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/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);