@monoes/monograph 1.1.0 → 1.2.1

package/dist/src/skills/platform-skills.js

@@ -0,0 +1,179 @@
+/**
+ * Multi-platform IDE Skill File Installer
+ *
+ * Generates and installs per-community skill files for various IDE/platform
+ * targets (Claude, Cursor, VS Code, Zed, Codex, Gemini, Aider, Copilot, Kiro).
+ * Each platform gets one file per community describing exported symbols from
+ * that community.
+ */
+import fs from 'fs/promises';
+import fsSync from 'fs';
+import path from 'path';
+// ============================================================================
+// SUPPORTED PLATFORMS
+// ============================================================================
+export const SUPPORTED_PLATFORMS = [
+    'claude',
+    'cursor',
+    'vscode',
+    'zed',
+    'codex',
+    'gemini',
+    'aider',
+    'copilot',
+    'kiro',
+];
+// ============================================================================
+// PLATFORM CONFIG
+// ============================================================================
+const PLATFORM_DEFAULTS = {
+    claude: { subPath: ['.claude', 'skills'], ext: '.md' },
+    cursor: { subPath: ['.cursor', 'rules'], ext: '.md' },
+    vscode: { subPath: ['.vscode'], ext: '.json' },
+    zed: { subPath: ['.zed'], ext: '.md' },
+    codex: { subPath: [], ext: '.md' },
+    gemini: { subPath: [], ext: '.md' },
+    aider: { subPath: [], ext: '.md' },
+    copilot: { subPath: ['.github'], ext: '.md' },
+    kiro: { subPath: ['.kiro', 'steering'], ext: '.md' },
+};
+/**
+ * Fixed file names for single-file platforms (no per-community files).
+ * When defined, a single skill file is written regardless of communities.
+ */
+const PLATFORM_FIXED_FILE = {
+    codex: 'AGENTS.md',
+    gemini: 'GEMINI.md',
+    aider: 'AGENTS.md',
+    copilot: 'copilot-instructions.md',
+    kiro: 'monograph.md',
+};
+// ============================================================================
+// SYNC INSTALLER (for new platforms + compatibility)
+// ============================================================================
+/**
+ * Synchronously install a skill file for a specific platform into the repo.
+ * Returns { filesWritten } where filesWritten contains absolute paths to written files.
+ *
+ * New single-file platforms (codex, gemini, aider, copilot, kiro) always write
+ * one file regardless of communities. Existing multi-file platforms write one
+ * file per community entry.
+ */
+export function installPlatformSkill(repoPath, platform, communities) {
+    const platformConfig = PLATFORM_DEFAULTS[platform];
+    if (!platformConfig) {
+        return { filesWritten: [] };
+    }
+    const outputDir = platformConfig.subPath.length > 0
+        ? path.join(repoPath, ...platformConfig.subPath)
+        : repoPath;
+    fsSync.mkdirSync(outputDir, { recursive: true });
+    const filesWritten = [];
+    const fixedFileName = PLATFORM_FIXED_FILE[platform];
+    if (fixedFileName) {
+        // Single-file platform: write one skill overview file
+        const filePath = path.join(outputDir, fixedFileName);
+        const content = renderMonographSkillDoc(platform);
+        fsSync.writeFileSync(filePath, content, 'utf-8');
+        filesWritten.push(filePath);
+    }
+    else {
+        // Multi-file platform: one file per community (existing behavior)
+        const ext = platformConfig.ext;
+        const normalised = communities.map(c => typeof c === 'string' ? { name: c, symbols: [] } : c);
+        for (const community of normalised) {
+            const fileName = `${community.name}-skills${ext}`;
+            const filePath = path.join(outputDir, fileName);
+            let content;
+            if (ext === '.json') {
+                content = renderVsCodeSnippet(community);
+            }
+            else {
+                content = renderMarkdown(community);
+            }
+            fsSync.writeFileSync(filePath, content, 'utf-8');
+            filesWritten.push(filePath);
+        }
+    }
+    return { filesWritten };
+}
+// ============================================================================
+// MAIN EXPORT
+// ============================================================================
+/**
+ * Install skill files for a specific platform into the repo.
+ *
+ * Platform output directories (relative to repoPath):
+ *   claude  → .claude/skills/
+ *   cursor  → .cursor/rules/
+ *   vscode  → .vscode/
+ *   zed     → .zed/
+ *
+ * Each platform gets one file per community. File names use the community name.
+ * Format:
+ *   claude/cursor/zed → <communityName>-skills.md
+ *   vscode            → <communityName>-skills.json (VS Code snippets format)
+ */
+export async function installSkillsForPlatform(repoPath, communities, config) {
+    const platformConfig = PLATFORM_DEFAULTS[config.platform];
+    const outputDir = config.outputDir ?? path.join(repoPath, ...platformConfig.subPath);
+    if (communities.length === 0) {
+        return { platform: config.platform, filesWritten: [], outputDir };
+    }
+    await fs.mkdir(outputDir, { recursive: true });
+    const filesWritten = [];
+    const ext = platformConfig.ext;
+    for (const community of communities) {
+        const fileName = `${community.name}-skills${ext}`;
+        const filePath = path.join(outputDir, fileName);
+        let content;
+        if (ext === '.json') {
+            content = renderVsCodeSnippet(community);
+        }
+        else {
+            content = renderMarkdown(community);
+        }
+        await fs.writeFile(filePath, content, 'utf-8');
+        filesWritten.push(filePath);
+    }
+    return { platform: config.platform, filesWritten, outputDir };
+}
+// ============================================================================
+// RENDERERS
+// ============================================================================
+function renderMonographSkillDoc(platform) {
+    const lines = [];
+    lines.push(`# Monograph Skills — ${platform.charAt(0).toUpperCase() + platform.slice(1)}`);
+    lines.push('');
+    lines.push('This file was generated by Monograph to document available skills for this platform.');
+    lines.push('');
+    lines.push('## Usage');
+    lines.push('');
+    lines.push('Monograph indexes your codebase and exposes symbol-level knowledge to AI assistants.');
+    lines.push('Run `monograph build` to update the knowledge graph and regenerate skill files.');
+    lines.push('');
+    return lines.join('\n');
+}
+function renderMarkdown(community) {
+    const lines = [];
+    lines.push(`# ${community.name} Skills`);
+    lines.push('');
+    for (const symbol of community.symbols) {
+        lines.push(`- ${symbol}`);
+    }
+    lines.push('');
+    return lines.join('\n');
+}
+function renderVsCodeSnippet(community) {
+    const snippetKey = community.name;
+    const body = community.symbols;
+    const snippet = {
+        [snippetKey]: {
+            prefix: community.name,
+            body,
+            description: `${community.name} monograph skill`,
+        },
+    };
+    return JSON.stringify(snippet, null, 2);
+}
+//# sourceMappingURL=platform-skills.js.map

package/dist/src/skills/platform-skills.js.map

@@ -0,0 +1 @@
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package/dist/src/staleness/git-staleness.d.ts

@@ -0,0 +1,11 @@
+import type { MonographDb } from '../storage/db.js';
+export interface StalenessReport {
+    isStale: boolean;
+    indexedAt: string | null;
+    indexedCommit: string | null;
+    currentCommit: string | null;
+    changedSince: string[];
+    staleSince: string | null;
+}
+export declare function checkStaleness(db: MonographDb, repoPath: string): StalenessReport;
+//# sourceMappingURL=git-staleness.d.ts.map

package/dist/src/staleness/git-staleness.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/staleness/git-staleness.js

@@ -0,0 +1,46 @@
+import { execSync } from 'child_process';
+export function checkStaleness(db, repoPath) {
+    // 1. Get stored commit hash
+    const row = db.prepare("SELECT value FROM index_meta WHERE key = 'last_commit_hash'").get();
+    const indexedCommitFull = row?.value ?? null;
+    // 2. Get current HEAD (full SHA — --short output length varies by repo size)
+    let currentCommit = null;
+    try {
+        currentCommit = execSync('git rev-parse HEAD', { cwd: repoPath, encoding: 'utf8' }).trim();
+    }
+    catch {
+        // Not a git repo or git not available
+        return { isStale: false, indexedAt: null, indexedCommit: null, currentCommit: null, changedSince: [], staleSince: null };
+    }
+    // Display short SHA (7 chars) for the interface field; compare short SHAs for staleness
+    const indexedCommitShort = indexedCommitFull ? indexedCommitFull.slice(0, 7) : null;
+    const currentCommitShort = currentCommit ? currentCommit.slice(0, 7) : null;
+    // 3. If no stored commit or short SHAs match, not stale
+    if (!indexedCommitFull || indexedCommitShort === currentCommitShort) {
+        return { isStale: false, indexedAt: null, indexedCommit: indexedCommitShort, currentCommit: currentCommitShort, changedSince: [], staleSince: null };
+    }
+    // Guard: indexedCommitFull is read from SQLite — validate before shell interpolation
+    if (!/^[0-9a-f]{7,40}$/i.test(indexedCommitFull)) {
+        return { isStale: true, indexedAt: null, indexedCommit: indexedCommitShort, currentCommit: currentCommitShort, changedSince: [], staleSince: null };
+    }
+    // 4. Get changed files between indexed commit and HEAD
+    let changedSince = [];
+    try {
+        const diff = execSync(`git diff --name-only ${indexedCommitFull}..HEAD`, { cwd: repoPath, encoding: 'utf8' });
+        changedSince = diff.trim().split('\n').filter(Boolean);
+    }
+    catch {
+        changedSince = [];
+    }
+    // 5. Get staleSince timestamp (first diverging commit after indexed commit)
+    let staleSince = null;
+    try {
+        const firstCommit = execSync(`git log --format="%ai" ${indexedCommitFull}..HEAD --reverse --max-count=1`, { cwd: repoPath, encoding: 'utf8' }).trim();
+        staleSince = firstCommit || null;
+    }
+    catch {
+        staleSince = null;
+    }
+    return { isStale: true, indexedAt: null, indexedCommit: indexedCommitShort, currentCommit: currentCommitShort, changedSince, staleSince };
+}
+//# sourceMappingURL=git-staleness.js.map

package/dist/src/staleness/git-staleness.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"git-staleness.js","sourceRoot":"","sources":["../../../src/staleness/git-staleness.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAYzC,MAAM,UAAU,cAAc,CAAC,EAAe,EAAE,QAAgB;IAC9D,4BAA4B;IAC5B,MAAM,GAAG,GAAG,EAAE,CAAC,OAAO,CAAC,6DAA6D,CAAC,CAAC,GAAG,EAAmC,CAAC;IAC7H,MAAM,iBAAiB,GAAG,GAAG,EAAE,KAAK,IAAI,IAAI,CAAC;IAE7C,6EAA6E;IAC7E,IAAI,aAAa,GAAkB,IAAI,CAAC;IACxC,IAAI,CAAC;QACH,aAAa,GAAG,QAAQ,CAAC,oBAAoB,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;IAC7F,CAAC;IAAC,MAAM,CAAC;QACP,sCAAsC;QACtC,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC;IAC3H,CAAC;IAED,wFAAwF;IACxF,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,CAAC,CAAC,iBAAiB,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACpF,MAAM,kBAAkB,GAAG,aAAa,CAAC,CAAC,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAE5E,wDAAwD;IACxD,IAAI,CAAC,iBAAiB,IAAI,kBAAkB,KAAK,kBAAkB,EAAE,CAAC;QACpE,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,aAAa,EAAE,kBAAkB,EAAE,aAAa,EAAE,kBAAkB,EAAE,YAAY,EAAE,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC;IACvJ,CAAC;IAED,qFAAqF;IACrF,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,iBAAiB,CAAC,EAAE,CAAC;QACjD,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,aAAa,EAAE,kBAAkB,EAAE,aAAa,EAAE,kBAAkB,EAAE,YAAY,EAAE,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC;IACtJ,CAAC;IAED,uDAAuD;IACvD,IAAI,YAAY,GAAa,EAAE,CAAC;IAChC,IAAI,CAAC;QACH,MAAM,IAAI,GAAG,QAAQ,CAAC,wBAAwB,iBAAiB,QAAQ,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC;QAC9G,YAAY,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;IACzD,CAAC;IAAC,MAAM,CAAC;QACP,YAAY,GAAG,EAAE,CAAC;IACpB,CAAC;IAED,4EAA4E;IAC5E,IAAI,UAAU,GAAkB,IAAI,CAAC;IACrC,IAAI,CAAC;QACH,MAAM,WAAW,GAAG,QAAQ,CAC1B,0BAA0B,iBAAiB,gCAAgC,EAC3E,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,CACpC,CAAC,IAAI,EAAE,CAAC;QACT,UAAU,GAAG,WAAW,IAAI,IAAI,CAAC;IACnC,CAAC;IAAC,MAAM,CAAC;QACP,UAAU,GAAG,IAAI,CAAC;IACpB,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,aAAa,EAAE,kBAAkB,EAAE,aAAa,EAAE,kBAAkB,EAAE,YAAY,EAAE,UAAU,EAAE,CAAC;AAC5I,CAAC"}

package/dist/src/storage/db.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"db.d.ts","sourceRoot":"","sources":["../../../src/storage/db.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AAStC,MAAM,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC;AAE5C,wBAAgB,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,WAAW,CAWlD;AAED,wBAAgB,OAAO,CAAC,EAAE,EAAE,WAAW,GAAG,IAAI,CAE7C;AAYD,+DAA+D;AAC/D,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC,EAAE,EAAE,WAAW,KAAK,IAAI,GAAG,IAAI,CActF"}
+{"version":3,"file":"db.d.ts","sourceRoot":"","sources":["../../../src/storage/db.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AAUtC,MAAM,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC;AAE5C,wBAAgB,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,WAAW,CAWlD;AAED,wBAAgB,OAAO,CAAC,EAAE,EAAE,WAAW,GAAG,IAAI,CAE7C;AAyBD,+DAA+D;AAC/D,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC,EAAE,EAAE,WAAW,KAAK,IAAI,GAAG,IAAI,CActF"}

package/dist/src/storage/db.js

@@ -1,7 +1,7 @@
 import Database from 'better-sqlite3';
 import { mkdirSync, existsSync, renameSync, unlinkSync } from 'fs';
 import { dirname } from 'path';
-import { CREATE_NODES, CREATE_EDGES, CREATE_COMMUNITIES, CREATE_INDEX_META, CREATE_NODES_FTS, CREATE_INDEXES, FTS_SYNC_TRIGGERS, } from './schema.js';
+import { CREATE_NODES, CREATE_EDGES, CREATE_COMMUNITIES, CREATE_INDEX_META, CREATE_NODES_FTS, CREATE_INDEXES, FTS_SYNC_TRIGGERS, CREATE_EMBEDDINGS, CREATE_WIKI_PAGES, } from './schema.js';
 import { MonographError } from '../types.js';
 export function openDb(dbPath) {
     try {
@@ -28,6 +28,20 @@ function applyMigrations(db) {
     for (const idx of CREATE_INDEXES)
         db.exec(idx);
     db.exec(FTS_SYNC_TRIGGERS);
+    db.exec(CREATE_EMBEDDINGS);
+    db.exec(CREATE_WIKI_PAGES);
+    // Schema version table — tracks incremental column additions.
+    db.exec(`CREATE TABLE IF NOT EXISTS schema_version (version INTEGER PRIMARY KEY)`);
+    const row = db.prepare('SELECT MAX(version) AS v FROM schema_version').get();
+    const current = row?.v ?? 0;
+    if (current < 1) {
+        // v1: added `reason TEXT` to edges
+        try {
+            db.exec('ALTER TABLE edges ADD COLUMN reason TEXT');
+        }
+        catch { /* already present */ }
+        db.prepare('INSERT OR REPLACE INTO schema_version VALUES (1)').run();
+    }
 }
 /** Write to a .tmp file then rename for atomic replacement. */
 export function atomicRebuild(dbPath, buildFn) {

package/dist/src/storage/db.js.map

@@ -1 +1 @@
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+{"version":3,"file":"db.js","sourceRoot":"","sources":["../../../src/storage/db.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,IAAI,CAAC;AACnE,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAC;AAC/B,OAAO,EACL,YAAY,EAAE,YAAY,EAAE,kBAAkB,EAC9C,iBAAiB,EAAE,gBAAgB,EAAE,cAAc,EAAE,iBAAiB,EACtE,iBAAiB,EAAE,iBAAiB,GACrC,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAI7C,MAAM,UAAU,MAAM,CAAC,MAAc;IACnC,IAAI,CAAC;QACH,SAAS,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QAChD,MAAM,EAAE,GAAG,IAAI,QAAQ,CAAC,MAAM,CAAC,CAAC;QAChC,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;QAChC,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC;QAC/B,eAAe,CAAC,EAAE,CAAC,CAAC;QACpB,OAAO,EAAE,CAAC;IACZ,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,IAAI,cAAc,CAAC,8BAA8B,MAAM,EAAE,EAAE,GAAG,CAAC,CAAC;IACxE,CAAC;AACH,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,EAAe;IACrC,EAAE,CAAC,KAAK,EAAE,CAAC;AACb,CAAC;AAED,SAAS,eAAe,CAAC,EAAe;IACtC,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IACtB,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IACtB,EAAE,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC;IAC5B,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAC3B,EAAE,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;IAC1B,KAAK,MAAM,GAAG,IAAI,cAAc;QAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IAC/C,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAC3B,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAC3B,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAE3B,8DAA8D;IAC9D,EAAE,CAAC,IAAI,CAAC,yEAAyE,CAAC,CAAC;IACnF,MAAM,GAAG,GAAG,EAAE,CAAC,OAAO,CAAC,8CAA8C,CAAC,CAAC,GAAG,EAA0B,CAAC;IACrG,MAAM,OAAO,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,CAAC;IAE5B,IAAI,OAAO,GAAG,CAAC,EAAE,CAAC;QAChB,mCAAmC;QACnC,IAAI,CAAC;YAAC,EAAE,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAC;QAAC,CAAC;QAAC,MAAM,CAAC,CAAC,qBAAqB,CAAC,CAAC;QAC5F,EAAE,CAAC,OAAO,CAAC,kDAAkD,CAAC,CAAC,GAAG,EAAE,CAAC;IACvE,CAAC;AACH,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,aAAa,CAAC,MAAc,EAAE,OAAkC;IAC9E,MAAM,OAAO,GAAG,MAAM,GAAG,MAAM,CAAC;IAChC,MAAM,EAAE,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC;IAC3B,IAAI,CAAC;QACH,OAAO,CAAC,EAAE,CAAC,CAAC;QACZ,EAAE,CAAC,KAAK,EAAE,CAAC;QACX,UAAU,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;IAC9B,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,EAAE,CAAC,KAAK,EAAE,CAAC;QACX,IAAI,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YACxB,IAAI,CAAC;gBAAC,UAAU,CAAC,OAAO,CAAC,CAAC;YAAC,CAAC;YAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC;QACrD,CAAC;QACD,MAAM,GAAG,CAAC;IACZ,CAAC;AACH,CAAC"}

package/dist/src/storage/edge-store.d.ts

@@ -2,6 +2,8 @@ import type Database from 'better-sqlite3';
 import type { MonographEdge } from '../types.js';
 export declare function insertEdge(db: Database.Database, edge: MonographEdge): void;
 export declare function insertEdges(db: Database.Database, edges: MonographEdge[]): void;
+/** Batch-fetch edges for multiple source IDs using a single SQL IN query. Batches at 50 IDs. */
+export declare function getEdgesForSources(db: Database.Database, sourceIds: string[]): MonographEdge[];
 export declare function getEdgesForSource(db: Database.Database, sourceId: string): MonographEdge[];
 export declare function getEdgesForTarget(db: Database.Database, targetId: string): MonographEdge[];
 export declare function deleteEdgesForFile(db: Database.Database, filePath: string): void;

package/dist/src/storage/edge-store.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"edge-store.d.ts","sourceRoot":"","sources":["../../../src/storage/edge-store.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAC3C,OAAO,KAAK,EAAiB,aAAa,EAAE,MAAM,aAAa,CAAC;AAEhE,wBAAgB,UAAU,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,IAAI,EAAE,aAAa,GAAG,IAAI,CAc3E;AAOD,wBAAgB,WAAW,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,KAAK,EAAE,aAAa,EAAE,GAAG,IAAI,CAmB/E;AAED,gGAAgG;AAChG,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,aAAa,EAAE,CAa9F;AAED,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,QAAQ,EAAE,MAAM,GAAG,aAAa,EAAE,CAK1F;AAED,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,QAAQ,EAAE,MAAM,GAAG,aAAa,EAAE,CAK1F;AAED,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,QAAQ,EAAE,MAAM,GAAG,IAAI,CAIhF;AAED,wBAAgB,UAAU,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,MAAM,CAGxD"}

package/dist/src/storage/edge-store.js

@@ -1,17 +1,42 @@
 export function insertEdge(db, edge) {
     db.prepare(`
-    INSERT OR REPLACE INTO edges (id, source_id, target_id, relation, confidence, confidence_score)
-    VALUES (?, ?, ?, ?, ?, ?)
-  `).run(edge.id, edge.sourceId, edge.targetId, edge.relation, edge.confidence, edge.confidenceScore);
+    INSERT OR REPLACE INTO edges (id, source_id, target_id, relation, confidence, confidence_score, reason, evidence)
+    VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+  `).run(edge.id, edge.sourceId, edge.targetId, edge.relation, edge.confidence, edge.confidenceScore, edge.reason ?? null, edge.evidence != null ? JSON.stringify(edge.evidence) : null);
 }
+const INSERT_EDGE_SQL = `
+    INSERT OR REPLACE INTO edges (id, source_id, target_id, relation, confidence, confidence_score, reason, evidence)
+    VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+  `;
 export function insertEdges(db, edges) {
+    if (edges.length === 0)
+        return;
+    // Prepare once and reuse across all rows — avoids N redundant prepare calls
+    const stmt = db.prepare(INSERT_EDGE_SQL);
     const insertMany = db.transaction((rows) => {
         for (const e of rows) {
-            insertEdge(db, e);
+            stmt.run(e.id, e.sourceId, e.targetId, e.relation, e.confidence, e.confidenceScore, e.reason ?? null, e.evidence != null ? JSON.stringify(e.evidence) : null);
         }
     });
     insertMany(edges);
 }
+/** Batch-fetch edges for multiple source IDs using a single SQL IN query. Batches at 50 IDs. */
+export function getEdgesForSources(db, sourceIds) {
+    if (sourceIds.length === 0)
+        return [];
+    const BATCH = 50;
+    const results = [];
+    for (let i = 0; i < sourceIds.length; i += BATCH) {
+        const chunk = sourceIds.slice(i, i + BATCH);
+        const placeholders = chunk.map(() => '?').join(',');
+        const rows = db
+            .prepare(`SELECT * FROM edges WHERE source_id IN (${placeholders})`)
+            .all(...chunk);
+        for (const row of rows)
+            results.push(rowToEdge(row));
+    }
+    return results;
+}
 export function getEdgesForSource(db, sourceId) {
     const rows = db
         .prepare('SELECT * FROM edges WHERE source_id = ?')
@@ -41,6 +66,8 @@ function rowToEdge(row) {
         relation: row.relation,
         confidence: row.confidence,
         confidenceScore: row.confidence_score,
+        reason: row.reason,
+        evidence: row.evidence ? JSON.parse(row.evidence) : undefined,
     };
 }
 //# sourceMappingURL=edge-store.js.map

package/dist/src/storage/edge-store.js.map

@@ -1 +1 @@
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package/dist/src/storage/embedding-store.d.ts

@@ -0,0 +1,29 @@
+import type Database from 'better-sqlite3';
+/**
+ * CRUD operations for the embeddings table.
+ *
+ * Vectors are stored as BLOBs (raw Float32Array bytes) and reconstructed on read.
+ */
+/**
+ * Ensure the embeddings table has the content_hash column introduced in a later
+ * schema version. Call this ONCE before a batch of upserts rather than inside
+ * upsertEmbedding itself to avoid running ALTER TABLE on every row write.
+ */
+export declare function ensureEmbeddingSchema(db: Database.Database): void;
+export declare function upsertEmbedding(db: Database.Database, nodeId: string, vector: Float32Array, contentHash?: string): void;
+/**
+ * Bulk-upsert multiple embeddings in a single transaction.
+ * Calls ensureEmbeddingSchema once before writing, then wraps all inserts in
+ * a transaction for 10-100x faster throughput vs per-row upsertEmbedding calls.
+ */
+export declare function batchUpsertEmbeddings(db: Database.Database, entries: Array<{
+    nodeId: string;
+    vector: Float32Array;
+    contentHash?: string;
+}>): void;
+export declare function getEmbeddingContentHash(db: Database.Database, nodeId: string): string | null;
+export declare function isEmbeddingStale(db: Database.Database, nodeId: string, currentHash: string): boolean;
+export declare function getEmbedding(db: Database.Database, nodeId: string): Float32Array | null;
+export declare function getAllEmbeddings(db: Database.Database): Map<string, Float32Array>;
+export declare function countEmbeddings(db: Database.Database): number;
+//# sourceMappingURL=embedding-store.d.ts.map

package/dist/src/storage/embedding-store.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/storage/embedding-store.js

@@ -0,0 +1,77 @@
+/**
+ * CRUD operations for the embeddings table.
+ *
+ * Vectors are stored as BLOBs (raw Float32Array bytes) and reconstructed on read.
+ */
+/**
+ * Ensure the embeddings table has the content_hash column introduced in a later
+ * schema version. Call this ONCE before a batch of upserts rather than inside
+ * upsertEmbedding itself to avoid running ALTER TABLE on every row write.
+ */
+export function ensureEmbeddingSchema(db) {
+    try {
+        db.exec('ALTER TABLE embeddings ADD COLUMN content_hash TEXT');
+    }
+    catch {
+        // Column already exists — ignore.
+    }
+}
+export function upsertEmbedding(db, nodeId, vector, contentHash) {
+    const buf = Buffer.from(vector.buffer, vector.byteOffset, vector.byteLength);
+    db
+        .prepare('INSERT OR REPLACE INTO embeddings (node_id, vector, content_hash) VALUES (?, ?, ?)')
+        .run(nodeId, buf, contentHash ?? null);
+}
+/**
+ * Bulk-upsert multiple embeddings in a single transaction.
+ * Calls ensureEmbeddingSchema once before writing, then wraps all inserts in
+ * a transaction for 10-100x faster throughput vs per-row upsertEmbedding calls.
+ */
+export function batchUpsertEmbeddings(db, entries) {
+    if (entries.length === 0)
+        return;
+    ensureEmbeddingSchema(db);
+    const stmt = db.prepare('INSERT OR REPLACE INTO embeddings (node_id, vector, content_hash) VALUES (?, ?, ?)');
+    const insertMany = db.transaction((rows) => {
+        for (const e of rows) {
+            const buf = Buffer.from(e.vector.buffer, e.vector.byteOffset, e.vector.byteLength);
+            stmt.run(e.nodeId, buf, e.contentHash ?? null);
+        }
+    });
+    insertMany(entries);
+}
+export function getEmbeddingContentHash(db, nodeId) {
+    const row = db
+        .prepare('SELECT content_hash FROM embeddings WHERE node_id = ?')
+        .get(nodeId);
+    return row?.content_hash ?? null;
+}
+export function isEmbeddingStale(db, nodeId, currentHash) {
+    const stored = getEmbeddingContentHash(db, nodeId);
+    return stored !== currentHash;
+}
+export function getEmbedding(db, nodeId) {
+    const row = db.prepare('SELECT vector FROM embeddings WHERE node_id = ?').get(nodeId);
+    if (!row)
+        return null;
+    return bufToFloat32(row.vector);
+}
+export function getAllEmbeddings(db) {
+    const rows = db.prepare('SELECT node_id, vector FROM embeddings').all();
+    const result = new Map();
+    for (const row of rows) {
+        result.set(row.node_id, bufToFloat32(row.vector));
+    }
+    return result;
+}
+export function countEmbeddings(db) {
+    const row = db.prepare('SELECT COUNT(*) AS n FROM embeddings').get();
+    return row.n;
+}
+// ── Internal helpers ──────────────────────────────────────────────────────────
+function bufToFloat32(buf) {
+    // Copy to a fresh ArrayBuffer so slice offset doesn't cause issues
+    const ab = buf.buffer.slice(buf.byteOffset, buf.byteOffset + buf.byteLength);
+    return new Float32Array(ab);
+}
+//# sourceMappingURL=embedding-store.js.map

package/dist/src/storage/embedding-store.js.map

@@ -0,0 +1 @@
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package/dist/src/storage/file-cache.d.ts

@@ -0,0 +1,23 @@
+import type { MonographDb } from './db.js';
+export interface FileCacheEntry {
+    filePath: string;
+    contentHash: string;
+    lastParsed: number;
+    nodeCount: number;
+    edgeCount: number;
+}
+export declare function hashFileContent(content: string): string;
+export declare function isFileCached(db: MonographDb, filePath: string, contentHash: string): boolean;
+export declare function updateFileCache(db: MonographDb, entry: FileCacheEntry): void;
+/**
+ * Bulk-upsert multiple file cache entries in a single transaction.
+ * Prefer this over calling updateFileCache in a loop for pipeline batch writes.
+ */
+export declare function batchUpdateFileCache(db: MonographDb, entries: FileCacheEntry[]): void;
+export declare function getFileCacheStats(db: MonographDb): {
+    totalCached: number;
+    hitRate: number;
+    stalePaths: string[];
+};
+export declare function clearFileCache(db: MonographDb): void;
+//# sourceMappingURL=file-cache.d.ts.map

package/dist/src/storage/file-cache.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"file-cache.d.ts","sourceRoot":"","sources":["../../../src/storage/file-cache.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,SAAS,CAAC;AAE3C,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAEvD;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,CAK5F;AAED,wBAAgB,eAAe,CAAC,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE,cAAc,GAAG,IAAI,CAK5E;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,EAAE,GAAG,IAAI,CAYrF;AAED,wBAAgB,iBAAiB,CAAC,EAAE,EAAE,WAAW,GAAG;IAClD,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,EAAE,CAAC;CACtB,CAsBA;AAED,wBAAgB,cAAc,CAAC,EAAE,EAAE,WAAW,GAAG,IAAI,CAEpD"}

package/dist/src/storage/file-cache.js

@@ -0,0 +1,56 @@
+import { createHash } from 'crypto';
+export function hashFileContent(content) {
+    return createHash('sha256').update(content).digest('hex');
+}
+export function isFileCached(db, filePath, contentHash) {
+    const row = db.prepare('SELECT content_hash FROM file_cache WHERE file_path = ?').get(filePath);
+    return row?.content_hash === contentHash;
+}
+export function updateFileCache(db, entry) {
+    db.prepare(`
+    INSERT OR REPLACE INTO file_cache (file_path, content_hash, last_parsed, node_count, edge_count)
+    VALUES (?, ?, ?, ?, ?)
+  `).run(entry.filePath, entry.contentHash, entry.lastParsed, entry.nodeCount, entry.edgeCount);
+}
+/**
+ * Bulk-upsert multiple file cache entries in a single transaction.
+ * Prefer this over calling updateFileCache in a loop for pipeline batch writes.
+ */
+export function batchUpdateFileCache(db, entries) {
+    if (entries.length === 0)
+        return;
+    const stmt = db.prepare(`
+    INSERT OR REPLACE INTO file_cache (file_path, content_hash, last_parsed, node_count, edge_count)
+    VALUES (?, ?, ?, ?, ?)
+  `);
+    const insertMany = db.transaction((rows) => {
+        for (const e of rows) {
+            stmt.run(e.filePath, e.contentHash, e.lastParsed, e.nodeCount, e.edgeCount);
+        }
+    });
+    insertMany(entries);
+}
+export function getFileCacheStats(db) {
+    // Single query: count cached entries and distinct indexed file paths in one pass.
+    const counts = db.prepare(`
+    SELECT
+      (SELECT COUNT(*) FROM file_cache) AS total_cached,
+      (SELECT COUNT(DISTINCT file_path) FROM nodes WHERE file_path IS NOT NULL) AS total_indexed
+  `).get();
+    const totalCached = counts.total_cached;
+    const hitRate = counts.total_indexed > 0 ? totalCached / counts.total_indexed : 0;
+    // Find stale paths via SQL LEFT JOIN — avoids loading all rows into JS memory.
+    const stalePaths = db.prepare(`
+    SELECT fc.file_path
+    FROM file_cache fc
+    LEFT JOIN (
+      SELECT DISTINCT file_path FROM nodes WHERE file_path IS NOT NULL
+    ) n ON fc.file_path = n.file_path
+    WHERE n.file_path IS NULL
+  `).all().map(r => r.file_path);
+    return { totalCached, hitRate, stalePaths };
+}
+export function clearFileCache(db) {
+    db.prepare('DELETE FROM file_cache').run();
+}
+//# sourceMappingURL=file-cache.js.map

package/dist/src/storage/file-cache.js.map

@@ -0,0 +1 @@
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package/dist/src/storage/fts-store.d.ts

@@ -6,6 +6,24 @@ export interface FtsResult {
     filePath: string | null;
     label: string;
     rank: number;
+    /** First line of the symbol in its source file (1-based, null if unknown). */
+    startLine: number | null;
+    /** Last line of the symbol in its source file (1-based, null if unknown). */
+    endLine: number | null;
 }
 export declare function ftsSearch(db: Database.Database, query: string, limit: number, label?: string): FtsResult[];
+export interface HybridSearchResult extends FtsResult {
+    combinedScore: number;
+    matchStrategy: 'fts' | 'like' | 'fuzzy';
+}
+/**
+ * Hybrid search combining three strategies:
+ *  1. FTS5 (trigram) BM25 match via `ftsSearch`
+ *  2. LIKE fallback for short queries (≤3 chars) or when FTS returns 0 results
+ *  3. In-memory fuzzy character-sequence scoring applied to all candidates
+ *
+ * Results are deduped by id (highest combinedScore wins), re-ranked, and
+ * trimmed to `limit`. The existing `ftsSearch` is left unchanged.
+ */
+export declare function hybridSearch(db: Database.Database, query: string, limit: number, label?: string): HybridSearchResult[];
 //# sourceMappingURL=fts-store.d.ts.map

package/dist/src/storage/fts-store.d.ts.map

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