feat(TRUEREF-0009): implement indexing pipeline and job queue

Implements the end-to-end indexing pipeline with a SQLite-backed job
queue, startup recovery, and REST API endpoints for job status.

- IndexingPipeline: orchestrates crawl → parse → atomic replace → embed
  → repo stats update with progress tracking at each stage
- JobQueue: sequential SQLite-backed queue (no external broker), deduplicates
  active jobs per repository, drains queued jobs on startup
- startup.ts: stale job recovery (running→failed), repo state reset, singleton
  initialization wired from hooks.server.ts
- GET /api/v1/jobs with repositoryId/status/limit filtering
- GET /api/v1/jobs/[id] single job lookup
- hooks.server.ts: initializes DB and pipeline on server start
- 18 unit tests covering queue, pipeline stages, recovery, and atomicity

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

src/hooks.server.ts

@@ -0,0 +1,72 @@
+/**
+ * SvelteKit server hooks (TRUEREF-0009).
+ *
+ * Runs once when the Node.js server process starts. Initialises the database
+ * and kicks off the indexing pipeline + job queue so queued jobs resume
+ * automatically after a restart.
+ */
+
+import { initializeDatabase } from '$lib/server/db/index.js';
+import { getClient } from '$lib/server/db/client.js';
+import { initializePipeline } from '$lib/server/pipeline/startup.js';
+import { EMBEDDING_CONFIG_KEY, createProviderFromConfig, defaultEmbeddingConfig } from '$lib/server/embeddings/factory.js';
+import { EmbeddingService } from '$lib/server/embeddings/embedding.service.js';
+import type { EmbeddingConfig } from '$lib/server/embeddings/factory.js';
+import type { Handle } from '@sveltejs/kit';
+
+// ---------------------------------------------------------------------------
+// Server initialisation — runs once on startup
+// ---------------------------------------------------------------------------
+
+try {
+	initializeDatabase();
+
+	const db = getClient();
+
+	// Load persisted embedding configuration (if any).
+	const configRow = db
+		.prepare<[string], { value: string }>(`SELECT value FROM settings WHERE key = ?`)
+		.get(EMBEDDING_CONFIG_KEY);
+
+	let embeddingService: EmbeddingService | null = null;
+
+	if (configRow) {
+		try {
+			const config: EmbeddingConfig =
+				typeof configRow.value === 'string'
+					? JSON.parse(configRow.value)
+					: (configRow.value as EmbeddingConfig);
+
+			if (config.provider !== 'none') {
+				const provider = createProviderFromConfig(config);
+				embeddingService = new EmbeddingService(db, provider);
+			}
+		} catch (err) {
+			console.warn(
+				`[hooks.server] Could not load embedding config: ${err instanceof Error ? err.message : String(err)}`
+			);
+		}
+	} else {
+		// Use the default (noop) config so the pipeline is still wired up.
+		const config = defaultEmbeddingConfig();
+		if (config.provider !== 'none') {
+			const provider = createProviderFromConfig(config);
+			embeddingService = new EmbeddingService(db, provider);
+		}
+	}
+
+	initializePipeline(db, embeddingService);
+	console.log('[hooks.server] Indexing pipeline initialised.');
+} catch (err) {
+	console.error(
+		`[hooks.server] Failed to initialise server: ${err instanceof Error ? err.message : String(err)}`
+	);
+}
+
+// ---------------------------------------------------------------------------
+// Request handler (pass-through)
+// ---------------------------------------------------------------------------
+
+export const handle: Handle = async ({ event, resolve }) => {
+	return resolve(event);
+};