fix: search index corruption on incremental updates and compile indexing

packages/cli/src/commands/search.ts

@@ -135,6 +135,12 @@ export async function search(term: string, opts: SearchOpts) {
 
 	spinner.stop();
 
+	// Filter results by scope when loaded from cache (cache contains all scopes)
+	if (scope !== "all") {
+		const scopeDir = scope === "wiki" ? "/wiki/" : "/raw/";
+		results = results.filter((r) => r.path.includes(scopeDir));
+	}
+
 	if (opts.json) {
 		console.log(JSON.stringify(results, null, 2));
 		return;

packages/cli/src/commands/watch.test.ts

@@ -57,7 +57,10 @@ describe("watch: HTTP server /ingest", () => {
 	});
 
 	test("builds correct markdown without url", () => {
-		const body = { content: "Body text", title: "Title Only" };
+		const body: { content: string; title: string; url?: string } = {
+			content: "Body text",
+			title: "Title Only",
+		};
 		const fullContent = body.title
 			? `# ${body.title}\n\n${body.url ? `Source: ${body.url}\n\n` : ""}${body.content}`
 			: body.content;

packages/core/src/compile/compiler.ts

@@ -700,6 +700,35 @@ async function compileVaultInner(
 
 		await saveManifest(root, manifest);
 
+		// Update search index with newly compiled wiki articles
+		try {
+			const { SearchIndex } = await import("../search/engine.js");
+			const searchIndex = new SearchIndex();
+			await searchIndex.load(root);
+			for (const op of allOperations) {
+				if ((op.op === "create" || op.op === "update") && op.content) {
+					const { frontmatter, body } = parseFrontmatter(op.content);
+					const title =
+						(frontmatter.title as string) ?? op.path.split("/").pop()?.replace(/\.md$/, "") ?? "";
+					const tags = Array.isArray(frontmatter.tags) ? (frontmatter.tags as string[]) : [];
+					const date =
+						(frontmatter.created as string) ??
+						(frontmatter.updated as string) ??
+						new Date().toISOString().slice(0, 10);
+					searchIndex.addDocument({
+						path: join(root, op.path),
+						title,
+						content: body,
+						tags,
+						date,
+					});
+				}
+			}
+			await searchIndex.save(root);
+		} catch {
+			// Search index update is best-effort — don't fail the compile
+		}
+
 		// Log compile activity
 		const parts = [`${sourcesToCompile.length} sources compiled`];
 		if (totalCreated > 0) parts.push(`${totalCreated} articles created`);

packages/core/src/daemon/folder-watcher.ts

@@ -25,14 +25,14 @@ export function matchGlob(filename: string, pattern: string): boolean {
 
 	// Handle *.{ext1,ext2} pattern
 	const braceMatch = pattern.match(/^\*\.\{(.+)\}$/);
-	if (braceMatch) {
+	if (braceMatch?.[1]) {
 		const extensions = braceMatch[1].split(",").map((e) => `.${e.trim()}`);
 		return extensions.includes(extname(filename).toLowerCase());
 	}
 
 	// Handle *.ext pattern
 	const extMatch = pattern.match(/^\*(\..+)$/);
-	if (extMatch) {
+	if (extMatch?.[1]) {
 		return extname(filename).toLowerCase() === extMatch[1].toLowerCase();
 	}
 
@@ -105,7 +105,7 @@ export async function scanFolder(folder: WatchFolder): Promise<string[]> {
 	try {
 		const files = await readdir(absPath, { recursive: folder.recursive });
 		for (const file of files) {
-			const name = typeof file === "string" ? file : file.toString();
+			const name = String(file);
 			const base = name.includes("/") ? name.split("/").pop()! : name;
 			if (!base.startsWith(".") && matchGlob(base, folder.glob)) {
 				matches.push(join(absPath, name));

packages/core/src/recovery.ts

@@ -145,7 +145,7 @@ export async function repairVault(root: string): Promise<RecoveryIssue[]> {
 						.sort()
 						.reverse();
 
-					if (backups.length > 0) {
+					if (backups[0]) {
 						const latest = join(backupsDir, backups[0]);
 						try {
 							const backup = await readFile(latest, "utf-8");

packages/core/src/search/engine.ts

@@ -406,7 +406,7 @@ export class SearchIndex {
 				path: d.path,
 				title: d.title,
 				snippet: d.content.slice(0, 200),
-				tokenCount: d.tokens.length,
+				tokenCount: d.tokenCount,
 				termFreqs: [...d.termFreqs.entries()],
 				tags: d.tags,
 				date: d.date,
@@ -436,9 +436,10 @@ export class SearchIndex {
 
 		try {
 			const raw = await readFile(path, "utf-8");
-			const data = JSON.parse(raw) as SerializedIndex & { version: number };
+			const data = JSON.parse(raw) as SerializedIndex;
+			const version = data.version as number;
 
-			if (data.version !== 1 && data.version !== 2) return false;
+			if (version !== 1 && version !== 2) return false;
 
 			this.documents = data.documents.map((d) => ({
 				path: d.path,
@@ -507,12 +508,10 @@ export class SearchIndex {
 		const docFreq = new Map<string, number>();
 
 		for (const doc of this.documents) {
-			const seen = new Set<string>();
-			for (const token of doc.tokens) {
-				if (!seen.has(token)) {
-					docFreq.set(token, (docFreq.get(token) ?? 0) + 1);
-					seen.add(token);
-				}
+			// Use termFreqs.keys() instead of tokens — loaded docs have tokens: []
+			// but termFreqs is always populated (from serialization or addDocument)
+			for (const term of doc.termFreqs.keys()) {
+				docFreq.set(term, (docFreq.get(term) ?? 0) + 1);
 			}
 		}
 

packages/core/src/skills/registry.ts

@@ -235,13 +235,13 @@ async function installFromGitHub(
 	skillsDir: string,
 ): Promise<InstallResult> {
 	// repo format: "user/repo" or "user/repo#branch"
-	const [repoPath, branch] = repo.split("#");
+	const [repoPath, branch] = repo.split("#") as [string, string | undefined];
 	const parts = repoPath.split("/");
-	if (parts.length !== 2) {
+	if (parts.length !== 2 || !parts[1]) {
 		throw new Error(`Invalid GitHub repo format: "${repo}". Expected "user/repo"`);
 	}
 
-	const repoName = parts[1];
+	const repoName: string = parts[1];
 	const destDir = join(skillsDir, repoName);
 
 	if (existsSync(destDir)) {