monomind 1.9.16 → 1.10.0

package/packages/@monomind/cli/dist/src/commands/monograph.d.ts

@@ -1,8 +0,0 @@
-/**
- * Monograph CLI Command
- * Knowledge graph for code and documents — build, search, inspect.
- */
-import type { Command } from '../types.js';
-export declare const monographCommand: Command;
-export default monographCommand;
-//# sourceMappingURL=monograph.d.ts.map

package/packages/@monomind/cli/dist/src/commands/monograph.js

@@ -1,526 +0,0 @@
-/**
- * Monograph CLI Command
- * Knowledge graph for code and documents — build, search, inspect.
- */
-import { join, resolve, extname } from 'path';
-import { readdirSync, statSync, existsSync } from 'fs';
-import { output } from '../output.js';
-const DOC_EXTENSIONS = new Set(['.md', '.mdx', '.txt', '.rst', '.pdf']);
-const IGNORE_DIRS = new Set([
-    'node_modules', '.git', 'dist', 'build', '__pycache__',
-    '.cache', 'coverage', '.monomind', 'vendor', 'target',
-]);
-function getDbPath(root) {
-    return join(root, '.monomind', 'monograph.db');
-}
-function walkDocs(dir, ignore) {
-    const extraIgnore = new Set(ignore);
-    const results = [];
-    function walk(d) {
-        let entries;
-        try {
-            entries = readdirSync(d);
-        }
-        catch {
-            return;
-        }
-        for (const entry of entries) {
-            if (IGNORE_DIRS.has(entry) || extraIgnore.has(entry))
-                continue;
-            const full = join(d, entry);
-            let st;
-            try {
-                st = statSync(full);
-            }
-            catch {
-                continue;
-            }
-            if (st.isDirectory()) {
-                walk(full);
-                continue;
-            }
-            const ext = extname(entry).toLowerCase();
-            if (DOC_EXTENSIONS.has(ext))
-                results.push({ path: full, ext });
-        }
-    }
-    walk(dir);
-    return results;
-}
-// ── build subcommand ──────────────────────────────────────────────────────────
-const buildCommand = {
-    name: 'build',
-    description: 'Build the knowledge graph from code, docs (md/txt/rst), and PDFs',
-    options: [
-        { name: 'path', short: 'p', type: 'string', description: 'Root path to index (default: cwd)' },
-        { name: 'code-only', type: 'boolean', description: 'Index only code files, skip documents' },
-        { name: 'llm', type: 'boolean', description: 'Enable Claude-powered semantic extraction (requires ANTHROPIC_API_KEY)' },
-        { name: 'llm-sections', type: 'number', description: 'Max sections to enrich with LLM (default 50)', default: '50' },
-        { name: 'force', short: 'f', type: 'boolean', description: 'Force full rebuild even if index is fresh' },
-    ],
-    examples: [
-        { command: 'monomind monograph build', description: 'Index code + all documents' },
-        { command: 'monomind monograph build --llm', description: 'Also extract semantic relationships with Claude' },
-        { command: 'monomind monograph build --code-only', description: 'Code only, skip docs' },
-        { command: 'monomind monograph build -p ./docs', description: 'Index a specific path' },
-    ],
-    action: async (ctx) => {
-        const root = resolve(ctx.flags.path ?? process.cwd());
-        const codeOnly = ctx.flags['code-only'] === true;
-        const force = ctx.flags.force === true;
-        const llmFlag = ctx.flags.llm === true;
-        const llmSections = parseInt(ctx.flags['llm-sections'] || '50', 10);
-        const hasApiKey = !!process.env.ANTHROPIC_API_KEY;
-        const llmMaxSections = (llmFlag && hasApiKey) ? llmSections : 0;
-        if (llmFlag && !hasApiKey) {
-            output.printWarning('--llm passed but ANTHROPIC_API_KEY is not set — LLM extraction disabled');
-        }
-        output.writeln();
-        output.writeln(output.bold('Monograph — Knowledge Graph Build'));
-        output.writeln(output.dim('─'.repeat(60)));
-        output.writeln(`  Path    : ${root}`);
-        output.writeln(`  Mode    : ${codeOnly ? 'Code only' : 'Code + Documents + PDFs'}`);
-        if (llmMaxSections > 0) {
-            output.writeln(`  Claude  : Enriching up to ${llmMaxSections} sections`);
-        }
-        output.writeln();
-        // Pre-scan to show what will be indexed
-        if (!codeOnly) {
-            const docs = walkDocs(root, []);
-            const byExt = new Map();
-            for (const { ext } of docs)
-                byExt.set(ext, (byExt.get(ext) ?? 0) + 1);
-            if (docs.length > 0) {
-                output.writeln(output.dim(`  Found ${docs.length} document files:`));
-                for (const [ext, count] of [...byExt.entries()].sort()) {
-                    output.writeln(output.dim(`    ${ext.padEnd(6)} ${count} files`));
-                }
-                output.writeln();
-            }
-        }
-        const spinner = output.createSpinner({ text: 'Building knowledge graph…', spinner: 'dots' });
-        spinner.start();
-        const startTime = Date.now();
-        const progressLines = [];
-        try {
-            const { buildAsync } = await import('@monoes/monograph');
-            await buildAsync(root, {
-                codeOnly,
-                force,
-                llmMaxSections,
-                onProgress: (p) => {
-                    const msg = `[${p.phase}] ${p.message ?? ''}`;
-                    progressLines.push(msg);
-                    spinner.setText(msg.slice(0, 60));
-                },
-            });
-            const elapsed = ((Date.now() - startTime) / 1000).toFixed(1);
-            spinner.succeed(`Build complete in ${elapsed}s`);
-            // Show per-phase summary
-            output.writeln();
-            output.writeln(output.bold('  Build phases:'));
-            for (const line of progressLines) {
-                output.writeln(output.dim(`    ${line}`));
-            }
-            // Show graph stats
-            output.writeln();
-            await printStats(root);
-            return { success: true };
-        }
-        catch (err) {
-            spinner.fail('Build failed');
-            output.printError(err instanceof Error ? err.message : String(err));
-            return { success: false, exitCode: 1 };
-        }
-    },
-};
-// ── wiki subcommand ───────────────────────────────────────────────────────────
-const wikiCommand = {
-    name: 'wiki',
-    description: 'Scan all docs and PDFs in the project and build a searchable knowledge graph',
-    options: [
-        { name: 'path', short: 'p', type: 'string', description: 'Root path (default: cwd)' },
-        { name: 'llm', type: 'boolean', description: 'Enrich with Claude semantic extraction (requires ANTHROPIC_API_KEY)' },
-        { name: 'llm-sections', type: 'number', description: 'Max sections for LLM enrichment (default 100)', default: '100' },
-        { name: 'force', short: 'f', type: 'boolean', description: 'Force full rebuild' },
-    ],
-    examples: [
-        { command: 'monomind monograph wiki', description: 'Build knowledge graph from all docs and PDFs' },
-        { command: 'monomind monograph wiki --llm', description: 'Also extract semantic relationships with Claude' },
-        { command: 'monomind monograph wiki --llm --llm-sections 200', description: 'Process 200 sections with Claude' },
-    ],
-    action: async (ctx) => {
-        const root = resolve(ctx.flags.path ?? process.cwd());
-        const force = ctx.flags.force === true;
-        const llmFlag = ctx.flags.llm === true;
-        const llmSections = parseInt(ctx.flags['llm-sections'] || '100', 10);
-        const hasApiKey = !!process.env.ANTHROPIC_API_KEY;
-        const llmMaxSections = (llmFlag && hasApiKey) ? llmSections : 0;
-        if (llmFlag && !hasApiKey) {
-            output.printWarning('--llm passed but ANTHROPIC_API_KEY is not set — LLM extraction disabled');
-        }
-        // Pre-scan docs
-        const docs = walkDocs(root, []);
-        const byExt = new Map();
-        for (const { ext } of docs)
-            byExt.set(ext, (byExt.get(ext) ?? 0) + 1);
-        output.writeln();
-        output.writeln(output.bold('Monograph — Wiki & Document Knowledge Graph'));
-        output.writeln(output.dim('─'.repeat(60)));
-        output.writeln(`  Path : ${root}`);
-        output.writeln();
-        if (docs.length === 0) {
-            output.printWarning('No document files found (.md .mdx .txt .rst .pdf)');
-            output.writeln(output.dim(`  Searched: ${root}`));
-            output.writeln(output.dim('  Make sure you\'re in the right directory.'));
-            return { success: false, exitCode: 1 };
-        }
-        output.writeln(output.bold(`  Discovered ${docs.length} files:`));
-        for (const [ext, count] of [...byExt.entries()].sort()) {
-            const label = ext === '.pdf' ? '(PDF chunks will be created)' :
-                ext === '.md' || ext === '.mdx' ? '(headings → Section nodes)' :
-                    '(plain text → Section nodes)';
-            output.writeln(`    ${output.success(ext.padEnd(6))} ${String(count).padStart(4)} files  ${output.dim(label)}`);
-        }
-        if (llmMaxSections > 0) {
-            output.writeln();
-            output.writeln(`  ${output.success('Claude enrichment')} enabled — up to ${llmMaxSections} sections`);
-            output.writeln(output.dim('  Extracts typed semantic relationships (DESCRIBES, CAUSES, PART_OF, …)'));
-        }
-        else if (!llmFlag) {
-            output.writeln();
-            output.writeln(output.dim('  Tip: add --llm to extract Claude-inferred semantic relationships'));
-        }
-        output.writeln();
-        const spinner = output.createSpinner({ text: 'Building…', spinner: 'dots' });
-        spinner.start();
-        const startTime = Date.now();
-        const progressLines = [];
-        try {
-            const { buildAsync } = await import('@monoes/monograph');
-            await buildAsync(root, {
-                codeOnly: false,
-                force,
-                llmMaxSections,
-                onProgress: (p) => {
-                    const msg = `[${p.phase}] ${p.message ?? ''}`;
-                    progressLines.push(msg);
-                    if (p.phase.includes('docs') || p.phase.includes('pdf') ||
-                        p.phase.includes('contextual') || p.phase.includes('llm') ||
-                        p.phase.includes('embed')) {
-                        spinner.setText(msg.slice(0, 70));
-                    }
-                },
-            });
-            const elapsed = ((Date.now() - startTime) / 1000).toFixed(1);
-            spinner.succeed(`Done in ${elapsed}s`);
-            output.writeln();
-            output.writeln(output.bold('  Knowledge graph phases:'));
-            for (const line of progressLines.filter(l => l.includes('docs') || l.includes('pdf') || l.includes('contextual') ||
-                l.includes('llm') || l.includes('embed') || l.includes('structure'))) {
-                output.writeln(output.dim(`    ${line}`));
-            }
-            output.writeln();
-            await printStats(root);
-            output.writeln();
-            output.writeln(output.bold('  Next steps:'));
-            output.printList([
-                'monomind monograph search "your query"   — search the wiki',
-                'monomind monograph stats                 — full node/edge breakdown',
-                'monomind monograph watch                 — rebuild on file changes',
-            ]);
-            return { success: true };
-        }
-        catch (err) {
-            spinner.fail('Build failed');
-            output.printError(err instanceof Error ? err.message : String(err));
-            return { success: false, exitCode: 1 };
-        }
-    },
-};
-// ── search subcommand ─────────────────────────────────────────────────────────
-const searchCommand = {
-    name: 'search',
-    description: 'Search the knowledge graph (BM25, semantic, or hybrid)',
-    options: [
-        { name: 'query', short: 'q', type: 'string', description: 'Search query', required: true },
-        { name: 'limit', short: 'l', type: 'number', description: 'Max results (default 15)', default: '15' },
-        { name: 'label', type: 'string', description: 'Filter by node type: Section, Function, Concept, File, etc.' },
-        { name: 'mode', short: 'm', type: 'string', description: 'Search mode: bm25 | semantic | hybrid (default: hybrid)', default: 'hybrid' },
-        { name: 'path', short: 'p', type: 'string', description: 'Root path (default: cwd)' },
-    ],
-    examples: [
-        { command: 'monomind monograph search -q "authentication flow"', description: 'Hybrid search across all nodes' },
-        { command: 'monomind monograph search -q "API design" --label Section', description: 'Search only doc sections' },
-        { command: 'monomind monograph search -q "pipeline" --mode semantic', description: 'Semantic (embedding) search' },
-    ],
-    action: async (ctx) => {
-        const query = ctx.flags.query;
-        const limit = parseInt(ctx.flags.limit || '15', 10);
-        const label = ctx.flags.label;
-        const mode = ctx.flags.mode ?? 'hybrid';
-        const root = resolve(ctx.flags.path ?? process.cwd());
-        const dbPath = getDbPath(root);
-        if (!query) {
-            output.printError('--query is required');
-            return { success: false, exitCode: 1 };
-        }
-        if (!existsSync(dbPath)) {
-            output.printWarning('No knowledge graph found. Run: monomind monograph build');
-            return { success: false, exitCode: 1 };
-        }
-        output.writeln();
-        output.writeln(output.bold(`Monograph Search — "${query}"`));
-        output.writeln(output.dim(`  mode: ${mode}${label ? `  label: ${label}` : ''}  limit: ${limit}`));
-        output.writeln();
-        try {
-            const { openDb, closeDb, ftsSearch, semanticSearch } = await import('@monoes/monograph');
-            const db = openDb(dbPath);
-            let results = [];
-            const K = 60;
-            if (mode === 'semantic') {
-                results = semanticSearch(db, query, limit, label).map(r => ({ ...r }));
-            }
-            else if (mode === 'bm25') {
-                results = ftsSearch(db, query, limit, label).map(r => ({ ...r }));
-            }
-            else {
-                // hybrid: RRF merge
-                const bm25 = ftsSearch(db, query, limit * 2, label);
-                const sem = semanticSearch(db, query, limit * 2, label);
-                const scores = new Map();
-                const meta = new Map();
-                bm25.forEach((r, i) => { scores.set(r.id, (scores.get(r.id) ?? 0) + 1 / (K + i)); meta.set(r.id, r); });
-                sem.forEach((r, i) => { scores.set(r.id, (scores.get(r.id) ?? 0) + 1 / (K + i)); if (!meta.has(r.id))
-                    meta.set(r.id, r); });
-                results = [...scores.entries()]
-                    .sort((a, b) => b[1] - a[1])
-                    .slice(0, limit)
-                    .map(([id, score]) => ({ ...meta.get(id), score }));
-            }
-            closeDb(db);
-            if (results.length === 0) {
-                output.printWarning('No results found.');
-                output.writeln(output.dim('  Try: --mode semantic  or  monomind monograph build to rebuild the index'));
-                return { success: true, data: [] };
-            }
-            output.printTable({
-                columns: [
-                    { key: 'label', header: 'Type', width: 12 },
-                    { key: 'name', header: 'Name', width: 32 },
-                    { key: 'file', header: 'File', width: 30 },
-                    { key: 'score', header: 'Score', width: 8 },
-                ],
-                data: results.map(r => ({
-                    label: output.dim(r.label),
-                    name: r.name.length > 30 ? r.name.slice(0, 27) + '…' : r.name,
-                    file: r.filePath ? (r.filePath.length > 28 ? '…' + r.filePath.slice(-27) : r.filePath) : output.dim('—'),
-                    score: r.score != null ? output.dim(r.score.toFixed(4)) : output.dim('—'),
-                })),
-            });
-            output.writeln(output.dim(`\n  ${results.length} results`));
-            return { success: true, data: results };
-        }
-        catch (err) {
-            output.printError(err instanceof Error ? err.message : String(err));
-            return { success: false, exitCode: 1 };
-        }
-    },
-};
-// ── stats subcommand ──────────────────────────────────────────────────────────
-const statsCommand = {
-    name: 'stats',
-    description: 'Show knowledge graph statistics — node counts, edge types, top concepts',
-    options: [
-        { name: 'path', short: 'p', type: 'string', description: 'Root path (default: cwd)' },
-        { name: 'top', type: 'number', description: 'Number of top concepts to show (default 10)', default: '10' },
-    ],
-    examples: [
-        { command: 'monomind monograph stats', description: 'Show graph statistics' },
-        { command: 'monomind monograph stats --top 20', description: 'Show top 20 concepts' },
-    ],
-    action: async (ctx) => {
-        const root = resolve(ctx.flags.path ?? process.cwd());
-        const top = parseInt(ctx.flags.top || '10', 10);
-        const dbPath = getDbPath(root);
-        if (!existsSync(dbPath)) {
-            output.printWarning('No knowledge graph found. Run: monomind monograph build');
-            return { success: false, exitCode: 1 };
-        }
-        output.writeln();
-        output.writeln(output.bold('Monograph — Knowledge Graph Statistics'));
-        output.writeln(output.dim('─'.repeat(60)));
-        output.writeln();
-        try {
-            await printStats(root, top, true);
-            return { success: true };
-        }
-        catch (err) {
-            output.printError(err instanceof Error ? err.message : String(err));
-            return { success: false, exitCode: 1 };
-        }
-    },
-};
-// ── watch subcommand ──────────────────────────────────────────────────────────
-const watchCommand = {
-    name: 'watch',
-    description: 'Watch for file changes and incrementally rebuild the knowledge graph',
-    options: [
-        { name: 'path', short: 'p', type: 'string', description: 'Root path (default: cwd)' },
-        { name: 'llm', type: 'boolean', description: 'Enable LLM enrichment on rebuild (requires ANTHROPIC_API_KEY)' },
-    ],
-    examples: [
-        { command: 'monomind monograph watch', description: 'Watch and rebuild on changes' },
-    ],
-    action: async (ctx) => {
-        const root = resolve(ctx.flags.path ?? process.cwd());
-        const llmFlag = ctx.flags.llm === true;
-        const hasApiKey = !!process.env.ANTHROPIC_API_KEY;
-        const llmMaxSections = (llmFlag && hasApiKey) ? 50 : 0;
-        output.writeln();
-        output.writeln(output.bold('Monograph — Watch Mode'));
-        output.writeln(output.dim(`  Watching: ${root}`));
-        output.writeln(output.dim('  Press Ctrl+C to stop'));
-        output.writeln();
-        try {
-            const { watchAsync } = await import('@monoes/monograph');
-            const watcher = await watchAsync(root, {
-                codeOnly: false,
-                llmMaxSections,
-                onProgress: (p) => {
-                    output.writeln(output.dim(`  [${p.phase}] ${p.message ?? ''}`));
-                },
-            });
-            output.printSuccess('Watching for changes…');
-            output.writeln();
-            await new Promise(resolve => {
-                process.on('SIGINT', () => {
-                    watcher?.stop?.();
-                    output.writeln();
-                    output.writeln(output.dim('Watch stopped.'));
-                    resolve();
-                });
-            });
-            return { success: true };
-        }
-        catch (err) {
-            output.printError(err instanceof Error ? err.message : String(err));
-            return { success: false, exitCode: 1 };
-        }
-    },
-};
-// ── shared helper ─────────────────────────────────────────────────────────────
-async function printStats(root, topN = 10, detailed = false) {
-    const { openDb, closeDb } = await import('@monoes/monograph');
-    const db = openDb(getDbPath(root));
-    try {
-        // Node counts by label
-        const nodeCounts = db.prepare(`SELECT label, COUNT(*) as n FROM nodes GROUP BY label ORDER BY n DESC`).all();
-        // Edge counts by relation
-        const edgeCounts = db.prepare(`SELECT relation, COUNT(*) as n FROM edges GROUP BY relation ORDER BY n DESC`).all();
-        // Top concepts by importance
-        const topConcepts = db.prepare(`
-      SELECT name,
-             COALESCE(json_extract(properties, '$.importance'), 1) as importance,
-             (SELECT COUNT(*) FROM edges WHERE target_id = nodes.id AND relation = 'TAGGED_AS') as sections
-      FROM nodes WHERE label = 'Concept'
-      ORDER BY importance DESC, sections DESC
-      LIMIT ?
-    `).all(topN);
-        output.writeln(output.bold('  Nodes'));
-        output.printTable({
-            columns: [
-                { key: 'label', header: 'Type', width: 18 },
-                { key: 'count', header: 'Count', width: 10 },
-                { key: 'bar', header: '', width: 30 },
-            ],
-            data: nodeCounts.map(r => {
-                const n = r.n;
-                const max = nodeCounts[0]?.n ?? 1;
-                const bars = Math.round((n / max) * 20);
-                return {
-                    label: r.label,
-                    count: String(n),
-                    bar: output.dim('█'.repeat(bars) + '░'.repeat(20 - bars)),
-                };
-            }),
-        });
-        if (detailed) {
-            output.writeln();
-            output.writeln(output.bold('  Edges'));
-            output.printTable({
-                columns: [
-                    { key: 'relation', header: 'Relation', width: 22 },
-                    { key: 'count', header: 'Count', width: 10 },
-                ],
-                data: edgeCounts.map(r => ({ relation: r.relation, count: String(r.n) })),
-            });
-        }
-        if (topConcepts.length > 0) {
-            output.writeln();
-            output.writeln(output.bold(`  Top ${topN} Concepts by Importance`));
-            output.printTable({
-                columns: [
-                    { key: 'name', header: 'Concept', width: 28 },
-                    { key: 'importance', header: 'Importance', width: 12 },
-                    { key: 'sections', header: 'Sections', width: 10 },
-                ],
-                data: topConcepts.map(r => ({
-                    name: r.name,
-                    importance: output.dim('★'.repeat(r.importance) + '☆'.repeat(5 - r.importance)),
-                    sections: String(r.sections ?? 0),
-                })),
-            });
-        }
-        // CO_OCCURS enrichment hint
-        const coOccurCount = db.prepare(`SELECT COUNT(*) as n FROM edges WHERE relation = 'CO_OCCURS'`).get().n;
-        const llmCount = db.prepare(`SELECT COUNT(*) as n FROM edges WHERE confidence = 'INFERRED'`).get().n;
-        output.writeln();
-        output.writeln(output.dim(`  CO_OCCURS edges: ${coOccurCount}   Inferred (LLM) edges: ${llmCount}`));
-        output.writeln(output.dim(`  Database: ${getDbPath(root)}`));
-    }
-    finally {
-        closeDb(db);
-    }
-}
-// ── root command ──────────────────────────────────────────────────────────────
-export const monographCommand = {
-    name: 'monograph',
-    description: 'Knowledge graph for code and documents — build, search, explore',
-    aliases: ['kg'],
-    subcommands: [buildCommand, wikiCommand, searchCommand, statsCommand, watchCommand],
-    examples: [
-        { command: 'monomind monograph wiki', description: 'Build KG from all docs and PDFs' },
-        { command: 'monomind monograph wiki --llm', description: 'Build KG with Claude semantic extraction' },
-        { command: 'monomind monograph build', description: 'Build KG from code + docs' },
-        { command: 'monomind monograph search -q "authentication"', description: 'Search the knowledge graph' },
-        { command: 'monomind monograph stats', description: 'Show graph statistics' },
-        { command: 'monomind monograph watch', description: 'Watch for changes and rebuild' },
-    ],
-    action: async () => {
-        output.writeln();
-        output.writeln(output.bold('Monograph — Knowledge Graph'));
-        output.writeln(output.dim('Code intelligence + Document wiki in one unified graph'));
-        output.writeln();
-        output.writeln('Commands:');
-        output.printList([
-            'wiki      — Scan all docs & PDFs → searchable knowledge graph',
-            'build     — Full build (code + docs + PDFs)',
-            'search    — Search across code, sections, and concepts',
-            'stats     — Node/edge counts, top concepts',
-            'watch     — Auto-rebuild on file changes',
-        ]);
-        output.writeln();
-        output.writeln('Examples:');
-        output.printList([
-            'monomind monograph wiki',
-            'monomind monograph wiki --llm',
-            'monomind monograph search -q "pipeline architecture"',
-        ]);
-        output.writeln();
-        output.writeln(output.dim('Add --llm to any build command to extract semantic relationships with Claude'));
-        return { success: true };
-    },
-};
-export default monographCommand;
-//# sourceMappingURL=monograph.js.map

package/packages/@monomind/cli/dist/src/commands/neural.d.ts

@@ -1,10 +0,0 @@
-/**
- * CLI Neural Command
- * Neural pattern training, MoE, Flash Attention, pattern learning
- *
- * github.com/nokhodian/monomind
- */
-import type { Command } from '../types.js';
-export declare const neuralCommand: Command;
-export default neuralCommand;
-//# sourceMappingURL=neural.d.ts.map