monomind 1.10.0 → 1.10.2

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

@@ -0,0 +1,8 @@
+/**
+ * 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

@@ -0,0 +1,526 @@
+/**
+ * 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

@@ -0,0 +1,10 @@
+/**
+ * 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