@andespindola/brainlink 0.1.0-beta.4 → 0.1.0-beta.40

package/dist/application/get-graph-layout.js

@@ -1,26 +1,41 @@
+import { createHash } from 'node:crypto';
+import { stat } from 'node:fs/promises';
 import { createCauliflowerGraphLayout } from '../domain/graph-layout.js';
-import { getGraph } from './get-graph.js';
+import { indexStoragePath } from '../infrastructure/file-index.js';
+import { getGraphSummary } from './get-graph-summary.js';
 const graphLayoutCache = new Map();
+const readDatabaseSignature = async (vaultPath) => {
+    try {
+        const info = await stat(indexStoragePath(vaultPath));
+        return `${Math.floor(info.mtimeMs)}:${info.size}`;
+    }
+    catch {
+        return '0:0';
+    }
+};
 const createGraphSignature = (graph) => {
     const nodesSignature = graph.nodes.map((node) => `${node.id}|${node.agentId}|${node.title}|${node.path}`).join('\n');
     const edgesSignature = graph.edges
         .map((edge) => `${edge.source}|${edge.target ?? ''}|${edge.targetTitle}|${edge.weight}|${edge.priority}`)
         .join('\n');
-    return `${graph.nodes.length}:${nodesSignature}|${graph.edges.length}:${edgesSignature}`;
+    return createHash('sha256')
+        .update(`${graph.nodes.length}:${nodesSignature}|${graph.edges.length}:${edgesSignature}`)
+        .digest('hex');
 };
 export const getGraphLayout = async (vaultPath, agentId) => {
-    const graph = await getGraph(vaultPath, agentId);
-    const signature = createGraphSignature(graph);
+    const databaseSignature = await readDatabaseSignature(vaultPath);
     const cacheKey = `${vaultPath}:${agentId ?? ''}`;
     const cached = graphLayoutCache.get(cacheKey);
-    if (cached?.signature === signature) {
+    if (cached?.databaseSignature === databaseSignature) {
         return {
-            signature,
+            signature: cached.signature,
             layout: cached.layout
         };
     }
+    const graph = await getGraphSummary(vaultPath, agentId);
+    const signature = createGraphSignature(graph);
     const layout = createCauliflowerGraphLayout(graph);
-    graphLayoutCache.set(cacheKey, { signature, layout });
+    graphLayoutCache.set(cacheKey, { databaseSignature, signature, layout });
     return {
         signature,
         layout

package/dist/application/get-graph-node.js

@@ -0,0 +1,12 @@
+import { ensureVault } from '../infrastructure/file-system-vault.js';
+import { openFileIndex } from '../infrastructure/file-index.js';
+export const getGraphNode = async (vaultPath, id, agentId) => {
+    const absoluteVaultPath = await ensureVault(vaultPath);
+    const index = openFileIndex(absoluteVaultPath);
+    try {
+        return await index.getGraphNode(id, agentId);
+    }
+    finally {
+        index.close();
+    }
+};

package/dist/application/get-graph-summary.js

@@ -0,0 +1,12 @@
+import { ensureVault } from '../infrastructure/file-system-vault.js';
+import { openFileIndex } from '../infrastructure/file-index.js';
+export const getGraphSummary = async (vaultPath, agentId) => {
+    const absoluteVaultPath = await ensureVault(vaultPath);
+    const index = openFileIndex(absoluteVaultPath);
+    try {
+        return await index.getGraphSummary(agentId);
+    }
+    finally {
+        index.close();
+    }
+};

package/dist/application/get-graph.js

@@ -1,10 +1,10 @@
 import { ensureVault } from '../infrastructure/file-system-vault.js';
-import { openSqliteIndex } from '../infrastructure/sqlite-index.js';
+import { openFileIndex } from '../infrastructure/file-index.js';
 export const getGraph = async (vaultPath, agentId) => {
     const absoluteVaultPath = await ensureVault(vaultPath);
-    const index = openSqliteIndex(absoluteVaultPath);
+    const index = openFileIndex(absoluteVaultPath);
     try {
-        return index.getGraph(agentId);
+        return await index.getGraph(agentId);
     }
     finally {
         index.close();

package/dist/application/import-legacy-sqlite.js

@@ -0,0 +1,296 @@
+import { execFile } from 'node:child_process';
+import { access } from 'node:fs/promises';
+import { basename, extname, join, relative, resolve } from 'node:path';
+import { pathToFileURL } from 'node:url';
+import { promisify } from 'node:util';
+import { extractTags, extractWikiLinks } from '../domain/markdown.js';
+import { sanitizeAgentId, sharedAgentId } from '../domain/agents.js';
+import { ensureVault, listVaultFiles, writeMarkdownFile } from '../infrastructure/file-system-vault.js';
+import { getBrainlinkHomePath } from '../infrastructure/paths.js';
+const execFileAsync = promisify(execFile);
+const fieldSeparator = '\u001f';
+const rowSeparator = '\u001e';
+const contentColumnCandidates = ['content', 'markdown', 'body', 'text', 'note'];
+const titleColumnCandidates = ['title', 'note_title', 'name', 'headline'];
+const pathColumnCandidates = ['path', 'file_path', 'filepath', 'source_path', 'source'];
+const agentColumnCandidates = ['agent', 'agent_id', 'namespace', 'scope'];
+const tagColumnCandidates = ['tags', 'tag_list', 'keywords'];
+const createdColumnCandidates = ['created_at', 'createdat', 'created', 'ctime'];
+const updatedColumnCandidates = ['updated_at', 'updatedat', 'updated', 'mtime'];
+const systemHubTitle = 'Memory Hub';
+const systemRootTitle = 'Knowledge Root';
+const normalizeTitle = (title) => title.trim().replace(/\.md$/i, '').toLowerCase();
+const slugify = (title) => title
+    .normalize('NFKD')
+    .replace(/[\u0300-\u036f]/g, '')
+    .toLowerCase()
+    .replace(/[^a-z0-9]+/g, '-')
+    .replace(/^-+|-+$/g, '');
+const quoteIdentifier = (value) => `"${value.replaceAll('"', '""')}"`;
+const pickColumn = (columns, candidates) => {
+    const byLower = new Map(columns.map((column) => [column.toLowerCase(), column]));
+    return candidates.map((candidate) => byLower.get(candidate)).find((column) => Boolean(column)) ?? null;
+};
+const parseDelimitedRows = (rawOutput) => {
+    const normalized = rawOutput.trim();
+    if (normalized.length === 0) {
+        return [];
+    }
+    return normalized
+        .split(rowSeparator)
+        .map((row) => row.trim())
+        .filter(Boolean)
+        .map((row) => row.split(fieldSeparator));
+};
+const runSqliteQuery = async (databasePath, sql) => {
+    const baseArgs = ['-noheader', '-separator', fieldSeparator, '-newline', rowSeparator, '-cmd', '.timeout 5000'];
+    const runQuery = async (args) => {
+        const { stdout } = await execFileAsync('sqlite3', [...args, sql], { maxBuffer: 1024 * 1024 * 64 });
+        return parseDelimitedRows(stdout);
+    };
+    try {
+        return await runQuery(['--readonly', ...baseArgs, databasePath]);
+    }
+    catch (error) {
+        const message = error instanceof Error ? error.message : String(error);
+        const lower = message.toLowerCase();
+        if (lower.includes('enoent') || lower.includes('not found')) {
+            throw new Error('sqlite3 CLI was not found. Install sqlite3 to use db-import.');
+        }
+        if (lower.includes('database is locked') || lower.includes('(5)')) {
+            try {
+                const uri = pathToFileURL(databasePath);
+                uri.search = 'mode=ro&immutable=1';
+                return await runQuery(['-uri', ...baseArgs, uri.toString()]);
+            }
+            catch (fallbackError) {
+                const fallbackMessage = fallbackError instanceof Error ? fallbackError.message : String(fallbackError);
+                throw new Error(`Unable to read SQLite database (locked). Close writers (server/watch/mcp) or rerun with DB idle. Details: ${fallbackMessage}`);
+            }
+        }
+        throw new Error(`Unable to read SQLite database: ${message}`);
+    }
+};
+const detectLegacyDbPath = async (vaultPath, explicitPath) => {
+    if (explicitPath) {
+        return resolve(explicitPath);
+    }
+    const vaultRoot = await ensureVault(vaultPath);
+    const candidates = [
+        join(vaultRoot, '.brainlink', 'brainlink.db'),
+        join(vaultRoot, '.brainlink', 'index.db'),
+        join(getBrainlinkHomePath(), 'brainlink.db'),
+        join(getBrainlinkHomePath(), 'vault', '.brainlink', 'brainlink.db')
+    ];
+    for (const candidate of candidates) {
+        try {
+            await access(candidate);
+            return candidate;
+        }
+        catch { }
+    }
+    throw new Error(`No legacy SQLite database found. Checked: ${candidates.join(', ')}. Use --db <path-to-db> to import explicitly.`);
+};
+const listTables = async (dbPath) => {
+    const rows = await runSqliteQuery(dbPath, `SELECT name
+     FROM sqlite_master
+     WHERE type = 'table' AND name NOT LIKE 'sqlite_%'
+     ORDER BY name`);
+    return rows.map((columns) => columns[0]).filter(Boolean);
+};
+const listColumns = async (dbPath, table) => {
+    const rows = await runSqliteQuery(dbPath, `PRAGMA table_info(${quoteIdentifier(table)})`);
+    return rows.map((columns) => columns[1]).filter(Boolean);
+};
+const tableScore = (columns) => {
+    const contentColumn = pickColumn(columns, contentColumnCandidates);
+    const titleColumn = pickColumn(columns, titleColumnCandidates);
+    const pathColumn = pickColumn(columns, pathColumnCandidates);
+    const agentColumn = pickColumn(columns, agentColumnCandidates);
+    return (contentColumn ? 6 : 0) + (titleColumn ? 4 : 0) + (pathColumn ? 2 : 0) + (agentColumn ? 1 : 0);
+};
+const detectTableMapping = async (dbPath, tableOverride) => {
+    const tables = await listTables(dbPath);
+    if (tables.length === 0) {
+        throw new Error('Legacy SQLite database has no readable tables.');
+    }
+    const mappings = await Promise.all(tables.map(async (table) => {
+        const columns = await listColumns(dbPath, table);
+        return {
+            table,
+            columns,
+            titleColumn: pickColumn(columns, titleColumnCandidates),
+            contentColumn: pickColumn(columns, contentColumnCandidates),
+            pathColumn: pickColumn(columns, pathColumnCandidates),
+            agentColumn: pickColumn(columns, agentColumnCandidates),
+            tagsColumn: pickColumn(columns, tagColumnCandidates),
+            createdColumn: pickColumn(columns, createdColumnCandidates),
+            updatedColumn: pickColumn(columns, updatedColumnCandidates),
+            score: tableScore(columns)
+        };
+    }));
+    if (tableOverride) {
+        const overridden = mappings.find((mapping) => mapping.table === tableOverride);
+        if (!overridden) {
+            throw new Error(`Table not found in SQLite database: ${tableOverride}`);
+        }
+        if (!overridden.contentColumn) {
+            throw new Error(`Table ${tableOverride} does not expose a readable content column.`);
+        }
+        return { mapping: overridden, detectedTables: tables };
+    }
+    const selected = [...mappings]
+        .filter((mapping) => mapping.contentColumn)
+        .sort((left, right) => right.score - left.score)[0];
+    if (!selected) {
+        throw new Error('Could not detect a legacy table with content column in SQLite database.');
+    }
+    return { mapping: selected, detectedTables: tables };
+};
+const hexExpression = (column) => column ? `hex(COALESCE(CAST(${quoteIdentifier(column)} AS BLOB), X''))` : `hex(X'')`;
+const decodeHexUtf8 = (value) => value ? Buffer.from(value, 'hex').toString('utf8') : '';
+const parseLegacyTags = (value) => Array.from(new Set(value
+    .split(/[\s,;|]+/)
+    .map((item) => item.trim().replace(/^#/, '').toLowerCase())
+    .filter((item) => /^[a-z0-9][a-z0-9_-]*$/i.test(item))));
+const titleFromPath = (pathValue) => basename(pathValue).replace(extname(pathValue), '').replace(/[-_]+/g, ' ').trim();
+const appendMissingTags = (content, tags) => {
+    if (tags.length === 0) {
+        return content;
+    }
+    const existingTags = new Set(extractTags(content).map((tag) => tag.toLowerCase()));
+    const missing = tags.filter((tag) => !existingTags.has(tag.toLowerCase()));
+    if (missing.length === 0) {
+        return content;
+    }
+    return `${content.trim()}\n\nTags: ${missing.map((tag) => `#${tag}`).join(' ')}`;
+};
+const buildNote = (title, content, agentId) => [
+    '---',
+    `title: "${title.replaceAll('"', '\\"')}"`,
+    `agent: "${agentId}"`,
+    '---',
+    '',
+    `# ${title}`,
+    '',
+    content.trim(),
+    ''
+].join('\n');
+const parseLegacyRow = (columns, rowIndex) => {
+    const [titleHex, contentHex, pathHex, agentHex, tagsHex] = columns;
+    const content = decodeHexUtf8(contentHex).trim();
+    const path = decodeHexUtf8(pathHex).trim();
+    const titleCandidate = decodeHexUtf8(titleHex).trim();
+    const fallbackTitleFromPath = path ? titleFromPath(path) : '';
+    const title = titleCandidate || fallbackTitleFromPath || `Imported Memory ${rowIndex + 1}`;
+    return {
+        title,
+        content,
+        path,
+        agent: decodeHexUtf8(agentHex).trim(),
+        tags: parseLegacyTags(decodeHexUtf8(tagsHex))
+    };
+};
+const noteRelativePath = (agentId, slug, suffix = 0) => `agents/${agentId}/${suffix > 0 ? `${slug}-${suffix + 1}` : slug || 'untitled'}.md`;
+const reserveUniquePath = (agentId, title, reserved) => {
+    const slug = slugify(title);
+    for (let suffix = 0; suffix < 10_000; suffix += 1) {
+        const relativePath = noteRelativePath(agentId, slug, suffix);
+        if (!reserved.has(relativePath)) {
+            reserved.add(relativePath);
+            return relativePath;
+        }
+    }
+    throw new Error(`Could not allocate unique path for imported note: ${title}`);
+};
+const ensureSystemNote = async (vaultPath, reserved, created, agentId, title, content, dryRun) => {
+    const filename = noteRelativePath(agentId, slugify(title));
+    if (reserved.has(filename)) {
+        return;
+    }
+    reserved.add(filename);
+    created.add(filename);
+    if (dryRun) {
+        return;
+    }
+    await writeMarkdownFile(vaultPath, filename, buildNote(title, content, agentId));
+};
+const applyConnectivityRule = async (vaultPath, reserved, created, title, content, agentId, dryRun) => {
+    const links = extractWikiLinks(content).filter((link) => normalizeTitle(link) !== normalizeTitle(title));
+    if (links.length > 0) {
+        return content.trim();
+    }
+    const normalized = normalizeTitle(title);
+    if (normalized === normalizeTitle(systemHubTitle)) {
+        await ensureSystemNote(vaultPath, reserved, created, agentId, systemRootTitle, `Entry point for agent memory. [[${systemHubTitle}]] #memory #root`, dryRun);
+        return `${content.trim()}\n\nRelated: [[${systemRootTitle}]]`;
+    }
+    await ensureSystemNote(vaultPath, reserved, created, agentId, systemHubTitle, 'Central memory index for this agent namespace. #memory #hub', dryRun);
+    return `${content.trim()}\n\nRelated: [[${systemHubTitle}]]`;
+};
+const importRowsFromMapping = async (vaultPath, dbPath, mapping, options, reserved) => {
+    const limit = Number.isFinite(options.limit) && (options.limit ?? 0) > 0 ? Math.floor(options.limit ?? 0) : undefined;
+    const sql = [
+        'SELECT',
+        `${hexExpression(mapping.titleColumn)} AS title_hex,`,
+        `${hexExpression(mapping.contentColumn)} AS content_hex,`,
+        `${hexExpression(mapping.pathColumn)} AS path_hex,`,
+        `${hexExpression(mapping.agentColumn)} AS agent_hex,`,
+        `${hexExpression(mapping.tagsColumn)} AS tags_hex,`,
+        `${hexExpression(mapping.createdColumn)} AS created_hex,`,
+        `${hexExpression(mapping.updatedColumn)} AS updated_hex`,
+        `FROM ${quoteIdentifier(mapping.table)}`,
+        ...(limit ? [`LIMIT ${limit}`] : [])
+    ].join(' ');
+    const rows = await runSqliteQuery(dbPath, sql);
+    const createdSystemNotes = new Set();
+    const importedFiles = [];
+    let imported = 0;
+    let skipped = 0;
+    for (let rowIndex = 0; rowIndex < rows.length; rowIndex += 1) {
+        const row = parseLegacyRow(rows[rowIndex], rowIndex);
+        if (!row.content) {
+            skipped += 1;
+            continue;
+        }
+        const agentId = sanitizeAgentId(options.agentOverride || row.agent || sharedAgentId);
+        const filename = reserveUniquePath(agentId, row.title, reserved);
+        const mergedContent = appendMissingTags(row.content, row.tags);
+        const connectedContent = await applyConnectivityRule(vaultPath, reserved, createdSystemNotes, row.title, mergedContent, agentId, options.dryRun === true);
+        const note = buildNote(row.title, connectedContent, agentId);
+        if (options.dryRun !== true) {
+            await writeMarkdownFile(vaultPath, filename, note);
+        }
+        importedFiles.push(filename);
+        imported += 1;
+    }
+    return {
+        rowsRead: rows.length,
+        imported,
+        skipped,
+        createdSystemNotes: createdSystemNotes.size,
+        importedFiles
+    };
+};
+export const importLegacySqliteDatabase = async (vaultPath, options = {}) => {
+    const vault = await ensureVault(vaultPath);
+    const dbPath = await detectLegacyDbPath(vaultPath, options.dbPath);
+    const { mapping, detectedTables } = await detectTableMapping(dbPath, options.table);
+    const existingFiles = (await listVaultFiles(vaultPath))
+        .filter((path) => extname(path).toLowerCase() === '.md')
+        .map((path) => relative(vault, path));
+    const reserved = new Set(existingFiles);
+    const imported = await importRowsFromMapping(vaultPath, dbPath, mapping, options, reserved);
+    return {
+        vault,
+        dbPath,
+        table: mapping.table,
+        detectedTables,
+        rowsRead: imported.rowsRead,
+        imported: imported.imported,
+        skipped: imported.skipped,
+        createdSystemNotes: imported.createdSystemNotes,
+        dryRun: options.dryRun === true,
+        importedFiles: imported.importedFiles
+    };
+};

package/dist/application/index-vault.js

@@ -3,7 +3,8 @@ import { sharedAgentId } from '../domain/agents.js';
 import { createEmbeddingProvider } from '../domain/embeddings.js';
 import { loadBrainlinkConfig } from '../infrastructure/config.js';
 import { ensureVault, readMarkdownFiles } from '../infrastructure/file-system-vault.js';
-import { openSqliteIndex } from '../infrastructure/sqlite-index.js';
+import { buildSearchPacks } from '../infrastructure/search-packs.js';
+import { openFileIndex } from '../infrastructure/file-index.js';
 const toTitleKey = (title) => title.toLowerCase();
 const appendTitleEntry = (map, document) => {
     const key = toTitleKey(document.title);
@@ -59,10 +60,16 @@ export const indexVault = async (vaultPath) => {
     }));
     const titleMaps = createTitleMaps(documents);
     const indexedDocuments = await embedIndexedDocuments(documents.map((document) => createIndexedDocument(document, createScopedTitleResolver(document, titleMaps), config.chunkSize)), config.embeddingProvider);
-    const index = openSqliteIndex(absoluteVaultPath);
+    const index = openFileIndex(absoluteVaultPath);
     try {
-        index.reset();
-        index.saveDocuments(indexedDocuments);
+        await index.reset();
+        await index.saveDocuments(indexedDocuments);
+        try {
+            await buildSearchPacks(absoluteVaultPath, indexedDocuments);
+        }
+        catch {
+            // Pack generation is best-effort. The JSON index remains the primary path.
+        }
         return {
             documentCount: indexedDocuments.length,
             chunkCount: indexedDocuments.reduce((total, document) => total + document.chunks.length, 0),

package/dist/application/list-agents.js

@@ -1,10 +1,10 @@
 import { ensureVault } from '../infrastructure/file-system-vault.js';
-import { openSqliteIndex } from '../infrastructure/sqlite-index.js';
+import { openFileIndex } from '../infrastructure/file-index.js';
 export const listAgents = async (vaultPath) => {
     const absoluteVaultPath = await ensureVault(vaultPath);
-    const index = openSqliteIndex(absoluteVaultPath);
+    const index = openFileIndex(absoluteVaultPath);
     try {
-        return index.listAgents();
+        return await index.listAgents();
     }
     finally {
         index.close();

package/dist/application/list-links.js

@@ -1,10 +1,10 @@
 import { ensureVault } from '../infrastructure/file-system-vault.js';
-import { openSqliteIndex } from '../infrastructure/sqlite-index.js';
+import { openFileIndex } from '../infrastructure/file-index.js';
 export const listLinks = async (vaultPath, agentId) => {
     const absoluteVaultPath = await ensureVault(vaultPath);
-    const index = openSqliteIndex(absoluteVaultPath);
+    const index = openFileIndex(absoluteVaultPath);
     try {
-        return index.listLinks(agentId);
+        return await index.listLinks(agentId);
     }
     finally {
         index.close();
@@ -12,9 +12,9 @@ export const listLinks = async (vaultPath, agentId) => {
 };
 export const listBacklinks = async (vaultPath, title, agentId) => {
     const absoluteVaultPath = await ensureVault(vaultPath);
-    const index = openSqliteIndex(absoluteVaultPath);
+    const index = openFileIndex(absoluteVaultPath);
     try {
-        return index.listBacklinks(title, agentId);
+        return await index.listBacklinks(title, agentId);
     }
     finally {
         index.close();

package/dist/application/migrate-vault.js

@@ -0,0 +1,91 @@
+import { chmod, mkdir, readFile, writeFile } from 'node:fs/promises';
+import { dirname, extname, isAbsolute, join, relative } from 'node:path';
+import { ensureVault, isBucketVaultPath, listVaultFiles, resolveVaultPath, writeMarkdownFile } from '../infrastructure/file-system-vault.js';
+const directoryMode = 0o700;
+const fileMode = 0o600;
+const isMarkdownPath = (path) => extname(path).toLowerCase() === '.md';
+const timestamp = () => new Date().toISOString().replace(/[-:]/g, '').replace(/\..+$/, 'Z');
+const isPathInside = (parent, child) => {
+    const path = relative(parent, child);
+    return path === '' || (!path.startsWith('..') && !isAbsolute(path));
+};
+const conflictPath = (targetPath) => {
+    const extension = extname(targetPath);
+    const base = extension ? targetPath.slice(0, -extension.length) : targetPath;
+    return `${base}.conflict-${timestamp()}${extension}`;
+};
+const writePreservedFile = async (absolutePath, content) => {
+    await mkdir(dirname(absolutePath), { recursive: true, mode: directoryMode });
+    await writeFile(absolutePath, content, { mode: fileMode });
+    await chmod(absolutePath, fileMode);
+};
+const writeMigratedFile = async (targetVault, targetRoot, absolutePath, content) => {
+    if (isBucketVaultPath(targetVault)) {
+        await writeMarkdownFile(targetVault, relative(targetRoot, absolutePath), content.toString('utf8'));
+        return;
+    }
+    await writePreservedFile(absolutePath, content);
+};
+export const planVaultMigration = async (source, target) => {
+    const sourceFiles = (await listVaultFiles(source)).filter(isMarkdownPath);
+    return sourceFiles.reduce(async (statePromise, sourceFile) => {
+        const state = await statePromise;
+        const targetFile = join(target, relative(source, sourceFile));
+        if (!isPathInside(target, targetFile)) {
+            return state;
+        }
+        const sourceContent = await readFile(sourceFile);
+        try {
+            const targetContent = await readFile(targetFile);
+            if (sourceContent.equals(targetContent)) {
+                return [...state, { kind: 'unchanged', sourcePath: sourceFile, targetPath: targetFile, sourceContent }];
+            }
+            return [...state, { kind: 'conflict', sourcePath: sourceFile, targetPath: conflictPath(targetFile), sourceContent }];
+        }
+        catch (error) {
+            if (!(error instanceof Error) || !('code' in error) || error.code !== 'ENOENT') {
+                throw error;
+            }
+            return [...state, { kind: 'copy', sourcePath: sourceFile, targetPath: targetFile, sourceContent }];
+        }
+    }, Promise.resolve([]));
+};
+export const previewVaultMigration = async (sourceVault, targetVault) => {
+    const source = await ensureVault(sourceVault);
+    const target = await ensureVault(targetVault);
+    if (source === target) {
+        return { source, target, copied: 0, unchanged: 0, conflicted: 0 };
+    }
+    const actions = await planVaultMigration(source, target);
+    const copied = actions.filter((action) => action.kind === 'copy').length;
+    const unchanged = actions.filter((action) => action.kind === 'unchanged').length;
+    const conflicted = actions.filter((action) => action.kind === 'conflict').length;
+    return { source, target, copied, unchanged, conflicted };
+};
+export const migrateVaultContent = async (sourceVault, targetVault) => {
+    const source = await ensureVault(sourceVault);
+    const target = await ensureVault(targetVault);
+    if (source === target) {
+        return { source, target, copied: 0, unchanged: 0, conflicted: 0 };
+    }
+    const actions = await planVaultMigration(source, target);
+    for (const action of actions) {
+        if (action.kind === 'unchanged') {
+            continue;
+        }
+        await writeMigratedFile(targetVault, target, action.targetPath, action.sourceContent);
+    }
+    const copied = actions.filter((action) => action.kind === 'copy').length;
+    const unchanged = actions.filter((action) => action.kind === 'unchanged').length;
+    const conflicted = actions.filter((action) => action.kind === 'conflict').length;
+    return { source, target, copied, unchanged, conflicted };
+};
+export const shouldMigrateDefaultVault = async (sourceVault, targetVault) => {
+    const source = resolveVaultPath(sourceVault);
+    const target = resolveVaultPath(targetVault);
+    if (source === target) {
+        return false;
+    }
+    const [sourceFiles, targetFiles] = await Promise.all([listVaultFiles(source), listVaultFiles(target)]);
+    return sourceFiles.filter(isMarkdownPath).length > 0 && targetFiles.filter(isMarkdownPath).length === 0;
+};

package/dist/application/search-graph-node-ids.js

@@ -0,0 +1,12 @@
+import { ensureVault } from '../infrastructure/file-system-vault.js';
+import { openFileIndex } from '../infrastructure/file-index.js';
+export const searchGraphNodeIds = async (vaultPath, query, limit, agentId) => {
+    const absoluteVaultPath = await ensureVault(vaultPath);
+    const index = openFileIndex(absoluteVaultPath);
+    try {
+        return await index.searchGraphNodeIds(query, limit, agentId);
+    }
+    finally {
+        index.close();
+    }
+};

package/dist/application/search-knowledge.js

@@ -1,19 +1,89 @@
+import { stat } from 'node:fs/promises';
 import { ensureVault } from '../infrastructure/file-system-vault.js';
-import { openSqliteIndex } from '../infrastructure/sqlite-index.js';
+import { ensurePrivatePacksFromLegacyIndex, searchInPacks } from '../infrastructure/search-packs.js';
+import { indexStoragePath, openFileIndex } from '../infrastructure/file-index.js';
 import { createEmbeddingProvider } from '../domain/embeddings.js';
 import { loadBrainlinkConfig, sanitizeSearchMode } from '../infrastructure/config.js';
+const hybridCacheTtlMs = 30_000;
+const hybridCacheMaxEntries = 200;
+const hybridSearchCache = new Map();
+const readIndexMtimeMs = async (vaultPath) => {
+    try {
+        return (await stat(indexStoragePath(vaultPath))).mtimeMs;
+    }
+    catch {
+        return 0;
+    }
+};
+const toCacheKey = (vaultPath, query, limit, agentId) => JSON.stringify({
+    vaultPath,
+    query: query.trim().toLowerCase(),
+    limit,
+    agentId: agentId?.trim().toLowerCase() ?? '*'
+});
+const cacheGet = (key, indexMtimeMs) => {
+    const entry = hybridSearchCache.get(key);
+    if (!entry) {
+        return undefined;
+    }
+    const fresh = Date.now() - entry.createdAt <= hybridCacheTtlMs && entry.indexMtimeMs === indexMtimeMs;
+    if (!fresh) {
+        hybridSearchCache.delete(key);
+        return undefined;
+    }
+    return entry.results;
+};
+const cacheSet = (entry) => {
+    hybridSearchCache.set(entry.key, entry);
+    if (hybridSearchCache.size <= hybridCacheMaxEntries) {
+        return;
+    }
+    const overflow = hybridSearchCache.size - hybridCacheMaxEntries;
+    const keys = Array.from(hybridSearchCache.keys()).slice(0, overflow);
+    keys.forEach((key) => hybridSearchCache.delete(key));
+};
 export const searchKnowledge = async (vaultPath, query, limit, agentId, mode) => {
     const absoluteVaultPath = await ensureVault(vaultPath);
     const config = await loadBrainlinkConfig();
     const searchMode = sanitizeSearchMode(mode, config.defaultSearchMode);
+    await ensurePrivatePacksFromLegacyIndex(absoluteVaultPath);
+    const cacheKey = searchMode === 'hybrid' ? toCacheKey(absoluteVaultPath, query, limit, agentId) : undefined;
+    const indexMtimeMs = cacheKey ? await readIndexMtimeMs(absoluteVaultPath) : 0;
+    const cached = cacheKey ? cacheGet(cacheKey, indexMtimeMs) : undefined;
+    if (cached) {
+        return cached;
+    }
     const provider = createEmbeddingProvider(config.embeddingProvider);
     const shouldEmbedQuery = searchMode !== 'fts' && provider.name !== 'none';
     const queryEmbedding = shouldEmbedQuery ? (await provider.embed([query]))[0] ?? [] : [];
-    const index = openSqliteIndex(absoluteVaultPath);
     try {
-        return index.search(query, limit, agentId, searchMode, queryEmbedding);
+        const index = openFileIndex(absoluteVaultPath);
+        try {
+            const results = await index.search(query, limit, agentId, searchMode, queryEmbedding);
+            if (cacheKey) {
+                cacheSet({
+                    key: cacheKey,
+                    createdAt: Date.now(),
+                    indexMtimeMs,
+                    results
+                });
+            }
+            return results;
+        }
+        finally {
+            index.close();
+        }
     }
-    finally {
-        index.close();
+    catch {
+        const fallbackResults = await searchInPacks(absoluteVaultPath, query, limit, agentId);
+        if (cacheKey) {
+            cacheSet({
+                key: cacheKey,
+                createdAt: Date.now(),
+                indexMtimeMs,
+                results: fallbackResults
+            });
+        }
+        return fallbackResults;
     }
 };