feat(MULTIVERSION-0001): wire trueref.json into pipeline + per-version rules

- Add migration 0003: recreate repository_configs with nullable version_id
  column and two partial unique indexes (repo-wide: version_id IS NULL,
  per-version: (repository_id, version_id) WHERE version_id IS NOT NULL)
- Update schema.ts to reflect the new composite structure with uniqueIndex
  partial constraints via drizzle-orm sql helper
- IndexingPipeline: parse trueref.json / context7.json after crawl, apply
  excludeFiles filter before diff computation, update totalFiles accordingly
- IndexingPipeline: persist repo-wide rules (version_id=null) and
  version-specific rules (when versionId set) via upsertRepoConfig helper
- Add matchesExcludePattern static helper supporting plain filename,
  glob prefix (docs/legacy*), and exact path patterns
- context endpoint: split getRules into repo-wide + version-specific lookup
  with dedup merge; pass versionId at call site
- Update test DB loaders to include migration 0003
- Add pipeline tests for excludeFiles, repo-wide rules persistence, and
  per-version rules persistence
- Add integration tests for merged rules, repo-only rules, and dedup logic

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

src/routes/api/v1/api-contract.integration.test.ts

@@ -55,6 +55,7 @@ function createTestDb(): Database.Database {
 	const migration0 = readFileSync(join(migrationsFolder, '0000_large_master_chief.sql'), 'utf-8');
 	const migration1 = readFileSync(join(migrationsFolder, '0001_quick_nighthawk.sql'), 'utf-8');
 	const migration2 = readFileSync(join(migrationsFolder, '0002_silky_stellaris.sql'), 'utf-8');
+	const migration3 = readFileSync(join(migrationsFolder, '0003_multiversion_config.sql'), 'utf-8');
 
 	// Apply first migration
 	const statements0 = migration0
@@ -85,6 +86,15 @@ function createTestDb(): Database.Database {
 		client.exec(statement);
 	}
 
+	const statements3 = migration3
+		.split('--> statement-breakpoint')
+		.map((statement) => statement.trim())
+		.filter(Boolean);
+
+	for (const statement of statements3) {
+		client.exec(statement);
+	}
+
 	client.exec(readFileSync(ftsFile, 'utf-8'));
 
 	return client;
@@ -487,6 +497,95 @@ describe('API contract integration', () => {
 		});
 	});
 
+	it('GET /api/v1/context returns merged repo-wide and version-specific rules', async () => {
+		const repositoryId = seedRepo(db);
+		const versionId = seedVersion(db, repositoryId, 'v2.0.0');
+		const documentId = seedDocument(db, repositoryId, versionId);
+
+		// Insert repo-wide rules (version_id IS NULL).
+		db.prepare(
+			`INSERT INTO repository_configs (repository_id, version_id, rules, updated_at)
+			 VALUES (?, NULL, ?, ?)`
+		).run(repositoryId, JSON.stringify(['Repo-wide rule']), NOW_S);
+
+		// Insert version-specific rules.
+		db.prepare(
+			`INSERT INTO repository_configs (repository_id, version_id, rules, updated_at)
+			 VALUES (?, ?, ?, ?)`
+		).run(repositoryId, versionId, JSON.stringify(['Version-specific rule']), NOW_S);
+
+		seedSnippet(db, {
+			documentId,
+			repositoryId,
+			versionId,
+			content: 'some versioned content'
+		});
+
+		const response = await getContext({
+			url: new URL(
+				`http://test/api/v1/context?libraryId=${encodeURIComponent(`${repositoryId}/v2.0.0`)}&query=${encodeURIComponent('versioned content')}`
+			)
+		} as never);
+
+		expect(response.status).toBe(200);
+		const body = await response.json();
+		// Both repo-wide and version-specific rules should appear (deduped).
+		expect(body.rules).toEqual(['Repo-wide rule', 'Version-specific rule']);
+	});
+
+	it('GET /api/v1/context returns only repo-wide rules when no version is requested', async () => {
+		const repositoryId = seedRepo(db);
+		const documentId = seedDocument(db, repositoryId);
+
+		// Insert repo-wide rules (version_id IS NULL).
+		db.prepare(
+			`INSERT INTO repository_configs (repository_id, version_id, rules, updated_at)
+			 VALUES (?, NULL, ?, ?)`
+		).run(repositoryId, JSON.stringify(['Repo-wide rule only']), NOW_S);
+
+		seedSnippet(db, { documentId, repositoryId, content: 'some content' });
+
+		const response = await getContext({
+			url: new URL(
+				`http://test/api/v1/context?libraryId=${encodeURIComponent(repositoryId)}&query=${encodeURIComponent('some content')}`
+			)
+		} as never);
+
+		expect(response.status).toBe(200);
+		const body = await response.json();
+		expect(body.rules).toEqual(['Repo-wide rule only']);
+	});
+
+	it('GET /api/v1/context deduplicates rules that appear in both repo-wide and version config', async () => {
+		const repositoryId = seedRepo(db);
+		const versionId = seedVersion(db, repositoryId, 'v3.0.0');
+		const documentId = seedDocument(db, repositoryId, versionId);
+
+		const sharedRule = 'Use TypeScript strict mode';
+		db.prepare(
+			`INSERT INTO repository_configs (repository_id, version_id, rules, updated_at)
+			 VALUES (?, NULL, ?, ?)`
+		).run(repositoryId, JSON.stringify([sharedRule]), NOW_S);
+
+		db.prepare(
+			`INSERT INTO repository_configs (repository_id, version_id, rules, updated_at)
+			 VALUES (?, ?, ?, ?)`
+		).run(repositoryId, versionId, JSON.stringify([sharedRule, 'Version-only rule']), NOW_S);
+
+		seedSnippet(db, { documentId, repositoryId, versionId, content: 'dedup test content' });
+
+		const response = await getContext({
+			url: new URL(
+				`http://test/api/v1/context?libraryId=${encodeURIComponent(`${repositoryId}/v3.0.0`)}&query=${encodeURIComponent('dedup test')}`
+			)
+		} as never);
+
+		expect(response.status).toBe(200);
+		const body = await response.json();
+		// sharedRule appears once, version-only rule appended.
+		expect(body.rules).toEqual([sharedRule, 'Version-only rule']);
+	});
+
 	it('GET /api/v1/context returns 404 with VERSION_NOT_FOUND when version does not exist', async () => {
 		const repositoryId = seedRepo(db);
 

src/routes/api/v1/context/+server.ts

@@ -54,24 +54,52 @@ interface RawRepoConfig {
 	rules: string | null;
 }
 
-function getRules(db: ReturnType<typeof getClient>, repositoryId: string): string[] {
-	const row = db
-		.prepare<
-			[string],
-			RawRepoConfig
-		>(`SELECT rules FROM repository_configs WHERE repository_id = ?`)
-		.get(repositoryId);
-
-	if (!row?.rules) return [];
-
+function parseRulesJson(raw: string | null | undefined): string[] {
+	if (!raw) return [];
 	try {
-		const parsed = JSON.parse(row.rules);
+		const parsed = JSON.parse(raw);
 		return Array.isArray(parsed) ? (parsed as string[]) : [];
 	} catch {
 		return [];
 	}
 }
 
+function getRules(
+	db: ReturnType<typeof getClient>,
+	repositoryId: string,
+	versionId?: string
+): string[] {
+	// Repo-wide rules (version_id IS NULL).
+	const repoRow = db
+		.prepare<
+			[string],
+			RawRepoConfig
+		>(`SELECT rules FROM repository_configs WHERE repository_id = ? AND version_id IS NULL`)
+		.get(repositoryId);
+
+	const repoRules = parseRulesJson(repoRow?.rules);
+
+	if (!versionId) return repoRules;
+
+	// Version-specific rules.
+	const versionRow = db
+		.prepare<
+			[string, string],
+			RawRepoConfig
+		>(`SELECT rules FROM repository_configs WHERE repository_id = ? AND version_id = ?`)
+		.get(repositoryId, versionId);
+
+	const versionRules = parseRulesJson(versionRow?.rules);
+
+	// Merge: repo-wide first, then version-specific (deduped by content).
+	const seen = new Set(repoRules);
+	const merged = [...repoRules];
+	for (const r of versionRules) {
+		if (!seen.has(r)) merged.push(r);
+	}
+	return merged;
+}
+
 interface RawRepoState {
 	state: 'pending' | 'indexing' | 'indexed' | 'error';
 	id: string;
@@ -283,8 +311,8 @@ export const GET: RequestHandler = async ({ url }) => {
 			snippetVersions
 		};
 
-		// Load rules from repository_configs.
-		const rules = getRules(db, parsed.repositoryId);
+		// Load rules from repository_configs (repo-wide + version-specific merged).
+		const rules = getRules(db, parsed.repositoryId, versionId);
 
 		if (responseType === 'txt') {
 			const text = formatContextTxt(selectedResults, rules, metadata);