@tekmidian/pai 0.2.2 → 0.3.0

package/dist/vault-indexer-Bo2aPSzP.mjs

@@ -0,0 +1,499 @@
+import { t as chunkMarkdown } from "./chunker-CbnBe0s0.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
+/**
+* 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
+*/
+/** 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.
+*/
+const VAULT_SKIP_DIRS = new Set([
+	".git",
+	"node_modules",
+	"vendor",
+	"Pods",
+	"dist",
+	"build",
+	"out",
+	"DerivedData",
+	".next",
+	".venv",
+	"venv",
+	"__pycache__",
+	".cache",
+	".bun",
+	".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}:${endLine}`).digest("hex");
+}
+function yieldToEventLoop() {
+	return new Promise((resolve) => setImmediate(resolve));
+}
+/**
+* Recursively collect all .md files under a vault root, following symlinks.
+*
+* Symlink-following behaviour:
+*  - Symbolic links to files: followed if the target is a .md file
+*  - Symbolic links to directories: followed with cycle detection via inode
+*
+* Cycle detection is based on the real inode of each visited directory.
+* Using the real stat (not lstat) ensures that symlinked dirs resolve to
+* their actual inode, preventing infinite loops.
+*
+* @param dir        Directory to scan.
+* @param vaultRoot  Absolute root of the vault (for computing vaultRelPath).
+* @param acc        Shared accumulator (mutated in place for early exit).
+* @param visited    Set of "device:inode" strings for visited directories.
+* @param depth      Current recursion depth.
+*/
+function walkVaultMdFiles(vaultRoot, opts) {
+	const maxFiles = opts?.maxFiles ?? VAULT_MAX_FILES;
+	const maxDepth = opts?.maxDepth ?? VAULT_MAX_DEPTH;
+	const results = [];
+	const visitedDirs = /* @__PURE__ */ new Set();
+	function walk(dir, depth) {
+		if (results.length >= maxFiles) return;
+		if (depth > maxDepth) return;
+		let dirStat;
+		try {
+			dirStat = statSync(dir);
+		} catch {
+			return;
+		}
+		const dirKey = `${dirStat.dev}:${dirStat.ino}`;
+		if (visitedDirs.has(dirKey)) return;
+		visitedDirs.add(dirKey);
+		let entries;
+		try {
+			entries = readdirSync(dir, {
+				withFileTypes: true,
+				encoding: "utf8"
+			});
+		} catch {
+			return;
+		}
+		for (const entry of entries) {
+			if (results.length >= maxFiles) break;
+			if (VAULT_SKIP_DIRS.has(entry.name)) continue;
+			const full = join(dir, entry.name);
+			if (entry.isSymbolicLink()) {
+				let targetStat;
+				try {
+					targetStat = statSync(full);
+				} catch {
+					continue;
+				}
+				if (targetStat.isDirectory()) {
+					if (!VAULT_SKIP_DIRS.has(entry.name)) walk(full, depth + 1);
+				} else if (targetStat.isFile() && entry.name.endsWith(".md")) results.push({
+					absPath: full,
+					vaultRelPath: relative(vaultRoot, full),
+					inode: targetStat.ino,
+					device: targetStat.dev
+				});
+			} else if (entry.isDirectory()) walk(full, depth + 1);
+			else if (entry.isFile() && entry.name.endsWith(".md")) {
+				let fileStat;
+				try {
+					fileStat = statSync(full);
+				} catch {
+					continue;
+				}
+				results.push({
+					absPath: full,
+					vaultRelPath: relative(vaultRoot, full),
+					inode: fileStat.ino,
+					device: fileStat.dev
+				});
+			}
+		}
+	}
+	if (existsSync(vaultRoot)) walk(vaultRoot, 0);
+	return results;
+}
+/**
+* Group vault files by inode identity (device + inode).
+*
+* Within each group, the canonical file is chosen as the one with the
+* fewest path separators (shallowest), breaking ties by shortest string.
+* All other group members become aliases.
+*/
+function deduplicateByInode(files) {
+	const groups = /* @__PURE__ */ new Map();
+	for (const file of files) {
+		const key = `${file.device}:${file.inode}`;
+		const existing = groups.get(key);
+		if (existing) existing.push(file);
+		else groups.set(key, [file]);
+	}
+	const result = [];
+	for (const group of groups.values()) {
+		if (group.length === 0) continue;
+		const [canonical, ...aliases] = [...group].sort((a, b) => {
+			const aDepth = (a.vaultRelPath.match(/\//g) ?? []).length;
+			const bDepth = (b.vaultRelPath.match(/\//g) ?? []).length;
+			if (aDepth !== bDepth) return aDepth - bDepth;
+			return a.vaultRelPath.length - b.vaultRelPath.length;
+		});
+		result.push({
+			canonical,
+			aliases
+		});
+	}
+	return result;
+}
+/**
+* Parse all [[wikilinks]] and ![[embeds]] from markdown content.
+*
+* Handles:
+*  - Standard wikilinks: [[Target Note]]
+*  - Aliased wikilinks: [[Target Note|Display Text]]
+*  - Heading anchors: [[Target Note#Heading]] (stripped for resolution)
+*  - Embeds: ![[Target Note]]
+*  - Frontmatter wikilinks (YAML between --- delimiters)
+*
+* @param content  Raw markdown file content.
+* @returns        Array of parsed links in document order.
+*/
+function parseWikilinks(content) {
+	const links = [];
+	const lines = content.split("\n");
+	let frontmatterEnd = 0;
+	if (content.startsWith("---")) {
+		const closingIdx = content.indexOf("\n---", 3);
+		if (closingIdx !== -1) frontmatterEnd = content.slice(0, closingIdx + 4).split("\n").length - 1;
+	}
+	const wikilinkRe = /(!?)\[\[([^\]]+?)\]\]/g;
+	for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {
+		const line = lines[lineIdx];
+		const lineNumber = lineIdx + 1;
+		wikilinkRe.lastIndex = 0;
+		let match;
+		while ((match = wikilinkRe.exec(line)) !== null) {
+			const isEmbed = match[1] === "!";
+			const inner = match[2];
+			const pipeIdx = inner.indexOf("|");
+			const beforePipe = pipeIdx === -1 ? inner : inner.slice(0, pipeIdx);
+			const alias = pipeIdx === -1 ? null : inner.slice(pipeIdx + 1);
+			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
+			});
+		}
+	}
+	return links;
+}
+/**
+* Build a name lookup index for Obsidian wikilink resolution.
+*
+* Maps lowercase filename (without .md extension) to all vault-relative paths
+* that share that name. Includes both canonical paths and alias paths so that
+* wikilinks resolve regardless of which path the file is accessed through.
+*/
+function buildNameIndex(files) {
+	const index = /* @__PURE__ */ new Map();
+	for (const file of files) {
+		const name = basename(file.vaultRelPath, ".md").toLowerCase();
+		const existing = index.get(name);
+		if (existing) existing.push(file.vaultRelPath);
+		else index.set(name, [file.vaultRelPath]);
+	}
+	return index;
+}
+/**
+* Resolve a wikilink target to a vault-relative path using Obsidian's rules.
+*
+* Resolution algorithm:
+*  1. If raw contains "/", attempt exact path match (with and without .md).
+*  2. Normalize: lowercase the raw target, strip .md extension.
+*  3. Look up in the name index (all files with that basename).
+*  4. If exactly one match, return it.
+*  5. If multiple matches, pick the one closest to the source file
+*     (longest common directory prefix, then shortest overall path).
+*  6. If no matches, return null (dead link).
+*
+* @param raw         The raw link target (heading-stripped, pipe-stripped).
+* @param nameIndex   Map from lowercase basename-without-ext to vault paths.
+* @param sourcePath  Vault-relative path of the file containing the link.
+* @returns           Vault-relative path of the resolved target, or null.
+*/
+function resolveWikilink(raw, nameIndex, sourcePath) {
+	if (!raw) return null;
+	if (raw.includes("/")) {
+		const normalized = normalize(raw);
+		const normalizedMd = normalized.endsWith(".md") ? normalized : normalized + ".md";
+		for (const [, paths] of nameIndex) for (const p of paths) {
+			if (p === normalizedMd || p === normalized) return p;
+			if (p.toLowerCase() === normalizedMd.toLowerCase()) return p;
+		}
+	}
+	const rawBase = basename(raw).replace(/\.md$/i, "").toLowerCase().trim();
+	if (!rawBase) return null;
+	const candidates = nameIndex.get(rawBase);
+	if (!candidates || candidates.length === 0) return null;
+	if (candidates.length === 1) return candidates[0];
+	const sourceDir = dirname(sourcePath);
+	let bestPath = null;
+	let bestPrefixLen = -1;
+	let bestPathLen = Infinity;
+	for (const candidate of candidates) {
+		const prefixLen = commonPrefixLength(sourceDir, dirname(candidate));
+		const pathLen = candidate.length;
+		if (prefixLen > bestPrefixLen || prefixLen === bestPrefixLen && pathLen < bestPathLen) {
+			bestPrefixLen = prefixLen;
+			bestPathLen = pathLen;
+			bestPath = candidate;
+		}
+	}
+	return bestPath;
+}
+/**
+* Compute the length of the common prefix between two directory paths,
+* measured in path segments (not raw characters).
+*
+* Example: "a/b/c" and "a/b/d" → 2 (common: "a", "b")
+*/
+function commonPrefixLength(a, b) {
+	if (a === "." && b === ".") return 0;
+	const aParts = a === "." ? [] : a.split("/");
+	const bParts = b === "." ? [] : b.split("/");
+	let count = 0;
+	const len = Math.min(aParts.length, bParts.length);
+	for (let i = 0; i < len; i++) if (aParts[i] === bParts[i]) count++;
+	else break;
+	return count;
+}
+/**
+* Index an entire Obsidian vault (or markdown knowledge base) into the
+* federation database.
+*
+* Steps:
+*  1. Walk vault root, following symlinks.
+*  2. Deduplicate by inode — each unique file is indexed once.
+*  3. Build a name index for wikilink resolution.
+*  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.
+*     d. Upsert vault_files row.
+*  5. Record aliases in vault_aliases.
+*  6. Rebuild vault_name_index table.
+*  7. Rebuild vault_links:
+*     a. Parse [[wikilinks]] from each canonical file.
+*     b. Resolve each link with resolveWikilink().
+*     c. Insert into vault_links.
+*  8. Compute and upsert health metrics (vault_health).
+*  9. Return statistics.
+*
+* @param db              Open federation database.
+* @param vaultProjectId  Registry project ID for the vault "project".
+* @param vaultRoot       Absolute path to the vault root directory.
+*/
+async function indexVault(db, vaultProjectId, vaultRoot) {
+	const startTime = Date.now();
+	const result = {
+		filesIndexed: 0,
+		chunksCreated: 0,
+		filesSkipped: 0,
+		aliasesRecorded: 0,
+		linksExtracted: 0,
+		deadLinksFound: 0,
+		orphansFound: 0,
+		elapsed: 0
+	};
+	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) {
+		if (filesSinceYield >= VAULT_YIELD_EVERY) {
+			await yieldToEventLoop();
+			filesSinceYield = 0;
+		}
+		filesSinceYield++;
+		const { canonical } = group;
+		let content;
+		try {
+			content = readFileSync(canonical.absPath, "utf8");
+		} catch {
+			result.filesSkipped++;
+			continue;
+		}
+		const hash = sha256File(content);
+		if (selectFileHash.get(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);
+		})();
+		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);
+		})();
+		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);
+	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);
+	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 = [];
+	for (const group of inodeGroups) {
+		const { canonical } = group;
+		let content;
+		try {
+			content = readFileSync(canonical.absPath, "utf8");
+		} catch {
+			continue;
+		}
+		const parsedLinks = parseWikilinks(content);
+		for (const link of parsedLinks) {
+			const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);
+			linkRows.push({
+				source: canonical.vaultRelPath,
+				raw: link.raw,
+				target,
+				linkType: link.isEmbed ? "embed" : "wikilink",
+				lineNumber: link.lineNumber
+			});
+		}
+	}
+	db.transaction((rows) => {
+		for (const row of rows) insertLink.run(row.source, row.raw, row.target, row.linkType, row.lineNumber);
+	})(linkRows);
+	result.linksExtracted = linkRows.length;
+	result.deadLinksFound = linkRows.filter((r) => r.target === 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 computedAt = Date.now();
+	let orphanCount = 0;
+	db.transaction((groups) => {
+		for (const group of groups) {
+			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;
+			if (isOrphan) orphanCount++;
+			upsertHealth.run(path, inbound, outbound, dead, isOrphan, computedAt);
+		}
+	})(inodeGroups);
+	result.orphansFound = orphanCount;
+	result.elapsed = Date.now() - startTime;
+	return result;
+}
+
+//#endregion
+export { indexVault };
+//# sourceMappingURL=vault-indexer-Bo2aPSzP.mjs.map

package/dist/vault-indexer-Bo2aPSzP.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"vault-indexer-Bo2aPSzP.mjs","names":[],"sources":["../src/memory/vault-indexer.ts"],"sourcesContent":["/**\n * Vault indexer for the PAI federation memory engine.\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.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 { createHash } from \"node:crypto\";\nimport { readFileSync, statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative, basename, dirname, normalize } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\nimport { chunkMarkdown } from \"./chunker.js\";\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport interface VaultFile {\n  absPath: string;\n  vaultRelPath: string;\n  inode: number;\n  device: number;\n}\n\nexport interface InodeGroup {\n  canonical: VaultFile;\n  aliases: VaultFile[];\n}\n\nexport interface ParsedLink {\n  raw: string;\n  alias: string | null;\n  lineNumber: number;\n  isEmbed: boolean;\n}\n\nexport interface VaultIndexResult {\n  filesIndexed: number;\n  chunksCreated: number;\n  filesSkipped: number;\n  aliasesRecorded: number;\n  linksExtracted: number;\n  deadLinksFound: number;\n  orphansFound: number;\n  elapsed: number;\n}\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\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/** Number of files to process before yielding to the event loop. */\nconst VAULT_YIELD_EVERY = 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// Utility\n// ---------------------------------------------------------------------------\n\nfunction sha256File(content: string): string {\n  return createHash(\"sha256\").update(content).digest(\"hex\");\n}\n\nfunction chunkId(\n  projectId: number,\n  path: string,\n  chunkIndex: number,\n  startLine: number,\n  endLine: number,\n): string {\n  return createHash(\"sha256\")\n    .update(`${projectId}:${path}:${chunkIndex}:${startLine}:${endLine}`)\n    .digest(\"hex\");\n}\n\nfunction yieldToEventLoop(): Promise<void> {\n  return new Promise((resolve) => setImmediate(resolve));\n}\n\n// ---------------------------------------------------------------------------\n// Vault directory walker (follows symlinks)\n// ---------------------------------------------------------------------------\n\n/**\n * Recursively collect all .md files under a vault root, following symlinks.\n *\n * Symlink-following behaviour:\n *  - Symbolic links to files: followed if the target is a .md file\n *  - Symbolic links to directories: followed with cycle detection via inode\n *\n * Cycle detection is based on the real inode of each visited directory.\n * Using the real stat (not lstat) ensures that symlinked dirs resolve to\n * their actual inode, preventing infinite loops.\n *\n * @param dir        Directory to scan.\n * @param vaultRoot  Absolute root of the vault (for computing vaultRelPath).\n * @param acc        Shared accumulator (mutated in place for early exit).\n * @param visited    Set of \"device:inode\" strings for visited directories.\n * @param depth      Current recursion depth.\n */\nexport function walkVaultMdFiles(\n  vaultRoot: string,\n  opts?: { maxFiles?: number; maxDepth?: number },\n): VaultFile[] {\n  const maxFiles = opts?.maxFiles ?? VAULT_MAX_FILES;\n  const maxDepth = opts?.maxDepth ?? VAULT_MAX_DEPTH;\n\n  const results: VaultFile[] = [];\n  const visitedDirs = new Set<string>();\n\n  function walk(dir: string, depth: number): void {\n    if (results.length >= maxFiles) return;\n    if (depth > maxDepth) return;\n\n    // Get the real inode of this directory (follows symlinks on the dir itself)\n    let dirStat: ReturnType<typeof statSync>;\n    try {\n      dirStat = statSync(dir);\n    } catch {\n      return; // Unreadable or broken symlink — skip\n    }\n\n    const dirKey = `${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// ---------------------------------------------------------------------------\n// Inode deduplication\n// ---------------------------------------------------------------------------\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// ---------------------------------------------------------------------------\n// Wikilink parser\n// ---------------------------------------------------------------------------\n\n/**\n * Parse all [[wikilinks]] and ![[embeds]] 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 *\n * @param content  Raw markdown file content.\n * @returns        Array of parsed links in document order.\n */\nexport function parseWikilinks(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  for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {\n    const line = lines[lineIdx]!;\n    const lineNumber = lineIdx + 1; // 1-indexed\n\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      // For frontmatter lines, mark as non-embed regardless of !\n      const isFrontmatter = lineIdx < frontmatterEnd;\n      links.push({\n        raw,\n        alias: alias?.trim() ?? null,\n        lineNumber,\n        isEmbed: isEmbed && !isFrontmatter,\n      });\n    }\n  }\n\n  return links;\n}\n\n// ---------------------------------------------------------------------------\n// Name index builder\n// ---------------------------------------------------------------------------\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// ---------------------------------------------------------------------------\n// Wikilink resolver\n// ---------------------------------------------------------------------------\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  // E.g. \"PAI/20-webseiten/_20-webseiten-master\" → \"_20-webseiten-master\"\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// ---------------------------------------------------------------------------\n// Main vault indexing orchestrator\n// ---------------------------------------------------------------------------\n\n/**\n * Index an entire Obsidian vault (or markdown knowledge base) into the\n * federation database.\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 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 db              Open federation database.\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  db: Database,\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  // ---------------------------------------------------------------------------\n  // Step 1: Walk vault, collecting all .md files (follows symlinks)\n  // ---------------------------------------------------------------------------\n\n  const allFiles = walkVaultMdFiles(vaultRoot);\n\n  // ---------------------------------------------------------------------------\n  // Step 2: Deduplicate by inode\n  // ---------------------------------------------------------------------------\n\n  const inodeGroups = deduplicateByInode(allFiles);\n\n  // ---------------------------------------------------------------------------\n  // Step 3: Build name index (from all files including aliases, for resolution)\n  // ---------------------------------------------------------------------------\n\n  const nameIndex = buildNameIndex(allFiles);\n\n  // ---------------------------------------------------------------------------\n  // Step 4: Prepare SQL statements\n  // ---------------------------------------------------------------------------\n\n  const selectFileHash = db.prepare(\n    \"SELECT hash FROM vault_files WHERE vault_path = ?\",\n  );\n\n  const deleteOldChunkIds = db.prepare(\n    \"SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  const deleteFts = db.prepare(\"DELETE FROM memory_fts WHERE id = ?\");\n\n  const deleteChunks = db.prepare(\n    \"DELETE FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  const insertChunk = db.prepare(`\n    INSERT INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const insertFts = db.prepare(`\n    INSERT INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const upsertVaultFile = db.prepare(`\n    INSERT INTO vault_files (vault_path, inode, device, hash, title, indexed_at)\n    VALUES (?, ?, ?, ?, ?, ?)\n    ON CONFLICT(vault_path) DO UPDATE SET\n      inode      = excluded.inode,\n      device     = excluded.device,\n      hash       = excluded.hash,\n      title      = excluded.title,\n      indexed_at = excluded.indexed_at\n  `);\n\n  // ---------------------------------------------------------------------------\n  // Step 4 (cont.): Index each canonical file\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n  let filesSinceYield = 0;\n\n  for (const group of inodeGroups) {\n    // Yield periodically to keep the IPC server responsive\n    if (filesSinceYield >= VAULT_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const { canonical } = group;\n\n    // Read file content\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 = selectFileHash.get(canonical.vaultRelPath) as\n      | { hash: string }\n      | undefined;\n\n    if (existing?.hash === hash) {\n      result.filesSkipped++;\n      continue;\n    }\n\n    // Delete old chunks for this vault path\n    const oldChunkIds = deleteOldChunkIds.all(\n      vaultProjectId,\n      canonical.vaultRelPath,\n    ) as Array<{ id: string }>;\n\n    db.transaction(() => {\n      for (const row of oldChunkIds) {\n        deleteFts.run(row.id);\n      }\n      deleteChunks.run(vaultProjectId, canonical.vaultRelPath);\n    })();\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    db.transaction(() => {\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        insertChunk.run(\n          id,\n          vaultProjectId,\n          \"vault\",\n          \"topic\",\n          canonical.vaultRelPath,\n          chunk.startLine,\n          chunk.endLine,\n          chunk.hash,\n          chunk.text,\n          updatedAt,\n        );\n        insertFts.run(\n          chunk.text,\n          id,\n          vaultProjectId,\n          canonical.vaultRelPath,\n          \"vault\",\n          \"topic\",\n          chunk.startLine,\n          chunk.endLine,\n        );\n      }\n      upsertVaultFile.run(\n        canonical.vaultRelPath,\n        canonical.inode,\n        canonical.device,\n        hash,\n        title,\n        updatedAt,\n      );\n    })();\n\n    result.filesIndexed++;\n    result.chunksCreated += chunks.length;\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 5: Record aliases in vault_aliases\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  // Clear old aliases for this vault before rebuilding\n  // (We identify vault aliases by checking which canonical paths belong to\n  //  the canonical files we just indexed — simpler to clear + rebuild all.)\n  db.exec(\"DELETE FROM vault_aliases\");\n\n  const insertAlias = db.prepare(`\n    INSERT OR REPLACE INTO vault_aliases (vault_path, canonical_path, inode, device)\n    VALUES (?, ?, ?, ?)\n  `);\n\n  const insertAliasesTx = db.transaction((groups: InodeGroup[]) => {\n    for (const group of groups) {\n      for (const alias of group.aliases) {\n        insertAlias.run(\n          alias.vaultRelPath,\n          group.canonical.vaultRelPath,\n          alias.inode,\n          alias.device,\n        );\n        result.aliasesRecorded++;\n      }\n    }\n  });\n  insertAliasesTx(inodeGroups);\n\n  // ---------------------------------------------------------------------------\n  // Step 6: Rebuild vault_name_index\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  db.exec(\"DELETE FROM vault_name_index\");\n\n  const insertNameIndex = db.prepare(`\n    INSERT OR REPLACE INTO vault_name_index (name, vault_path) VALUES (?, ?)\n  `);\n\n  const insertNameIndexTx = db.transaction(\n    (entries: Array<[string, string]>) => {\n      for (const [name, path] of entries) {\n        insertNameIndex.run(name, path);\n      }\n    },\n  );\n\n  const nameEntries: Array<[string, string]> = [];\n  for (const [name, paths] of nameIndex) {\n    for (const path of paths) {\n      nameEntries.push([name, path]);\n    }\n  }\n  insertNameIndexTx(nameEntries);\n\n  // ---------------------------------------------------------------------------\n  // Step 7: Rebuild vault_links\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  db.exec(\"DELETE FROM vault_links\");\n\n  const insertLink = db.prepare(`\n    INSERT OR IGNORE INTO vault_links\n      (source_path, target_raw, target_path, link_type, line_number)\n    VALUES (?, ?, ?, ?, ?)\n  `);\n\n  // Parse and resolve wikilinks in bulk transaction\n  const linkRows: Array<{\n    source: string;\n    raw: string;\n    target: string | null;\n    linkType: string;\n    lineNumber: number;\n  }> = [];\n\n  for (const group of inodeGroups) {\n    const { canonical } = group;\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      continue;\n    }\n\n    const parsedLinks = parseWikilinks(content);\n    for (const link of parsedLinks) {\n      const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);\n      linkRows.push({\n        source: canonical.vaultRelPath,\n        raw: link.raw,\n        target,\n        linkType: link.isEmbed ? \"embed\" : \"wikilink\",\n        lineNumber: link.lineNumber,\n      });\n    }\n  }\n\n  const insertLinksTx = db.transaction(\n    (\n      rows: Array<{\n        source: string;\n        raw: string;\n        target: string | null;\n        linkType: string;\n        lineNumber: number;\n      }>,\n    ) => {\n      for (const row of rows) {\n        insertLink.run(row.source, row.raw, row.target, row.linkType, row.lineNumber);\n      }\n    },\n  );\n  insertLinksTx(linkRows);\n\n  result.linksExtracted = linkRows.length;\n  result.deadLinksFound = linkRows.filter((r) => r.target === null).length;\n\n  // ---------------------------------------------------------------------------\n  // Step 8: Compute and upsert vault_health metrics\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  // Count outbound links per source\n  const outboundCounts = db\n    .prepare(\n      `SELECT source_path, COUNT(*) AS cnt FROM vault_links GROUP BY source_path`,\n    )\n    .all() as Array<{ source_path: string; cnt: number }>;\n\n  // Count dead links per source\n  const deadLinkCounts = db\n    .prepare(\n      `SELECT source_path, COUNT(*) AS cnt FROM vault_links\n       WHERE target_path IS NULL GROUP BY source_path`,\n    )\n    .all() as Array<{ source_path: string; cnt: number }>;\n\n  // Count inbound links per target\n  const inboundCounts = db\n    .prepare(\n      `SELECT target_path, COUNT(*) AS cnt FROM vault_links\n       WHERE target_path IS NOT NULL GROUP BY target_path`,\n    )\n    .all() as Array<{ target_path: string; cnt: number }>;\n\n  // Build maps for O(1) lookup\n  const outboundMap = new Map<string, number>(\n    outboundCounts.map((r) => [r.source_path, r.cnt]),\n  );\n  const deadMap = new Map<string, number>(\n    deadLinkCounts.map((r) => [r.source_path, r.cnt]),\n  );\n  const inboundMap = new Map<string, number>(\n    inboundCounts.map((r) => [r.target_path, r.cnt]),\n  );\n\n  const upsertHealth = db.prepare(`\n    INSERT INTO vault_health\n      (vault_path, inbound_count, outbound_count, dead_link_count, is_orphan, computed_at)\n    VALUES (?, ?, ?, ?, ?, ?)\n    ON CONFLICT(vault_path) DO UPDATE SET\n      inbound_count   = excluded.inbound_count,\n      outbound_count  = excluded.outbound_count,\n      dead_link_count = excluded.dead_link_count,\n      is_orphan       = excluded.is_orphan,\n      computed_at     = excluded.computed_at\n  `);\n\n  const computedAt = Date.now();\n  let orphanCount = 0;\n\n  const upsertHealthTx = db.transaction((groups: InodeGroup[]) => {\n    for (const group of groups) {\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 ? 1 : 0;\n      if (isOrphan) orphanCount++;\n      upsertHealth.run(path, inbound, outbound, dead, isOrphan, computedAt);\n    }\n  });\n  upsertHealthTx(inodeGroups);\n\n  result.orphansFound = orphanCount;\n  result.elapsed = Date.now() - startTime;\n\n  return result;\n}\n"],"mappings":";;;;;;;;;;;;;;;;;;;;;AA4DA,MAAM,kBAAkB;;AAGxB,MAAM,kBAAkB;;AAGxB,MAAM,oBAAoB;;;;;AAM1B,MAAM,kBAAkB,IAAI,IAAI;CAE9B;CAEA;CACA;CACA;CAEA;CACA;CACA;CACA;CACA;CAEA;CACA;CACA;CAEA;CACA;CAEA;CACA;CACD,CAAC;AAMF,SAAS,WAAW,SAAyB;AAC3C,QAAO,WAAW,SAAS,CAAC,OAAO,QAAQ,CAAC,OAAO,MAAM;;AAG3D,SAAS,QACP,WACA,MACA,YACA,WACA,SACQ;AACR,QAAO,WAAW,SAAS,CACxB,OAAO,GAAG,UAAU,GAAG,KAAK,GAAG,WAAW,GAAG,UAAU,GAAG,UAAU,CACpE,OAAO,MAAM;;AAGlB,SAAS,mBAAkC;AACzC,QAAO,IAAI,SAAS,YAAY,aAAa,QAAQ,CAAC;;;;;;;;;;;;;;;;;;;AAwBxD,SAAgB,iBACd,WACA,MACa;CACb,MAAM,WAAW,MAAM,YAAY;CACnC,MAAM,WAAW,MAAM,YAAY;CAEnC,MAAM,UAAuB,EAAE;CAC/B,MAAM,8BAAc,IAAI,KAAa;CAErC,SAAS,KAAK,KAAa,OAAqB;AAC9C,MAAI,QAAQ,UAAU,SAAU;AAChC,MAAI,QAAQ,SAAU;EAGtB,IAAI;AACJ,MAAI;AACF,aAAU,SAAS,IAAI;UACjB;AACN;;EAGF,MAAM,SAAS,GAAG,QAAQ,IAAI,GAAG,QAAQ;AACzC,MAAI,YAAY,IAAI,OAAO,CAAE;AAC7B,cAAY,IAAI,OAAO;EAEvB,IAAI;AACJ,MAAI;AACF,aAAU,YAAY,KAAK;IAAE,eAAe;IAAM,UAAU;IAAQ,CAAC;UAC/D;AACN;;AAGF,OAAK,MAAM,SAAS,SAAS;AAC3B,OAAI,QAAQ,UAAU,SAAU;AAChC,OAAI,gBAAgB,IAAI,MAAM,KAAK,CAAE;GAErC,MAAM,OAAO,KAAK,KAAK,MAAM,KAAK;AAElC,OAAI,MAAM,gBAAgB,EAAE;IAE1B,IAAI;AACJ,QAAI;AACF,kBAAa,SAAS,KAAK;YACrB;AACN;;AAGF,QAAI,WAAW,aAAa,EAC1B;SAAI,CAAC,gBAAgB,IAAI,MAAM,KAAK,CAClC,MAAK,MAAM,QAAQ,EAAE;eAEd,WAAW,QAAQ,IAAI,MAAM,KAAK,SAAS,MAAM,CAC1D,SAAQ,KAAK;KACX,SAAS;KACT,cAAc,SAAS,WAAW,KAAK;KACvC,OAAO,WAAW;KAClB,QAAQ,WAAW;KACpB,CAAC;cAEK,MAAM,aAAa,CAC5B,MAAK,MAAM,QAAQ,EAAE;YACZ,MAAM,QAAQ,IAAI,MAAM,KAAK,SAAS,MAAM,EAAE;IACvD,IAAI;AACJ,QAAI;AACF,gBAAW,SAAS,KAAK;YACnB;AACN;;AAEF,YAAQ,KAAK;KACX,SAAS;KACT,cAAc,SAAS,WAAW,KAAK;KACvC,OAAO,SAAS;KAChB,QAAQ,SAAS;KAClB,CAAC;;;;AAKR,KAAI,WAAW,UAAU,CACvB,MAAK,WAAW,EAAE;AAGpB,QAAO;;;;;;;;;AAcT,SAAgB,mBAAmB,OAAkC;CACnE,MAAM,yBAAS,IAAI,KAA0B;AAE7C,MAAK,MAAM,QAAQ,OAAO;EACxB,MAAM,MAAM,GAAG,KAAK,OAAO,GAAG,KAAK;EACnC,MAAM,WAAW,OAAO,IAAI,IAAI;AAChC,MAAI,SACF,UAAS,KAAK,KAAK;MAEnB,QAAO,IAAI,KAAK,CAAC,KAAK,CAAC;;CAI3B,MAAM,SAAuB,EAAE;AAE/B,MAAK,MAAM,SAAS,OAAO,QAAQ,EAAE;AACnC,MAAI,MAAM,WAAW,EAAG;EAUxB,MAAM,CAAC,WAAW,GAAG,WAPN,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,MAAM;GACvC,MAAM,UAAU,EAAE,aAAa,MAAM,MAAM,IAAI,EAAE,EAAE;GACnD,MAAM,UAAU,EAAE,aAAa,MAAM,MAAM,IAAI,EAAE,EAAE;AACnD,OAAI,WAAW,OAAQ,QAAO,SAAS;AACvC,UAAO,EAAE,aAAa,SAAS,EAAE,aAAa;IAC9C;AAGF,SAAO,KAAK;GAAE;GAAW;GAAS,CAAC;;AAGrC,QAAO;;;;;;;;;;;;;;;AAoBT,SAAgB,eAAe,SAA+B;CAC5D,MAAM,QAAsB,EAAE;CAC9B,MAAM,QAAQ,QAAQ,MAAM,KAAK;CAGjC,IAAI,iBAAiB;AACrB,KAAI,QAAQ,WAAW,MAAM,EAAE;EAC7B,MAAM,aAAa,QAAQ,QAAQ,SAAS,EAAE;AAC9C,MAAI,eAAe,GACjB,kBAAiB,QAAQ,MAAM,GAAG,aAAa,EAAE,CAAC,MAAM,KAAK,CAAC,SAAS;;CAK3E,MAAM,aAAa;AAEnB,MAAK,IAAI,UAAU,GAAG,UAAU,MAAM,QAAQ,WAAW;EACvD,MAAM,OAAO,MAAM;EACnB,MAAM,aAAa,UAAU;AAE7B,aAAW,YAAY;EACvB,IAAI;AACJ,UAAQ,QAAQ,WAAW,KAAK,KAAK,MAAM,MAAM;GAC/C,MAAM,UAAU,MAAM,OAAO;GAC7B,MAAM,QAAQ,MAAM;GAGpB,MAAM,UAAU,MAAM,QAAQ,IAAI;GAClC,MAAM,aAAa,YAAY,KAAK,QAAQ,MAAM,MAAM,GAAG,QAAQ;GACnE,MAAM,QAAQ,YAAY,KAAK,OAAO,MAAM,MAAM,UAAU,EAAE;GAG9D,MAAM,UAAU,WAAW,QAAQ,IAAI;GACvC,MAAM,MAAM,YAAY,KAAK,WAAW,MAAM,GAAG,WAAW,MAAM,GAAG,QAAQ,CAAC,MAAM;AAEpF,OAAI,CAAC,IAAK;GAGV,MAAM,gBAAgB,UAAU;AAChC,SAAM,KAAK;IACT;IACA,OAAO,OAAO,MAAM,IAAI;IACxB;IACA,SAAS,WAAW,CAAC;IACtB,CAAC;;;AAIN,QAAO;;;;;;;;;AAcT,SAAgB,eAAe,OAA2C;CACxE,MAAM,wBAAQ,IAAI,KAAuB;AAEzC,MAAK,MAAM,QAAQ,OAAO;EACxB,MAAM,OAAO,SAAS,KAAK,cAAc,MAAM,CAAC,aAAa;EAC7D,MAAM,WAAW,MAAM,IAAI,KAAK;AAChC,MAAI,SACF,UAAS,KAAK,KAAK,aAAa;MAEhC,OAAM,IAAI,MAAM,CAAC,KAAK,aAAa,CAAC;;AAIxC,QAAO;;;;;;;;;;;;;;;;;;;AAwBT,SAAgB,gBACd,KACA,WACA,YACe;AACf,KAAI,CAAC,IAAK,QAAO;AAGjB,KAAI,IAAI,SAAS,IAAI,EAAE;EACrB,MAAM,aAAa,UAAU,IAAI;EACjC,MAAM,eAAe,WAAW,SAAS,MAAM,GAAG,aAAa,aAAa;AAG5E,OAAK,MAAM,GAAG,UAAU,UACtB,MAAK,MAAM,KAAK,OAAO;AACrB,OAAI,MAAM,gBAAgB,MAAM,WAAY,QAAO;AACnD,OAAI,EAAE,aAAa,KAAK,aAAa,aAAa,CAAE,QAAO;;;CASjE,MAAM,UAAU,SAAS,IAAI,CAC1B,QAAQ,UAAU,GAAG,CACrB,aAAa,CACb,MAAM;AAET,KAAI,CAAC,QAAS,QAAO;CAErB,MAAM,aAAa,UAAU,IAAI,QAAQ;AAEzC,KAAI,CAAC,cAAc,WAAW,WAAW,EACvC,QAAO;AAGT,KAAI,WAAW,WAAW,EACxB,QAAO,WAAW;CAIpB,MAAM,YAAY,QAAQ,WAAW;CAErC,IAAI,WAA0B;CAC9B,IAAI,gBAAgB;CACpB,IAAI,cAAc;AAElB,MAAK,MAAM,aAAa,YAAY;EAElC,MAAM,YAAY,mBAAmB,WADhB,QAAQ,UAAU,CACsB;EAC7D,MAAM,UAAU,UAAU;AAE1B,MACE,YAAY,iBACX,cAAc,iBAAiB,UAAU,aAC1C;AACA,mBAAgB;AAChB,iBAAc;AACd,cAAW;;;AAIf,QAAO;;;;;;;;AAST,SAAS,mBAAmB,GAAW,GAAmB;AACxD,KAAI,MAAM,OAAO,MAAM,IAAK,QAAO;CACnC,MAAM,SAAS,MAAM,MAAM,EAAE,GAAG,EAAE,MAAM,IAAI;CAC5C,MAAM,SAAS,MAAM,MAAM,EAAE,GAAG,EAAE,MAAM,IAAI;CAC5C,IAAI,QAAQ;CACZ,MAAM,MAAM,KAAK,IAAI,OAAO,QAAQ,OAAO,OAAO;AAClD,MAAK,IAAI,IAAI,GAAG,IAAI,KAAK,IACvB,KAAI,OAAO,OAAO,OAAO,GACvB;KAEA;AAGJ,QAAO;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAiCT,eAAsB,WACpB,IACA,gBACA,WAC2B;CAC3B,MAAM,YAAY,KAAK,KAAK;CAE5B,MAAM,SAA2B;EAC/B,cAAc;EACd,eAAe;EACf,cAAc;EACd,iBAAiB;EACjB,gBAAgB;EAChB,gBAAgB;EAChB,cAAc;EACd,SAAS;EACV;CAMD,MAAM,WAAW,iBAAiB,UAAU;CAM5C,MAAM,cAAc,mBAAmB,SAAS;CAMhD,MAAM,YAAY,eAAe,SAAS;CAM1C,MAAM,iBAAiB,GAAG,QACxB,oDACD;CAED,MAAM,oBAAoB,GAAG,QAC3B,iEACD;CAED,MAAM,YAAY,GAAG,QAAQ,sCAAsC;CAEnE,MAAM,eAAe,GAAG,QACtB,8DACD;CAED,MAAM,cAAc,GAAG,QAAQ;;;IAG7B;CAEF,MAAM,YAAY,GAAG,QAAQ;;;IAG3B;CAEF,MAAM,kBAAkB,GAAG,QAAQ;;;;;;;;;IASjC;AAMF,OAAM,kBAAkB;CACxB,IAAI,kBAAkB;AAEtB,MAAK,MAAM,SAAS,aAAa;AAE/B,MAAI,mBAAmB,mBAAmB;AACxC,SAAM,kBAAkB;AACxB,qBAAkB;;AAEpB;EAEA,MAAM,EAAE,cAAc;EAGtB,IAAI;AACJ,MAAI;AACF,aAAU,aAAa,UAAU,SAAS,OAAO;UAC3C;AACN,UAAO;AACP;;EAGF,MAAM,OAAO,WAAW,QAAQ;AAOhC,MAJiB,eAAe,IAAI,UAAU,aAAa,EAI7C,SAAS,MAAM;AAC3B,UAAO;AACP;;EAIF,MAAM,cAAc,kBAAkB,IACpC,gBACA,UAAU,aACX;AAED,KAAG,kBAAkB;AACnB,QAAK,MAAM,OAAO,YAChB,WAAU,IAAI,IAAI,GAAG;AAEvB,gBAAa,IAAI,gBAAgB,UAAU,aAAa;IACxD,EAAE;EAGJ,MAAM,SAAS,cAAc,QAAQ;EACrC,MAAM,YAAY,KAAK,KAAK;EAG5B,MAAM,aAAa,cAAc,KAAK,QAAQ;EAC9C,MAAM,QAAQ,aACV,WAAW,GAAI,MAAM,GACrB,SAAS,UAAU,cAAc,MAAM;AAE3C,KAAG,kBAAkB;AACnB,QAAK,IAAI,IAAI,GAAG,IAAI,OAAO,QAAQ,KAAK;IACtC,MAAM,QAAQ,OAAO;IACrB,MAAM,KAAK,QACT,gBACA,UAAU,cACV,GACA,MAAM,WACN,MAAM,QACP;AACD,gBAAY,IACV,IACA,gBACA,SACA,SACA,UAAU,cACV,MAAM,WACN,MAAM,SACN,MAAM,MACN,MAAM,MACN,UACD;AACD,cAAU,IACR,MAAM,MACN,IACA,gBACA,UAAU,cACV,SACA,SACA,MAAM,WACN,MAAM,QACP;;AAEH,mBAAgB,IACd,UAAU,cACV,UAAU,OACV,UAAU,QACV,MACA,OACA,UACD;IACD,EAAE;AAEJ,SAAO;AACP,SAAO,iBAAiB,OAAO;;AAOjC,OAAM,kBAAkB;AAKxB,IAAG,KAAK,4BAA4B;CAEpC,MAAM,cAAc,GAAG,QAAQ;;;IAG7B;AAeF,CAbwB,GAAG,aAAa,WAAyB;AAC/D,OAAK,MAAM,SAAS,OAClB,MAAK,MAAM,SAAS,MAAM,SAAS;AACjC,eAAY,IACV,MAAM,cACN,MAAM,UAAU,cAChB,MAAM,OACN,MAAM,OACP;AACD,UAAO;;GAGX,CACc,YAAY;AAM5B,OAAM,kBAAkB;AAExB,IAAG,KAAK,+BAA+B;CAEvC,MAAM,kBAAkB,GAAG,QAAQ;;IAEjC;CAEF,MAAM,oBAAoB,GAAG,aAC1B,YAAqC;AACpC,OAAK,MAAM,CAAC,MAAM,SAAS,QACzB,iBAAgB,IAAI,MAAM,KAAK;GAGpC;CAED,MAAM,cAAuC,EAAE;AAC/C,MAAK,MAAM,CAAC,MAAM,UAAU,UAC1B,MAAK,MAAM,QAAQ,MACjB,aAAY,KAAK,CAAC,MAAM,KAAK,CAAC;AAGlC,mBAAkB,YAAY;AAM9B,OAAM,kBAAkB;AAExB,IAAG,KAAK,0BAA0B;CAElC,MAAM,aAAa,GAAG,QAAQ;;;;IAI5B;CAGF,MAAM,WAMD,EAAE;AAEP,MAAK,MAAM,SAAS,aAAa;EAC/B,MAAM,EAAE,cAAc;EAEtB,IAAI;AACJ,MAAI;AACF,aAAU,aAAa,UAAU,SAAS,OAAO;UAC3C;AACN;;EAGF,MAAM,cAAc,eAAe,QAAQ;AAC3C,OAAK,MAAM,QAAQ,aAAa;GAC9B,MAAM,SAAS,gBAAgB,KAAK,KAAK,WAAW,UAAU,aAAa;AAC3E,YAAS,KAAK;IACZ,QAAQ,UAAU;IAClB,KAAK,KAAK;IACV;IACA,UAAU,KAAK,UAAU,UAAU;IACnC,YAAY,KAAK;IAClB,CAAC;;;AAmBN,CAfsB,GAAG,aAErB,SAOG;AACH,OAAK,MAAM,OAAO,KAChB,YAAW,IAAI,IAAI,QAAQ,IAAI,KAAK,IAAI,QAAQ,IAAI,UAAU,IAAI,WAAW;GAGlF,CACa,SAAS;AAEvB,QAAO,iBAAiB,SAAS;AACjC,QAAO,iBAAiB,SAAS,QAAQ,MAAM,EAAE,WAAW,KAAK,CAAC;AAMlE,OAAM,kBAAkB;CAGxB,MAAM,iBAAiB,GACpB,QACC,4EACD,CACA,KAAK;CAGR,MAAM,iBAAiB,GACpB,QACC;uDAED,CACA,KAAK;CAGR,MAAM,gBAAgB,GACnB,QACC;2DAED,CACA,KAAK;CAGR,MAAM,cAAc,IAAI,IACtB,eAAe,KAAK,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,CAAC,CAClD;CACD,MAAM,UAAU,IAAI,IAClB,eAAe,KAAK,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,CAAC,CAClD;CACD,MAAM,aAAa,IAAI,IACrB,cAAc,KAAK,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,CAAC,CACjD;CAED,MAAM,eAAe,GAAG,QAAQ;;;;;;;;;;IAU9B;CAEF,MAAM,aAAa,KAAK,KAAK;CAC7B,IAAI,cAAc;AAalB,CAXuB,GAAG,aAAa,WAAyB;AAC9D,OAAK,MAAM,SAAS,QAAQ;GAC1B,MAAM,OAAO,MAAM,UAAU;GAC7B,MAAM,UAAU,WAAW,IAAI,KAAK,IAAI;GACxC,MAAM,WAAW,YAAY,IAAI,KAAK,IAAI;GAC1C,MAAM,OAAO,QAAQ,IAAI,KAAK,IAAI;GAClC,MAAM,WAAW,YAAY,IAAI,IAAI;AACrC,OAAI,SAAU;AACd,gBAAa,IAAI,MAAM,SAAS,UAAU,MAAM,UAAU,WAAW;;GAEvE,CACa,YAAY;AAE3B,QAAO,eAAe;AACtB,QAAO,UAAU,KAAK,KAAK,GAAG;AAE9B,QAAO"}