@tekmidian/pai 0.5.6 → 0.6.0

package/dist/{vault-indexer-DXWs9pDn.mjs → vault-indexer-Bi2cRmn7.mjs}

@@ -1,29 +1,15 @@
-import { t as chunkMarkdown } from "./chunker-CbnBe0s0.mjs";
+import { c as yieldToEventLoop, f as sha256File, l as chunkMarkdown, n as chunkId } from "./helpers-BEST-4Gx.mjs";
 import { existsSync, readFileSync, readdirSync, statSync } from "node:fs";
 import { basename, dirname, join, normalize, relative } from "node:path";
-import { createHash } from "node:crypto";
 
-//#region src/memory/vault-indexer.ts
+//#region src/memory/vault/walk.ts
 /**
-* Vault indexer for the PAI federation memory engine.
-*
-* Indexes an entire Obsidian vault (or any markdown knowledge base), following
-* symlinks, deduplicating files by inode, parsing wikilinks, and computing
-* per-file health metrics (orphan detection, dead links).
-*
-* Key differences from the project indexer (indexer.ts):
-*  - Follows symbolic links (project indexer skips them)
-*  - Deduplicates files with the same inode (same content reachable via multiple paths)
-*  - Parses [[wikilinks]] and builds a directed link graph
-*  - Resolves wikilinks using Obsidian's shortest-match algorithm
-*  - Computes health metrics per file: inbound/outbound link counts, dead links, orphans
+* Vault directory walker — follows symlinks with cycle detection.
 */
 /** Maximum number of .md files to collect from a vault. */
 const VAULT_MAX_FILES = 1e4;
 /** Maximum recursion depth for vault directory walks. */
 const VAULT_MAX_DEPTH = 10;
-/** Number of files to process before yielding to the event loop. */
-const VAULT_YIELD_EVERY = 10;
 /**
 * Directories to always skip, at any depth, during vault walks.
 * Includes standard build/VCS noise plus Obsidian-specific directories.
@@ -46,15 +32,6 @@ const VAULT_SKIP_DIRS = new Set([
 	".obsidian",
 	".trash"
 ]);
-function sha256File(content) {
-	return createHash("sha256").update(content).digest("hex");
-}
-function chunkId(projectId, path, chunkIndex, startLine, endLine) {
-	return createHash("sha256").update(`${projectId}:${path}:${chunkIndex}:${startLine}:${endLine}`).digest("hex");
-}
-function yieldToEventLoop() {
-	return new Promise((resolve) => setImmediate(resolve));
-}
 /**
 * Recursively collect all .md files under a vault root, following symlinks.
 *
@@ -66,11 +43,8 @@ function yieldToEventLoop() {
 * Using the real stat (not lstat) ensures that symlinked dirs resolve to
 * their actual inode, preventing infinite loops.
 *
-* @param dir        Directory to scan.
-* @param vaultRoot  Absolute root of the vault (for computing vaultRelPath).
-* @param acc        Shared accumulator (mutated in place for early exit).
-* @param visited    Set of "device:inode" strings for visited directories.
-* @param depth      Current recursion depth.
+* @param vaultRoot  Absolute path to the vault root directory.
+* @param opts       Optional overrides for maxFiles and maxDepth.
 */
 function walkVaultMdFiles(vaultRoot, opts) {
 	const maxFiles = opts?.maxFiles ?? VAULT_MAX_FILES;
@@ -137,6 +111,9 @@ function walkVaultMdFiles(vaultRoot, opts) {
 	if (existsSync(vaultRoot)) walk(vaultRoot, 0);
 	return results;
 }
+
+//#endregion
+//#region src/memory/vault/deduplicate.ts
 /**
 * Group vault files by inode identity (device + inode).
 *
@@ -168,8 +145,11 @@ function deduplicateByInode(files) {
 	}
 	return result;
 }
+
+//#endregion
+//#region src/memory/vault/parse-links.ts
 /**
-* Parse all [[wikilinks]] and ![[embeds]] from markdown content.
+* Parse all links from markdown content.
 *
 * Handles:
 *  - Standard wikilinks: [[Target Note]]
@@ -177,11 +157,16 @@ function deduplicateByInode(files) {
 *  - Heading anchors: [[Target Note#Heading]] (stripped for resolution)
 *  - Embeds: ![[Target Note]]
 *  - Frontmatter wikilinks (YAML between --- delimiters)
+*  - Markdown links: [text](path/to/note.md)
+*  - Markdown embeds: ![alt](image.png)
+*
+* External URLs (http://, https://, mailto:, etc.) are excluded — only
+* relative paths are treated as vault links.
 *
 * @param content  Raw markdown file content.
 * @returns        Array of parsed links in document order.
 */
-function parseWikilinks(content) {
+function parseLinks(content) {
 	const links = [];
 	const lines = content.split("\n");
 	let frontmatterEnd = 0;
@@ -190,9 +175,11 @@ function parseWikilinks(content) {
 		if (closingIdx !== -1) frontmatterEnd = content.slice(0, closingIdx + 4).split("\n").length - 1;
 	}
 	const wikilinkRe = /(!?)\[\[([^\]]+?)\]\]/g;
+	const mdLinkRe = /(!)?\[([^\]]*)\]\(([^)]+)\)/g;
 	for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {
 		const line = lines[lineIdx];
 		const lineNumber = lineIdx + 1;
+		const isFrontmatter = lineIdx < frontmatterEnd;
 		wikilinkRe.lastIndex = 0;
 		let match;
 		while ((match = wikilinkRe.exec(line)) !== null) {
@@ -204,17 +191,47 @@ function parseWikilinks(content) {
 			const hashIdx = beforePipe.indexOf("#");
 			const raw = hashIdx === -1 ? beforePipe.trim() : beforePipe.slice(0, hashIdx).trim();
 			if (!raw) continue;
-			const isFrontmatter = lineIdx < frontmatterEnd;
 			links.push({
 				raw,
 				alias: alias?.trim() ?? null,
 				lineNumber,
-				isEmbed: isEmbed && !isFrontmatter
+				isEmbed: isEmbed && !isFrontmatter,
+				isMdLink: false
 			});
 		}
+		if (!isFrontmatter) {
+			mdLinkRe.lastIndex = 0;
+			while ((match = mdLinkRe.exec(line)) !== null) {
+				const isEmbed = match[1] === "!";
+				const displayText = match[2];
+				let target = match[3].trim();
+				if (/^[a-z][a-z0-9+.-]*:/i.test(target)) continue;
+				if (target.startsWith("#")) continue;
+				const hashIdx = target.indexOf("#");
+				if (hashIdx !== -1) target = target.slice(0, hashIdx);
+				try {
+					target = decodeURIComponent(target);
+				} catch {}
+				const raw = target.replace(/\.md$/i, "").trim();
+				if (!raw) continue;
+				links.push({
+					raw,
+					alias: displayText || null,
+					lineNumber,
+					isEmbed,
+					isMdLink: true
+				});
+			}
+		}
 	}
 	return links;
 }
+
+//#endregion
+//#region src/memory/vault/name-index.ts
+/**
+* Name index builder for Obsidian wikilink resolution.
+*/
 /**
 * Build a name lookup index for Obsidian wikilink resolution.
 *
@@ -232,6 +249,12 @@ function buildNameIndex(files) {
 	}
 	return index;
 }
+
+//#endregion
+//#region src/memory/vault/resolve.ts
+/**
+* Wikilink resolver using Obsidian's shortest-match algorithm.
+*/
 /**
 * Resolve a wikilink target to a vault-relative path using Obsidian's rules.
 *
@@ -295,9 +318,28 @@ function commonPrefixLength(a, b) {
 	else break;
 	return count;
 }
+
+//#endregion
+//#region src/memory/vault/indexer.ts
 /**
-* Index an entire Obsidian vault (or markdown knowledge base) into the
-* federation database.
+* Main vault indexing orchestrator.
+*
+* Indexes an entire Obsidian vault (or any markdown knowledge base), following
+* symlinks, deduplicating files by inode, parsing wikilinks, and computing
+* per-file health metrics (orphan detection, dead links).
+*
+* Key differences from the project indexer (indexer/sync.ts):
+*  - Follows symbolic links (project indexer skips them)
+*  - Deduplicates files with the same inode (same content reachable via multiple paths)
+*  - Parses [[wikilinks]] and builds a directed link graph
+*  - Resolves wikilinks using Obsidian's shortest-match algorithm
+*  - Computes health metrics per file: inbound/outbound link counts, dead links, orphans
+*/
+/** Number of files to process before yielding to the event loop. */
+const VAULT_YIELD_EVERY = 1;
+/**
+* Index an entire Obsidian vault (or markdown knowledge base) using the
+* async StorageBackend interface.
 *
 * Steps:
 *  1. Walk vault root, following symlinks.
@@ -306,7 +348,7 @@ function commonPrefixLength(a, b) {
 *  4. For each canonical file:
 *     a. SHA-256 hash for change detection — skip unchanged files.
 *     b. Read content, chunk with chunkMarkdown().
-*     c. Insert chunks into memory_chunks and memory_fts.
+*     c. Insert chunks into backend (memory_chunks and memory_fts).
 *     d. Upsert vault_files row.
 *  5. Record aliases in vault_aliases.
 *  6. Rebuild vault_name_index table.
@@ -317,11 +359,11 @@ function commonPrefixLength(a, b) {
 *  8. Compute and upsert health metrics (vault_health).
 *  9. Return statistics.
 *
-* @param db              Open federation database.
+* @param backend         StorageBackend to write to.
 * @param vaultProjectId  Registry project ID for the vault "project".
 * @param vaultRoot       Absolute path to the vault root directory.
 */
-async function indexVault(db, vaultProjectId, vaultRoot) {
+async function indexVault(backend, vaultProjectId, vaultRoot) {
 	const startTime = Date.now();
 	const result = {
 		filesIndexed: 0,
@@ -336,28 +378,6 @@ async function indexVault(db, vaultProjectId, vaultRoot) {
 	const allFiles = walkVaultMdFiles(vaultRoot);
 	const inodeGroups = deduplicateByInode(allFiles);
 	const nameIndex = buildNameIndex(allFiles);
-	const selectFileHash = db.prepare("SELECT hash FROM vault_files WHERE vault_path = ?");
-	const deleteOldChunkIds = db.prepare("SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?");
-	const deleteFts = db.prepare("DELETE FROM memory_fts WHERE id = ?");
-	const deleteChunks = db.prepare("DELETE FROM memory_chunks WHERE project_id = ? AND path = ?");
-	const insertChunk = db.prepare(`
-    INSERT INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)
-    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-  `);
-	const insertFts = db.prepare(`
-    INSERT INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)
-    VALUES (?, ?, ?, ?, ?, ?, ?, ?)
-  `);
-	const upsertVaultFile = db.prepare(`
-    INSERT INTO vault_files (vault_path, inode, device, hash, title, indexed_at)
-    VALUES (?, ?, ?, ?, ?, ?)
-    ON CONFLICT(vault_path) DO UPDATE SET
-      inode      = excluded.inode,
-      device     = excluded.device,
-      hash       = excluded.hash,
-      title      = excluded.title,
-      indexed_at = excluded.indexed_at
-  `);
 	await yieldToEventLoop();
 	let filesSinceYield = 0;
 	for (const group of inodeGroups) {
@@ -375,120 +395,136 @@ async function indexVault(db, vaultProjectId, vaultRoot) {
 			continue;
 		}
 		const hash = sha256File(content);
-		if (selectFileHash.get(canonical.vaultRelPath)?.hash === hash) {
+		if ((await backend.getVaultFile(canonical.vaultRelPath))?.hash === hash) {
 			result.filesSkipped++;
 			continue;
 		}
-		const oldChunkIds = deleteOldChunkIds.all(vaultProjectId, canonical.vaultRelPath);
-		db.transaction(() => {
-			for (const row of oldChunkIds) deleteFts.run(row.id);
-			deleteChunks.run(vaultProjectId, canonical.vaultRelPath);
-		})();
+		await backend.deleteChunksForFile(vaultProjectId, canonical.vaultRelPath);
 		const chunks = chunkMarkdown(content);
 		const updatedAt = Date.now();
 		const titleMatch = /^#\s+(.+)$/m.exec(content);
 		const title = titleMatch ? titleMatch[1].trim() : basename(canonical.vaultRelPath, ".md");
-		db.transaction(() => {
-			for (let i = 0; i < chunks.length; i++) {
-				const chunk = chunks[i];
-				const id = chunkId(vaultProjectId, canonical.vaultRelPath, i, chunk.startLine, chunk.endLine);
-				insertChunk.run(id, vaultProjectId, "vault", "topic", canonical.vaultRelPath, chunk.startLine, chunk.endLine, chunk.hash, chunk.text, updatedAt);
-				insertFts.run(chunk.text, id, vaultProjectId, canonical.vaultRelPath, "vault", "topic", chunk.startLine, chunk.endLine);
-			}
-			upsertVaultFile.run(canonical.vaultRelPath, canonical.inode, canonical.device, hash, title, updatedAt);
-		})();
+		const chunkRows = [];
+		for (let i = 0; i < chunks.length; i++) {
+			const chunk = chunks[i];
+			const id = chunkId(vaultProjectId, canonical.vaultRelPath, i, chunk.startLine, chunk.endLine);
+			chunkRows.push({
+				id,
+				projectId: vaultProjectId,
+				source: "vault",
+				tier: "topic",
+				path: canonical.vaultRelPath,
+				startLine: chunk.startLine,
+				endLine: chunk.endLine,
+				hash: chunk.hash,
+				text: chunk.text,
+				updatedAt
+			});
+		}
+		if (chunkRows.length > 0) await backend.insertChunks(chunkRows);
+		const vaultFileRow = {
+			vaultPath: canonical.vaultRelPath,
+			inode: canonical.inode,
+			device: canonical.device,
+			hash,
+			title,
+			indexedAt: updatedAt
+		};
+		await backend.upsertVaultFile(vaultFileRow);
 		result.filesIndexed++;
 		result.chunksCreated += chunks.length;
 	}
 	await yieldToEventLoop();
-	db.exec("DELETE FROM vault_aliases");
-	const insertAlias = db.prepare(`
-    INSERT OR REPLACE INTO vault_aliases (vault_path, canonical_path, inode, device)
-    VALUES (?, ?, ?, ?)
-  `);
-	db.transaction((groups) => {
-		for (const group of groups) for (const alias of group.aliases) {
-			insertAlias.run(alias.vaultRelPath, group.canonical.vaultRelPath, alias.inode, alias.device);
-			result.aliasesRecorded++;
-		}
-	})(inodeGroups);
+	const allAliases = [];
+	for (const group of inodeGroups) for (const alias of group.aliases) {
+		allAliases.push({
+			vaultPath: alias.vaultRelPath,
+			canonicalPath: group.canonical.vaultRelPath,
+			inode: alias.inode,
+			device: alias.device
+		});
+		result.aliasesRecorded++;
+	}
+	const canonicalPaths = new Set(inodeGroups.map((g) => g.canonical.vaultRelPath));
+	for (const canonPath of canonicalPaths) await backend.deleteVaultAliases(canonPath);
+	if (allAliases.length > 0) await backend.upsertVaultAliases(allAliases);
 	await yieldToEventLoop();
-	db.exec("DELETE FROM vault_name_index");
-	const insertNameIndex = db.prepare(`
-    INSERT OR REPLACE INTO vault_name_index (name, vault_path) VALUES (?, ?)
-  `);
-	const insertNameIndexTx = db.transaction((entries) => {
-		for (const [name, path] of entries) insertNameIndex.run(name, path);
-	});
 	const nameEntries = [];
-	for (const [name, paths] of nameIndex) for (const path of paths) nameEntries.push([name, path]);
-	insertNameIndexTx(nameEntries);
+	for (const [name, paths] of nameIndex) for (const path of paths) nameEntries.push({
+		name,
+		vaultPath: path
+	});
+	await backend.replaceNameIndex(nameEntries);
 	await yieldToEventLoop();
-	db.exec("DELETE FROM vault_links");
-	const insertLink = db.prepare(`
-    INSERT OR IGNORE INTO vault_links
-      (source_path, target_raw, target_path, link_type, line_number)
-    VALUES (?, ?, ?, ?, ?)
-  `);
 	const linkRows = [];
+	const allSourcePaths = [];
+	let linkParseYield = 0;
 	for (const group of inodeGroups) {
+		if (linkParseYield++ % VAULT_YIELD_EVERY === 0) await yieldToEventLoop();
 		const { canonical } = group;
+		allSourcePaths.push(canonical.vaultRelPath);
 		let content;
 		try {
 			content = readFileSync(canonical.absPath, "utf8");
 		} catch {
 			continue;
 		}
-		const parsedLinks = parseWikilinks(content);
+		const parsedLinks = parseLinks(content);
 		for (const link of parsedLinks) {
 			const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);
+			let linkType;
+			if (link.isMdLink) linkType = link.isEmbed ? "md-embed" : "md-link";
+			else linkType = link.isEmbed ? "embed" : "wikilink";
 			linkRows.push({
-				source: canonical.vaultRelPath,
-				raw: link.raw,
-				target,
-				linkType: link.isEmbed ? "embed" : "wikilink",
+				sourcePath: canonical.vaultRelPath,
+				targetRaw: link.raw,
+				targetPath: target,
+				linkType,
 				lineNumber: link.lineNumber
 			});
 		}
 	}
-	db.transaction((rows) => {
-		for (const row of rows) insertLink.run(row.source, row.raw, row.target, row.linkType, row.lineNumber);
-	})(linkRows);
+	const LINK_BATCH_SIZE = 500;
+	for (let i = 0; i < allSourcePaths.length; i += LINK_BATCH_SIZE) {
+		const batchSources = allSourcePaths.slice(i, i + LINK_BATCH_SIZE);
+		const batchLinks = linkRows.filter((r) => batchSources.includes(r.sourcePath));
+		await backend.replaceLinksForSources(batchSources, batchLinks);
+		await yieldToEventLoop();
+	}
 	result.linksExtracted = linkRows.length;
-	result.deadLinksFound = linkRows.filter((r) => r.target === null).length;
+	result.deadLinksFound = linkRows.filter((r) => r.targetPath === null).length;
 	await yieldToEventLoop();
-	const outboundCounts = db.prepare(`SELECT source_path, COUNT(*) AS cnt FROM vault_links GROUP BY source_path`).all();
-	const deadLinkCounts = db.prepare(`SELECT source_path, COUNT(*) AS cnt FROM vault_links
-       WHERE target_path IS NULL GROUP BY source_path`).all();
-	const inboundCounts = db.prepare(`SELECT target_path, COUNT(*) AS cnt FROM vault_links
-       WHERE target_path IS NOT NULL GROUP BY target_path`).all();
-	const outboundMap = new Map(outboundCounts.map((r) => [r.source_path, r.cnt]));
-	const deadMap = new Map(deadLinkCounts.map((r) => [r.source_path, r.cnt]));
-	const inboundMap = new Map(inboundCounts.map((r) => [r.target_path, r.cnt]));
-	const upsertHealth = db.prepare(`
-    INSERT INTO vault_health
-      (vault_path, inbound_count, outbound_count, dead_link_count, is_orphan, computed_at)
-    VALUES (?, ?, ?, ?, ?, ?)
-    ON CONFLICT(vault_path) DO UPDATE SET
-      inbound_count   = excluded.inbound_count,
-      outbound_count  = excluded.outbound_count,
-      dead_link_count = excluded.dead_link_count,
-      is_orphan       = excluded.is_orphan,
-      computed_at     = excluded.computed_at
-  `);
+	const outboundMap = /* @__PURE__ */ new Map();
+	const deadMap = /* @__PURE__ */ new Map();
+	const inboundMap = /* @__PURE__ */ new Map();
+	for (const row of linkRows) {
+		outboundMap.set(row.sourcePath, (outboundMap.get(row.sourcePath) ?? 0) + 1);
+		if (row.targetPath === null) deadMap.set(row.sourcePath, (deadMap.get(row.sourcePath) ?? 0) + 1);
+		else inboundMap.set(row.targetPath, (inboundMap.get(row.targetPath) ?? 0) + 1);
+	}
 	const computedAt = Date.now();
 	let orphanCount = 0;
-	db.transaction((groups) => {
-		for (const group of groups) {
+	const HEALTH_BATCH_SIZE = 500;
+	for (let i = 0; i < inodeGroups.length; i += HEALTH_BATCH_SIZE) {
+		const healthRows = inodeGroups.slice(i, i + HEALTH_BATCH_SIZE).map((group) => {
 			const path = group.canonical.vaultRelPath;
 			const inbound = inboundMap.get(path) ?? 0;
 			const outbound = outboundMap.get(path) ?? 0;
 			const dead = deadMap.get(path) ?? 0;
-			const isOrphan = inbound === 0 ? 1 : 0;
+			const isOrphan = inbound === 0;
 			if (isOrphan) orphanCount++;
-			upsertHealth.run(path, inbound, outbound, dead, isOrphan, computedAt);
-		}
-	})(inodeGroups);
+			return {
+				vaultPath: path,
+				inboundCount: inbound,
+				outboundCount: outbound,
+				deadLinkCount: dead,
+				isOrphan,
+				computedAt
+			};
+		});
+		await backend.upsertVaultHealth(healthRows);
+		await yieldToEventLoop();
+	}
 	result.orphansFound = orphanCount;
 	result.elapsed = Date.now() - startTime;
 	return result;
@@ -496,4 +532,4 @@ async function indexVault(db, vaultProjectId, vaultRoot) {
 
 //#endregion
 export { indexVault };
-//# sourceMappingURL=vault-indexer-DXWs9pDn.mjs.map
+//# sourceMappingURL=vault-indexer-Bi2cRmn7.mjs.map

package/dist/vault-indexer-Bi2cRmn7.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"vault-indexer-Bi2cRmn7.mjs","names":[],"sources":["../src/memory/vault/walk.ts","../src/memory/vault/deduplicate.ts","../src/memory/vault/parse-links.ts","../src/memory/vault/name-index.ts","../src/memory/vault/resolve.ts","../src/memory/vault/indexer.ts"],"sourcesContent":["/**\n * Vault directory walker — follows symlinks with cycle detection.\n */\n\nimport { statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative } from \"node:path\";\nimport type { VaultFile } from \"./types.js\";\n\n/** Maximum number of .md files to collect from a vault. */\nconst VAULT_MAX_FILES = 10_000;\n\n/** Maximum recursion depth for vault directory walks. */\nconst VAULT_MAX_DEPTH = 10;\n\n/**\n * Directories to always skip, at any depth, during vault walks.\n * Includes standard build/VCS noise plus Obsidian-specific directories.\n */\nconst VAULT_SKIP_DIRS = new Set([\n  // Version control\n  \".git\",\n  // Dependency directories (any language)\n  \"node_modules\",\n  \"vendor\",\n  \"Pods\",\n  // Build / compile output\n  \"dist\",\n  \"build\",\n  \"out\",\n  \"DerivedData\",\n  \".next\",\n  // Python virtual environments and caches\n  \".venv\",\n  \"venv\",\n  \"__pycache__\",\n  // General caches\n  \".cache\",\n  \".bun\",\n  // Obsidian internals\n  \".obsidian\",\n  \".trash\",\n]);\n\n/**\n * Recursively collect all .md files under a vault root, following symlinks.\n *\n * Symlink-following behaviour:\n *  - Symbolic links to files: followed if the target is a .md file\n *  - Symbolic links to directories: followed with cycle detection via inode\n *\n * Cycle detection is based on the real inode of each visited directory.\n * Using the real stat (not lstat) ensures that symlinked dirs resolve to\n * their actual inode, preventing infinite loops.\n *\n * @param vaultRoot  Absolute path to the vault root directory.\n * @param opts       Optional overrides for maxFiles and maxDepth.\n */\nexport function walkVaultMdFiles(\n  vaultRoot: string,\n  opts?: { maxFiles?: number; maxDepth?: number },\n): VaultFile[] {\n  const maxFiles = opts?.maxFiles ?? VAULT_MAX_FILES;\n  const maxDepth = opts?.maxDepth ?? VAULT_MAX_DEPTH;\n\n  const results: VaultFile[] = [];\n  const visitedDirs = new Set<string>();\n\n  function walk(dir: string, depth: number): void {\n    if (results.length >= maxFiles) return;\n    if (depth > maxDepth) return;\n\n    // Get the real inode of this directory (follows symlinks on the dir itself)\n    let dirStat: ReturnType<typeof statSync>;\n    try {\n      dirStat = statSync(dir);\n    } catch {\n      return; // Unreadable or broken symlink — skip\n    }\n\n    const dirKey = `${dirStat.dev}:${dirStat.ino}`;\n    if (visitedDirs.has(dirKey)) return; // Cycle detected\n    visitedDirs.add(dirKey);\n\n    let entries: import(\"node:fs\").Dirent<string>[];\n    try {\n      entries = readdirSync(dir, { withFileTypes: true, encoding: \"utf8\" });\n    } catch {\n      return; // Unreadable directory — skip\n    }\n\n    for (const entry of entries) {\n      if (results.length >= maxFiles) break;\n      if (VAULT_SKIP_DIRS.has(entry.name)) continue;\n\n      const full = join(dir, entry.name);\n\n      if (entry.isSymbolicLink()) {\n        // Follow the symlink — resolve to real target\n        let targetStat: ReturnType<typeof statSync>;\n        try {\n          targetStat = statSync(full); // statSync follows symlinks\n        } catch {\n          continue; // Broken symlink — skip\n        }\n\n        if (targetStat.isDirectory()) {\n          if (!VAULT_SKIP_DIRS.has(entry.name)) {\n            walk(full, depth + 1);\n          }\n        } else if (targetStat.isFile() && entry.name.endsWith(\".md\")) {\n          results.push({\n            absPath: full,\n            vaultRelPath: relative(vaultRoot, full),\n            inode: targetStat.ino,\n            device: targetStat.dev,\n          });\n        }\n      } else if (entry.isDirectory()) {\n        walk(full, depth + 1);\n      } else if (entry.isFile() && entry.name.endsWith(\".md\")) {\n        let fileStat: ReturnType<typeof statSync>;\n        try {\n          fileStat = statSync(full);\n        } catch {\n          continue;\n        }\n        results.push({\n          absPath: full,\n          vaultRelPath: relative(vaultRoot, full),\n          inode: fileStat.ino,\n          device: fileStat.dev,\n        });\n      }\n    }\n  }\n\n  if (existsSync(vaultRoot)) {\n    walk(vaultRoot, 0);\n  }\n\n  return results;\n}\n","/**\n * Inode-based deduplication for vault files.\n */\n\nimport type { VaultFile, InodeGroup } from \"./types.js\";\n\n/**\n * Group vault files by inode identity (device + inode).\n *\n * Within each group, the canonical file is chosen as the one with the\n * fewest path separators (shallowest), breaking ties by shortest string.\n * All other group members become aliases.\n */\nexport function deduplicateByInode(files: VaultFile[]): InodeGroup[] {\n  const groups = new Map<string, VaultFile[]>();\n\n  for (const file of files) {\n    const key = `${file.device}:${file.inode}`;\n    const existing = groups.get(key);\n    if (existing) {\n      existing.push(file);\n    } else {\n      groups.set(key, [file]);\n    }\n  }\n\n  const result: InodeGroup[] = [];\n\n  for (const group of groups.values()) {\n    if (group.length === 0) continue;\n\n    // Sort: fewest path separators first, then shortest string\n    const sorted = [...group].sort((a, b) => {\n      const aDepth = (a.vaultRelPath.match(/\\//g) ?? []).length;\n      const bDepth = (b.vaultRelPath.match(/\\//g) ?? []).length;\n      if (aDepth !== bDepth) return aDepth - bDepth;\n      return a.vaultRelPath.length - b.vaultRelPath.length;\n    });\n\n    const [canonical, ...aliases] = sorted as [VaultFile, ...VaultFile[]];\n    result.push({ canonical, aliases });\n  }\n\n  return result;\n}\n","/**\n * Markdown link parser for vault files.\n *\n * Handles wikilinks ([[target]]), markdown links ([text](path)),\n * embeds (![[target]]), and frontmatter wikilinks.\n */\n\nimport type { ParsedLink } from \"./types.js\";\n\n/**\n * Parse all links from markdown content.\n *\n * Handles:\n *  - Standard wikilinks: [[Target Note]]\n *  - Aliased wikilinks: [[Target Note|Display Text]]\n *  - Heading anchors: [[Target Note#Heading]] (stripped for resolution)\n *  - Embeds: ![[Target Note]]\n *  - Frontmatter wikilinks (YAML between --- delimiters)\n *  - Markdown links: [text](path/to/note.md)\n *  - Markdown embeds: ![alt](image.png)\n *\n * External URLs (http://, https://, mailto:, etc.) are excluded — only\n * relative paths are treated as vault links.\n *\n * @param content  Raw markdown file content.\n * @returns        Array of parsed links in document order.\n */\nexport function parseLinks(content: string): ParsedLink[] {\n  const links: ParsedLink[] = [];\n  const lines = content.split(\"\\n\");\n\n  // Determine frontmatter range (YAML between opening and closing ---)\n  let frontmatterEnd = 0;\n  if (content.startsWith(\"---\")) {\n    const closingIdx = content.indexOf(\"\\n---\", 3);\n    if (closingIdx !== -1) {\n      frontmatterEnd = content.slice(0, closingIdx + 4).split(\"\\n\").length - 1;\n    }\n  }\n\n  // Regex for [[wikilinks]] and ![[embeds]]\n  const wikilinkRe = /(!?)\\[\\[([^\\]]+?)\\]\\]/g;\n\n  // Regex for markdown links [text](target) and embeds ![alt](target)\n  const mdLinkRe = /(!)?\\[([^\\]]*)\\]\\(([^)]+)\\)/g;\n\n  for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {\n    const line = lines[lineIdx]!;\n    const lineNumber = lineIdx + 1; // 1-indexed\n    const isFrontmatter = lineIdx < frontmatterEnd;\n\n    // --- Wikilinks ---\n    wikilinkRe.lastIndex = 0;\n    let match: RegExpExecArray | null;\n    while ((match = wikilinkRe.exec(line)) !== null) {\n      const isEmbed = match[1] === \"!\";\n      const inner = match[2]!;\n\n      // Split on first | for alias\n      const pipeIdx = inner.indexOf(\"|\");\n      const beforePipe = pipeIdx === -1 ? inner : inner.slice(0, pipeIdx);\n      const alias = pipeIdx === -1 ? null : inner.slice(pipeIdx + 1);\n\n      // Strip heading anchor (everything after #)\n      const hashIdx = beforePipe.indexOf(\"#\");\n      const raw = hashIdx === -1 ? beforePipe.trim() : beforePipe.slice(0, hashIdx).trim();\n\n      if (!raw) continue; // Skip links with empty targets (e.g. [[#Heading]])\n\n      links.push({\n        raw,\n        alias: alias?.trim() ?? null,\n        lineNumber,\n        isEmbed: isEmbed && !isFrontmatter,\n        isMdLink: false,\n      });\n    }\n\n    // --- Markdown links --- (skip inside frontmatter)\n    if (!isFrontmatter) {\n      mdLinkRe.lastIndex = 0;\n      while ((match = mdLinkRe.exec(line)) !== null) {\n        const isEmbed = match[1] === \"!\";\n        const displayText = match[2]!;\n        let target = match[3]!.trim();\n\n        // Skip external URLs\n        if (/^[a-z][a-z0-9+.-]*:/i.test(target)) continue;\n\n        // Skip pure anchor links (#heading)\n        if (target.startsWith(\"#\")) continue;\n\n        // Strip heading anchor from target\n        const hashIdx = target.indexOf(\"#\");\n        if (hashIdx !== -1) target = target.slice(0, hashIdx);\n\n        // URL-decode (Obsidian encodes spaces as %20 in md links)\n        try {\n          target = decodeURIComponent(target);\n        } catch {\n          // Malformed encoding — use as-is\n        }\n\n        // Strip .md extension for resolution (resolveWikilink adds it back)\n        const raw = target.replace(/\\.md$/i, \"\").trim();\n        if (!raw) continue;\n\n        links.push({\n          raw,\n          alias: displayText || null,\n          lineNumber,\n          isEmbed,\n          isMdLink: true,\n        });\n      }\n    }\n  }\n\n  return links;\n}\n\n/** @deprecated Use {@link parseLinks} instead. */\nexport const parseWikilinks = parseLinks;\n","/**\n * Name index builder for Obsidian wikilink resolution.\n */\n\nimport { basename } from \"node:path\";\nimport type { VaultFile } from \"./types.js\";\n\n/**\n * Build a name lookup index for Obsidian wikilink resolution.\n *\n * Maps lowercase filename (without .md extension) to all vault-relative paths\n * that share that name. Includes both canonical paths and alias paths so that\n * wikilinks resolve regardless of which path the file is accessed through.\n */\nexport function buildNameIndex(files: VaultFile[]): Map<string, string[]> {\n  const index = new Map<string, string[]>();\n\n  for (const file of files) {\n    const name = basename(file.vaultRelPath, \".md\").toLowerCase();\n    const existing = index.get(name);\n    if (existing) {\n      existing.push(file.vaultRelPath);\n    } else {\n      index.set(name, [file.vaultRelPath]);\n    }\n  }\n\n  return index;\n}\n","/**\n * Wikilink resolver using Obsidian's shortest-match algorithm.\n */\n\nimport { normalize, basename, dirname } from \"node:path\";\n\n/**\n * Resolve a wikilink target to a vault-relative path using Obsidian's rules.\n *\n * Resolution algorithm:\n *  1. If raw contains \"/\", attempt exact path match (with and without .md).\n *  2. Normalize: lowercase the raw target, strip .md extension.\n *  3. Look up in the name index (all files with that basename).\n *  4. If exactly one match, return it.\n *  5. If multiple matches, pick the one closest to the source file\n *     (longest common directory prefix, then shortest overall path).\n *  6. If no matches, return null (dead link).\n *\n * @param raw         The raw link target (heading-stripped, pipe-stripped).\n * @param nameIndex   Map from lowercase basename-without-ext to vault paths.\n * @param sourcePath  Vault-relative path of the file containing the link.\n * @returns           Vault-relative path of the resolved target, or null.\n */\nexport function resolveWikilink(\n  raw: string,\n  nameIndex: Map<string, string[]>,\n  sourcePath: string,\n): string | null {\n  if (!raw) return null;\n\n  // Case 1: path contains \"/\" — try exact match with and without .md\n  if (raw.includes(\"/\")) {\n    const normalized = normalize(raw);\n    const normalizedMd = normalized.endsWith(\".md\") ? normalized : normalized + \".md\";\n\n    // Check if any indexed path matches (case-insensitive for macOS compatibility)\n    for (const [, paths] of nameIndex) {\n      for (const p of paths) {\n        if (p === normalizedMd || p === normalized) return p;\n        if (p.toLowerCase() === normalizedMd.toLowerCase()) return p;\n      }\n    }\n    // Fall through to name lookup in case the path prefix was wrong\n  }\n\n  // Normalize the raw target for name lookup.\n  // Use the basename only — Obsidian resolves by filename, not full path.\n  const rawBase = basename(raw)\n    .replace(/\\.md$/i, \"\")\n    .toLowerCase()\n    .trim();\n\n  if (!rawBase) return null;\n\n  const candidates = nameIndex.get(rawBase);\n\n  if (!candidates || candidates.length === 0) {\n    return null; // Dead link\n  }\n\n  if (candidates.length === 1) {\n    return candidates[0]!;\n  }\n\n  // Multiple matches — pick the one closest to the source file\n  const sourceDir = dirname(sourcePath);\n\n  let bestPath: string | null = null;\n  let bestPrefixLen = -1;\n  let bestPathLen = Infinity;\n\n  for (const candidate of candidates) {\n    const candidateDir = dirname(candidate);\n    const prefixLen = commonPrefixLength(sourceDir, candidateDir);\n    const pathLen = candidate.length;\n\n    if (\n      prefixLen > bestPrefixLen ||\n      (prefixLen === bestPrefixLen && pathLen < bestPathLen)\n    ) {\n      bestPrefixLen = prefixLen;\n      bestPathLen = pathLen;\n      bestPath = candidate;\n    }\n  }\n\n  return bestPath;\n}\n\n/**\n * Compute the length of the common prefix between two directory paths,\n * measured in path segments (not raw characters).\n *\n * Example: \"a/b/c\" and \"a/b/d\" → 2 (common: \"a\", \"b\")\n */\nfunction commonPrefixLength(a: string, b: string): number {\n  if (a === \".\" && b === \".\") return 0;\n  const aParts = a === \".\" ? [] : a.split(\"/\");\n  const bParts = b === \".\" ? [] : b.split(\"/\");\n  let count = 0;\n  const len = Math.min(aParts.length, bParts.length);\n  for (let i = 0; i < len; i++) {\n    if (aParts[i] === bParts[i]) {\n      count++;\n    } else {\n      break;\n    }\n  }\n  return count;\n}\n","/**\n * Main vault indexing orchestrator.\n *\n * Indexes an entire Obsidian vault (or any markdown knowledge base), following\n * symlinks, deduplicating files by inode, parsing wikilinks, and computing\n * per-file health metrics (orphan detection, dead links).\n *\n * Key differences from the project indexer (indexer/sync.ts):\n *  - Follows symbolic links (project indexer skips them)\n *  - Deduplicates files with the same inode (same content reachable via multiple paths)\n *  - Parses [[wikilinks]] and builds a directed link graph\n *  - Resolves wikilinks using Obsidian's shortest-match algorithm\n *  - Computes health metrics per file: inbound/outbound link counts, dead links, orphans\n */\n\nimport { readFileSync } from \"node:fs\";\nimport { basename } from \"node:path\";\nimport type {\n  StorageBackend,\n  VaultFileRow,\n  VaultAliasRow,\n  VaultLinkRow,\n  VaultHealthRow,\n  VaultNameEntry,\n  ChunkRow,\n} from \"../../storage/interface.js\";\nimport { chunkMarkdown } from \"../chunker.js\";\nimport { sha256File, chunkId, yieldToEventLoop } from \"../indexer/helpers.js\";\nimport { walkVaultMdFiles } from \"./walk.js\";\nimport { deduplicateByInode } from \"./deduplicate.js\";\nimport { parseLinks } from \"./parse-links.js\";\nimport { buildNameIndex } from \"./name-index.js\";\nimport { resolveWikilink } from \"./resolve.js\";\nimport type { VaultIndexResult } from \"./types.js\";\n\n/** Number of files to process before yielding to the event loop. */\nconst VAULT_YIELD_EVERY = 1;\n\n/**\n * Index an entire Obsidian vault (or markdown knowledge base) using the\n * async StorageBackend interface.\n *\n * Steps:\n *  1. Walk vault root, following symlinks.\n *  2. Deduplicate by inode — each unique file is indexed once.\n *  3. Build a name index for wikilink resolution.\n *  4. For each canonical file:\n *     a. SHA-256 hash for change detection — skip unchanged files.\n *     b. Read content, chunk with chunkMarkdown().\n *     c. Insert chunks into backend (memory_chunks and memory_fts).\n *     d. Upsert vault_files row.\n *  5. Record aliases in vault_aliases.\n *  6. Rebuild vault_name_index table.\n *  7. Rebuild vault_links:\n *     a. Parse [[wikilinks]] from each canonical file.\n *     b. Resolve each link with resolveWikilink().\n *     c. Insert into vault_links.\n *  8. Compute and upsert health metrics (vault_health).\n *  9. Return statistics.\n *\n * @param backend         StorageBackend to write to.\n * @param vaultProjectId  Registry project ID for the vault \"project\".\n * @param vaultRoot       Absolute path to the vault root directory.\n */\nexport async function indexVault(\n  backend: StorageBackend,\n  vaultProjectId: number,\n  vaultRoot: string,\n): Promise<VaultIndexResult> {\n  const startTime = Date.now();\n\n  const result: VaultIndexResult = {\n    filesIndexed: 0,\n    chunksCreated: 0,\n    filesSkipped: 0,\n    aliasesRecorded: 0,\n    linksExtracted: 0,\n    deadLinksFound: 0,\n    orphansFound: 0,\n    elapsed: 0,\n  };\n\n  // Step 1: Walk vault, collecting all .md files (follows symlinks)\n  const allFiles = walkVaultMdFiles(vaultRoot);\n\n  // Step 2: Deduplicate by inode\n  const inodeGroups = deduplicateByInode(allFiles);\n\n  // Step 3: Build name index (from all files including aliases, for resolution)\n  const nameIndex = buildNameIndex(allFiles);\n\n  // Step 4: Index each canonical file\n  await yieldToEventLoop();\n  let filesSinceYield = 0;\n\n  for (const group of inodeGroups) {\n    if (filesSinceYield >= VAULT_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const { canonical } = group;\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      result.filesSkipped++;\n      continue;\n    }\n\n    const hash = sha256File(content);\n\n    // Change detection: skip if hash is unchanged\n    const existing = await backend.getVaultFile(canonical.vaultRelPath);\n    if (existing?.hash === hash) {\n      result.filesSkipped++;\n      continue;\n    }\n\n    // Delete old chunks for this vault path\n    await backend.deleteChunksForFile(vaultProjectId, canonical.vaultRelPath);\n\n    // Chunk the content\n    const chunks = chunkMarkdown(content);\n    const updatedAt = Date.now();\n\n    // Extract title from first H1 heading or filename\n    const titleMatch = /^#\\s+(.+)$/m.exec(content);\n    const title = titleMatch\n      ? titleMatch[1]!.trim()\n      : basename(canonical.vaultRelPath, \".md\");\n\n    // Build chunk rows\n    const chunkRows: ChunkRow[] = [];\n    for (let i = 0; i < chunks.length; i++) {\n      const chunk = chunks[i]!;\n      const id = chunkId(\n        vaultProjectId,\n        canonical.vaultRelPath,\n        i,\n        chunk.startLine,\n        chunk.endLine,\n      );\n      chunkRows.push({\n        id,\n        projectId: vaultProjectId,\n        source: \"vault\",\n        tier: \"topic\",\n        path: canonical.vaultRelPath,\n        startLine: chunk.startLine,\n        endLine: chunk.endLine,\n        hash: chunk.hash,\n        text: chunk.text,\n        updatedAt,\n      });\n    }\n\n    if (chunkRows.length > 0) {\n      await backend.insertChunks(chunkRows);\n    }\n\n    // Upsert vault file record\n    const vaultFileRow: VaultFileRow = {\n      vaultPath: canonical.vaultRelPath,\n      inode: canonical.inode,\n      device: canonical.device,\n      hash,\n      title,\n      indexedAt: updatedAt,\n    };\n    await backend.upsertVaultFile(vaultFileRow);\n\n    result.filesIndexed++;\n    result.chunksCreated += chunks.length;\n  }\n\n  // Step 5: Record aliases in vault_aliases\n  await yieldToEventLoop();\n\n  const allAliases: VaultAliasRow[] = [];\n  for (const group of inodeGroups) {\n    for (const alias of group.aliases) {\n      allAliases.push({\n        vaultPath: alias.vaultRelPath,\n        canonicalPath: group.canonical.vaultRelPath,\n        inode: alias.inode,\n        device: alias.device,\n      });\n      result.aliasesRecorded++;\n    }\n  }\n\n  const canonicalPaths = new Set(inodeGroups.map((g) => g.canonical.vaultRelPath));\n  for (const canonPath of canonicalPaths) {\n    await backend.deleteVaultAliases(canonPath);\n  }\n  if (allAliases.length > 0) {\n    await backend.upsertVaultAliases(allAliases);\n  }\n\n  // Step 6: Rebuild vault_name_index\n  await yieldToEventLoop();\n\n  const nameEntries: VaultNameEntry[] = [];\n  for (const [name, paths] of nameIndex) {\n    for (const path of paths) {\n      nameEntries.push({ name, vaultPath: path });\n    }\n  }\n  await backend.replaceNameIndex(nameEntries);\n\n  // Step 7: Rebuild vault_links\n  await yieldToEventLoop();\n\n  const linkRows: VaultLinkRow[] = [];\n  const allSourcePaths: string[] = [];\n\n  let linkParseYield = 0;\n  for (const group of inodeGroups) {\n    if (linkParseYield++ % VAULT_YIELD_EVERY === 0) {\n      await yieldToEventLoop();\n    }\n\n    const { canonical } = group;\n    allSourcePaths.push(canonical.vaultRelPath);\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      continue;\n    }\n\n    const parsedLinks = parseLinks(content);\n    for (const link of parsedLinks) {\n      const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);\n      let linkType: string;\n      if (link.isMdLink) {\n        linkType = link.isEmbed ? \"md-embed\" : \"md-link\";\n      } else {\n        linkType = link.isEmbed ? \"embed\" : \"wikilink\";\n      }\n      linkRows.push({\n        sourcePath: canonical.vaultRelPath,\n        targetRaw: link.raw,\n        targetPath: target,\n        linkType,\n        lineNumber: link.lineNumber,\n      });\n    }\n  }\n\n  // Replace all links for all sources in batches of 500\n  const LINK_BATCH_SIZE = 500;\n  for (let i = 0; i < allSourcePaths.length; i += LINK_BATCH_SIZE) {\n    const batchSources = allSourcePaths.slice(i, i + LINK_BATCH_SIZE);\n    const batchLinks = linkRows.filter((r) => batchSources.includes(r.sourcePath));\n    await backend.replaceLinksForSources(batchSources, batchLinks);\n    await yieldToEventLoop();\n  }\n\n  result.linksExtracted = linkRows.length;\n  result.deadLinksFound = linkRows.filter((r) => r.targetPath === null).length;\n\n  // Step 8: Compute and upsert vault_health metrics\n  await yieldToEventLoop();\n\n  const outboundMap = new Map<string, number>();\n  const deadMap = new Map<string, number>();\n  const inboundMap = new Map<string, number>();\n\n  for (const row of linkRows) {\n    outboundMap.set(row.sourcePath, (outboundMap.get(row.sourcePath) ?? 0) + 1);\n    if (row.targetPath === null) {\n      deadMap.set(row.sourcePath, (deadMap.get(row.sourcePath) ?? 0) + 1);\n    } else {\n      inboundMap.set(row.targetPath, (inboundMap.get(row.targetPath) ?? 0) + 1);\n    }\n  }\n\n  const computedAt = Date.now();\n  let orphanCount = 0;\n\n  const HEALTH_BATCH_SIZE = 500;\n  for (let i = 0; i < inodeGroups.length; i += HEALTH_BATCH_SIZE) {\n    const batch = inodeGroups.slice(i, i + HEALTH_BATCH_SIZE);\n    const healthRows: VaultHealthRow[] = batch.map((group) => {\n      const path = group.canonical.vaultRelPath;\n      const inbound = inboundMap.get(path) ?? 0;\n      const outbound = outboundMap.get(path) ?? 0;\n      const dead = deadMap.get(path) ?? 0;\n      const isOrphan = inbound === 0;\n      if (isOrphan) orphanCount++;\n      return {\n        vaultPath: path,\n        inboundCount: inbound,\n        outboundCount: outbound,\n        deadLinkCount: dead,\n        isOrphan,\n        computedAt,\n      };\n    });\n    await backend.upsertVaultHealth(healthRows);\n    await yieldToEventLoop();\n  }\n\n  result.orphansFound = orphanCount;\n  result.elapsed = Date.now() - startTime;\n\n  return 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