainPipeline = makePipeline({
+			files: [
+				{
+					path: 'trueref.json',
+					content: JSON.stringify({ rules: mainBranchRules }),
+					sha: 'sha-main-config',
+					language: 'json'
+				}
+			],
+			totalFiles: 1
+		});
+		const mainJob = makeJob('/test/repo'); // no versionId → main-branch job
+		await mainPipeline.run(mainJob as never);
+
+		// Confirm the repo-wide entry was written.
+		const afterMain = db
+			.prepare(
+				`SELECT rules FROM repository_configs WHERE repository_id = '/test/repo' AND version_id IS NULL`
+			)
+			.get() as { rules: string } | undefined;
+		expect(afterMain).toBeDefined();
+		expect(JSON.parse(afterMain!.rules)).toEqual(mainBranchRules);
+
+		// Act: index a version with different rules.
+		const versionId = insertVersion(db, { tag: 'v3.0.0', state: 'pending' });
+		const versionRules = ['v3 only: use the streaming API.'];
+		const versionPipeline = makePipeline({
+			files: [
+				{
+					path: 'trueref.json',
+					content: JSON.stringify({ rules: versionRules }),
+					sha: 'sha-v3-config',
+					language: 'json'
+				}
+			],
+			totalFiles: 1
+		});
+		const versionJob = makeJob('/test/repo', versionId);
+		await versionPipeline.run(versionJob as never);
+
+		// Assert: the repo-wide NULL entry must still contain the main-branch rules,
+		// not the version-specific ones.
+		const afterVersion = db
+			.prepare(
+				`SELECT rules FROM repository_configs WHERE repository_id = '/test/repo' AND version_id IS NULL`
+			)
+			.get() as { rules: string } | undefined;
+		expect(afterVersion).toBeDefined();
+		expect(JSON.parse(afterVersion!.rules)).toEqual(mainBranchRules);
+
+		// And the version-specific row must contain the version rules.
+		const versionRow = db
+			.prepare(
+				`SELECT rules FROM repository_configs WHERE repository_id = '/test/repo' AND version_id = ?`
+			)
+			.get(versionId) as { rules: string } | undefined;
+		expect(versionRow).toBeDefined();
+		expect(JSON.parse(versionRow!.rules)).toEqual(versionRules);
+	});
+
 	it('persists rules from CrawlResult.config even when trueref.json is absent from files (folders allowlist bug)', async () => {
 		// Regression test for MULTIVERSION-0001:
 		// When trueref.json specifies a `folders` allowlist (e.g. ["src/"]),

src/lib/server/pipeline/indexing.pipeline.ts

@@ -276,10 +276,13 @@ export class IndexingPipeline {
 
 			// ---- Stage 6: Persist rules from config ----------------------------
 			if (parsedConfig?.config.rules?.length) {
-				// Repo-wide rules (versionId = null).
+				if (!normJob.versionId) {
-				this.upsertRepoConfig(repo.id, null, parsedConfig.config.rules);
+					// Main-branch job: write the repo-wide entry only.
-				// Version-specific rules stored separately when indexing a version.
+					this.upsertRepoConfig(repo.id, null, parsedConfig.config.rules);
-				if (normJob.versionId) {
+				} else {
+					// Version job: write only the version-specific entry.
+					// Writing to the NULL row here would overwrite repo-wide rules
+					// with whatever the last-indexed version happened to carry.
 					this.upsertRepoConfig(repo.id, normJob.versionId, parsedConfig.config.rules);
 				}
 			}