@gzoo/cortex 0.5.9

package/package.json

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+{
+  "name": "@gzoo/cortex",
+  "version": "0.5.9",
+  "description": "Local-first knowledge graph that watches your project files, extracts entities and relationships via LLMs, and lets you query across projects in natural language.",
+  "type": "module",
+  "license": "MIT",
+  "author": "GZOO Media LLC <hello@gzoo.ai> (https://gzoo.ai)",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/gzoonet/cortex.git"
+  },
+  "homepage": "https://github.com/gzoonet/cortex",
+  "bugs": {
+    "url": "https://github.com/gzoonet/cortex/issues"
+  },
+  "keywords": [
+    "knowledge-graph",
+    "developer-tools",
+    "local-first",
+    "llm",
+    "cli",
+    "file-watcher",
+    "sqlite",
+    "vector-search",
+    "ollama",
+    "anthropic",
+    "gemini",
+    "openai-compatible",
+    "entity-extraction",
+    "cross-project",
+    "second-brain",
+    "mcp",
+    "web-dashboard"
+  ],
+  "workspaces": [
+    "packages/*"
+  ],
+  "scripts": {
+    "build": "tsc --build --force",
+    "build:clean": "tsc --build --clean && tsc --build --force",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage",
+    "dev": "npm run dev --workspace=packages/cli",
+    "lint": "tsc --noEmit",
+    "clean": "tsc --build --clean",
+    "cortex": "node packages/cli/dist/index.js",
+    "build:bundle": "npm run build && node scripts/bundle.cjs",
+    "build:mcp": "node scripts/bundle-mcp.cjs"
+  },
+  "bin": {
+    "cortex": "dist/cortex.mjs"
+  },
+  "engines": {
+    "node": ">=20.0.0",
+    "npm": ">=9.0.0"
+  },
+  "devDependencies": {
+    "@types/node": "^20.19.35",
+    "esbuild": "^0.27.3",
+    "typescript": "^5.9.3",
+    "vitest": "^4.0.18"
+  },
+  "dependencies": {
+    "@anthropic-ai/sdk": "^0.78.0",
+    "@lancedb/lancedb": "^0.26.2",
+    "@modelcontextprotocol/sdk": "^1.17.0",
+    "better-sqlite3": "^12.6.2",
+    "chalk": "^4.1.2",
+    "chokidar": "^5.0.0",
+    "cli-table3": "^0.6.5",
+    "commander": "^14.0.3",
+    "cors": "^2.8.5",
+    "express": "^4.21.0",
+    "inquirer": "^13.3.0",
+    "openai": "^4.0.0",
+    "ora": "^9.3.0",
+    "remark-parse": "^11.0.0",
+    "tree-sitter": "^0.21.1",
+    "tree-sitter-typescript": "^0.23.2",
+    "unified": "^11.0.5",
+    "ws": "^8.18.0",
+    "yaml": "^2.8.2",
+    "zod": "^3.25.76"
+  }
+}

package/packages/cli/dist/commands/config.d.ts

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+import { Command } from 'commander';
+export declare function registerConfigCommand(program: Command): void;
+export declare function registerExcludeCommand(program: Command): void;
+//# sourceMappingURL=config.d.ts.map

package/packages/cli/dist/commands/config.d.ts.map

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package/packages/cli/dist/commands/config.js

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+import { resolve, dirname } from 'node:path';
+import { homedir } from 'node:os';
+import { readFileSync, writeFileSync, mkdirSync } from 'node:fs';
+import chalk from 'chalk';
+import { loadConfig, getDefaultConfig, cortexConfigSchema, createLogger } from '@cortex/core';
+const logger = createLogger('cli:config');
+export function registerConfigCommand(program) {
+    const configCmd = program
+        .command('config')
+        .description('Read/write/validate configuration (includes exclude subcommand)');
+    configCmd
+        .command('get <key>')
+        .description('Get a configuration value')
+        .action(async (key) => {
+        const globals = program.opts();
+        await runConfigGet(key, globals);
+    });
+    configCmd
+        .command('set <key> <value>')
+        .description('Set a configuration value')
+        .action(async (key, value) => {
+        const globals = program.opts();
+        await runConfigSet(key, value, globals);
+    });
+    configCmd
+        .command('list')
+        .description('Show all non-default values')
+        .action(async () => {
+        const globals = program.opts();
+        await runConfigList(globals);
+    });
+    configCmd
+        .command('reset [key]')
+        .description('Reset to default (all if no key)')
+        .action(async (key) => {
+        const globals = program.opts();
+        await runConfigReset(key, globals);
+    });
+    configCmd
+        .command('validate')
+        .description('Validate configuration')
+        .action(async () => {
+        const globals = program.opts();
+        await runConfigValidate(globals);
+    });
+    // ── exclude subcommands ────────────────────────────────────────────────────
+    const excludeCmd = configCmd
+        .command('exclude')
+        .description('Manage which files and directories are ignored during watching');
+    excludeCmd
+        .command('list')
+        .description('Show all exclude patterns')
+        .action(async () => {
+        const globals = program.opts();
+        await runExcludeList(globals);
+    });
+    excludeCmd
+        .command('add <pattern>')
+        .description('Add an exclude pattern (file name, directory name, or glob like *.min.js)')
+        .action(async (pattern) => {
+        const globals = program.opts();
+        await runExcludeAdd(pattern, globals);
+    });
+    excludeCmd
+        .command('remove <pattern>')
+        .description('Remove an exclude pattern')
+        .action(async (pattern) => {
+        const globals = program.opts();
+        await runExcludeRemove(pattern, globals);
+    });
+}
+function getNestedValue(obj, path) {
+    const parts = path.split('.');
+    let current = obj;
+    for (const part of parts) {
+        if (current === null || current === undefined || typeof current !== 'object') {
+            return undefined;
+        }
+        current = current[part];
+    }
+    return current;
+}
+function setNestedValue(obj, path, value) {
+    const parts = path.split('.');
+    let current = obj;
+    for (let i = 0; i < parts.length - 1; i++) {
+        const part = parts[i];
+        if (current[part] === undefined || typeof current[part] !== 'object') {
+            current[part] = {};
+        }
+        current = current[part];
+    }
+    current[parts[parts.length - 1]] = value;
+}
+function parseValue(value) {
+    // Try JSON first (handles booleans, numbers, arrays, objects)
+    try {
+        return JSON.parse(value);
+    }
+    catch {
+        // Return as string
+        return value;
+    }
+}
+function getConfigFilePath(globals) {
+    if (globals.config) {
+        return resolve(globals.config, 'cortex.config.json');
+    }
+    // Search the same locations loadConfig uses: CWD first, then global ~/.cortex/
+    const cwdPath = resolve(process.cwd(), 'cortex.config.json');
+    try {
+        readFileSync(cwdPath);
+        return cwdPath;
+    }
+    catch {
+        // Fall back to global config
+        return resolve(homedir(), '.cortex', 'cortex.config.json');
+    }
+}
+function readConfigFile(path) {
+    try {
+        const content = readFileSync(path, 'utf-8');
+        return JSON.parse(content);
+    }
+    catch {
+        return {};
+    }
+}
+async function runConfigGet(key, globals) {
+    try {
+        const config = loadConfig({ configDir: globals.config ? resolve(globals.config) : undefined });
+        const value = getNestedValue(config, key);
+        if (value === undefined) {
+            if (globals.json) {
+                console.log(JSON.stringify({ error: `Key not found: ${key}` }));
+            }
+            else {
+                console.log(chalk.yellow(`Key not found: ${key}`));
+            }
+            return;
+        }
+        if (globals.json) {
+            console.log(JSON.stringify({ key, value }));
+        }
+        else {
+            const display = typeof value === 'object' ? JSON.stringify(value, null, 2) : String(value);
+            console.log(display);
+        }
+    }
+    catch (err) {
+        logger.error('Config get failed', { error: err instanceof Error ? err.message : String(err) });
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+async function runConfigSet(key, value, globals) {
+    try {
+        const configPath = getConfigFilePath(globals);
+        const raw = readConfigFile(configPath);
+        const parsed = parseValue(value);
+        setNestedValue(raw, key, parsed);
+        // Validate the new config
+        const result = cortexConfigSchema.safeParse(raw);
+        if (!result.success) {
+            const issues = result.error.issues.map((i) => `  ${i.path.join('.')}: ${i.message}`).join('\n');
+            if (globals.json) {
+                console.log(JSON.stringify({ error: 'Validation failed', issues: result.error.issues }));
+            }
+            else {
+                console.error(chalk.red('Validation failed:\n') + chalk.yellow(issues));
+            }
+            return;
+        }
+        // Write back
+        mkdirSync(dirname(configPath), { recursive: true });
+        writeFileSync(configPath, JSON.stringify(raw, null, 2) + '\n', 'utf-8');
+        if (globals.json) {
+            console.log(JSON.stringify({ key, value: parsed, saved: true }));
+        }
+        else {
+            console.log(chalk.green(`✓ Set ${key} = ${JSON.stringify(parsed)}`));
+        }
+    }
+    catch (err) {
+        logger.error('Config set failed', { error: err instanceof Error ? err.message : String(err) });
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+async function runConfigList(globals) {
+    try {
+        const config = loadConfig({ configDir: globals.config ? resolve(globals.config) : undefined });
+        const defaults = getDefaultConfig();
+        if (globals.json) {
+            console.log(JSON.stringify(config));
+            return;
+        }
+        console.log('');
+        console.log(chalk.bold.cyan('CORTEX CONFIGURATION'));
+        console.log(chalk.dim('─'.repeat(50)));
+        // Flatten and compare with defaults
+        const configFlat = flattenObject(config);
+        const defaultFlat = flattenObject(defaults);
+        let hasNonDefault = false;
+        for (const [key, value] of Object.entries(configFlat)) {
+            const defaultValue = defaultFlat[key];
+            const isDefault = JSON.stringify(value) === JSON.stringify(defaultValue);
+            if (!isDefault) {
+                hasNonDefault = true;
+                console.log(chalk.white(`  ${key}: `) +
+                    chalk.bold(JSON.stringify(value)) +
+                    chalk.dim(` (default: ${JSON.stringify(defaultValue)})`));
+            }
+        }
+        if (!hasNonDefault) {
+            console.log(chalk.dim('  All values are at defaults.'));
+        }
+        console.log('');
+    }
+    catch (err) {
+        logger.error('Config list failed', { error: err instanceof Error ? err.message : String(err) });
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+async function runConfigReset(key, globals) {
+    try {
+        const configPath = getConfigFilePath(globals);
+        const defaults = getDefaultConfig();
+        if (key) {
+            // Reset a single key
+            const raw = readConfigFile(configPath);
+            const defaultValue = getNestedValue(defaults, key);
+            if (defaultValue === undefined) {
+                if (globals.json) {
+                    console.log(JSON.stringify({ error: `Key not found: ${key}` }));
+                }
+                else {
+                    console.log(chalk.yellow(`Key not found: ${key}`));
+                }
+                return;
+            }
+            setNestedValue(raw, key, defaultValue);
+            writeFileSync(configPath, JSON.stringify(raw, null, 2) + '\n', 'utf-8');
+            if (globals.json) {
+                console.log(JSON.stringify({ key, value: defaultValue, reset: true }));
+            }
+            else {
+                console.log(chalk.green(`✓ Reset ${key} to default: ${JSON.stringify(defaultValue)}`));
+            }
+        }
+        else {
+            // Reset all — write defaults
+            writeFileSync(configPath, JSON.stringify(defaults, null, 2) + '\n', 'utf-8');
+            if (globals.json) {
+                console.log(JSON.stringify({ reset: 'all', saved: true }));
+            }
+            else {
+                console.log(chalk.green('✓ All configuration reset to defaults.'));
+            }
+        }
+    }
+    catch (err) {
+        logger.error('Config reset failed', { error: err instanceof Error ? err.message : String(err) });
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+async function runConfigValidate(globals) {
+    try {
+        const configPath = getConfigFilePath(globals);
+        const raw = readConfigFile(configPath);
+        const result = cortexConfigSchema.safeParse(raw);
+        if (result.success) {
+            if (globals.json) {
+                console.log(JSON.stringify({ valid: true }));
+            }
+            else {
+                console.log(chalk.green('✓ Configuration is valid.'));
+            }
+        }
+        else {
+            const issues = result.error.issues;
+            if (globals.json) {
+                console.log(JSON.stringify({ valid: false, issues }));
+            }
+            else {
+                console.log(chalk.red('✗ Configuration has errors:\n'));
+                for (const issue of issues) {
+                    console.log(chalk.yellow(`  ${issue.path.join('.')}: ${issue.message}`));
+                }
+            }
+        }
+    }
+    catch (err) {
+        logger.error('Config validate failed', { error: err instanceof Error ? err.message : String(err) });
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+async function runExcludeList(globals) {
+    try {
+        const config = loadConfig({ configDir: globals.config ? resolve(globals.config) : undefined });
+        const patterns = config.ingest.exclude;
+        if (globals.json) {
+            console.log(JSON.stringify(patterns));
+        }
+        else {
+            if (patterns.length === 0) {
+                console.log(chalk.dim('No exclude patterns configured.'));
+            }
+            else {
+                console.log(chalk.bold('Excluded patterns:'));
+                for (const p of patterns)
+                    console.log(`  ${p}`);
+            }
+        }
+    }
+    catch (err) {
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+async function runExcludeAdd(pattern, globals) {
+    try {
+        const configPath = getConfigFilePath(globals);
+        const raw = readConfigFile(configPath);
+        const ingest = (raw['ingest'] ?? {});
+        const current = Array.isArray(ingest['exclude']) ? ingest['exclude'] : [];
+        if (current.includes(pattern)) {
+            console.log(chalk.yellow(`Already excluded: ${pattern}`));
+            return;
+        }
+        ingest['exclude'] = [...current, pattern];
+        raw['ingest'] = ingest;
+        const result = cortexConfigSchema.safeParse(raw);
+        if (!result.success) {
+            const issues = result.error.issues.map((i) => `  ${i.path.join('.')}: ${i.message}`).join('\n');
+            console.error(chalk.red('Validation failed:\n') + chalk.yellow(issues));
+            return;
+        }
+        mkdirSync(dirname(configPath), { recursive: true });
+        writeFileSync(configPath, JSON.stringify(raw, null, 2) + '\n', 'utf-8');
+        if (globals.json) {
+            console.log(JSON.stringify({ added: pattern }));
+        }
+        else {
+            console.log(chalk.green(`✓ Added exclude: ${pattern}`));
+        }
+    }
+    catch (err) {
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+async function runExcludeRemove(pattern, globals) {
+    try {
+        const configPath = getConfigFilePath(globals);
+        const raw = readConfigFile(configPath);
+        const ingest = (raw['ingest'] ?? {});
+        const current = Array.isArray(ingest['exclude']) ? ingest['exclude'] : [];
+        if (!current.includes(pattern)) {
+            console.log(chalk.yellow(`Pattern not found: ${pattern}`));
+            return;
+        }
+        ingest['exclude'] = current.filter((p) => p !== pattern);
+        raw['ingest'] = ingest;
+        const result = cortexConfigSchema.safeParse(raw);
+        if (!result.success) {
+            const issues = result.error.issues.map((i) => `  ${i.path.join('.')}: ${i.message}`).join('\n');
+            console.error(chalk.red('Validation failed:\n') + chalk.yellow(issues));
+            return;
+        }
+        mkdirSync(dirname(configPath), { recursive: true });
+        writeFileSync(configPath, JSON.stringify(raw, null, 2) + '\n', 'utf-8');
+        if (globals.json) {
+            console.log(JSON.stringify({ removed: pattern }));
+        }
+        else {
+            console.log(chalk.green(`✓ Removed exclude: ${pattern}`));
+        }
+    }
+    catch (err) {
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+}
+export function registerExcludeCommand(program) {
+    const excludeCmd = program
+        .command('exclude')
+        .description('Manage which files and directories are ignored during watching');
+    excludeCmd
+        .command('add <pattern>')
+        .description('Add an exclude pattern (directory name, file name, or glob like *.log)')
+        .action(async (pattern) => {
+        const globals = program.opts();
+        await runExcludeAdd(pattern, globals);
+    });
+    excludeCmd
+        .command('remove <pattern>')
+        .description('Remove an exclude pattern')
+        .action(async (pattern) => {
+        const globals = program.opts();
+        await runExcludeRemove(pattern, globals);
+    });
+    excludeCmd
+        .command('list')
+        .description('Show all exclude patterns')
+        .action(async () => {
+        const globals = program.opts();
+        await runExcludeList(globals);
+    });
+}
+function flattenObject(obj, prefix = '') {
+    const result = {};
+    for (const [key, value] of Object.entries(obj)) {
+        const fullKey = prefix ? `${prefix}.${key}` : key;
+        if (value !== null && typeof value === 'object' && !Array.isArray(value)) {
+            Object.assign(result, flattenObject(value, fullKey));
+        }
+        else {
+            result[fullKey] = value;
+        }
+    }
+    return result;
+}
+//# sourceMappingURL=config.js.map

package/packages/cli/dist/commands/config.js.map

@@ -0,0 +1 @@
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package/packages/cli/dist/commands/contradictions.d.ts

@@ -0,0 +1,3 @@
+import { Command } from 'commander';
+export declare function registerContradictionsCommand(program: Command): void;
+//# sourceMappingURL=contradictions.d.ts.map

package/packages/cli/dist/commands/contradictions.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"contradictions.d.ts","sourceRoot":"","sources":["../../src/commands/contradictions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAWpC,wBAAgB,6BAA6B,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAUpE"}

package/packages/cli/dist/commands/contradictions.js

@@ -0,0 +1,74 @@
+import { resolve } from 'node:path';
+import chalk from 'chalk';
+import { loadConfig, createLogger } from '@cortex/core';
+import { SQLiteStore } from '@cortex/graph';
+const logger = createLogger('cli:contradictions');
+export function registerContradictionsCommand(program) {
+    program
+        .command('contradictions')
+        .description('List active contradictions')
+        .option('--all', 'Include resolved/dismissed', false)
+        .option('--severity <level>', 'Filter by severity: low, medium, high')
+        .action(async (opts) => {
+        const globals = program.opts();
+        await runContradictions(opts, globals);
+    });
+}
+async function runContradictions(opts, globals) {
+    const config = loadConfig({ configDir: globals.config ? resolve(globals.config) : undefined });
+    const store = new SQLiteStore({ dbPath: config.graph.dbPath, backupOnStartup: false });
+    try {
+        // Query contradictions table
+        const contradictions = await getContradictions(store, opts.all, opts.severity);
+        if (globals.json) {
+            console.log(JSON.stringify({ contradictions }));
+            store.close();
+            return;
+        }
+        console.log('');
+        console.log(chalk.bold.cyan('CONTRADICTIONS'));
+        console.log(chalk.dim('─'.repeat(60)));
+        if (contradictions.length === 0) {
+            console.log(chalk.dim('  No contradictions found.'));
+            console.log('');
+            store.close();
+            return;
+        }
+        for (const c of contradictions) {
+            const severityColor = c.severity === 'high'
+                ? chalk.red
+                : c.severity === 'medium' ? chalk.yellow : chalk.dim;
+            const statusIcon = c.status === 'active' ? '⚠' : '✓';
+            console.log('');
+            console.log(`${statusIcon} ${chalk.bold(c.id.slice(0, 8))}  ${severityColor(`[${c.severity}]`)}  ${chalk.dim(c.status)}`);
+            console.log(`  ${c.description}`);
+            // Show entity names
+            const entity1 = await store.getEntity(c.entityIds[0]);
+            const entity2 = await store.getEntity(c.entityIds[1]);
+            const name1 = entity1 ? entity1.name : c.entityIds[0].slice(0, 8);
+            const name2 = entity2 ? entity2.name : c.entityIds[1].slice(0, 8);
+            console.log(chalk.dim(`  Between: ${name1} ↔ ${name2}`));
+            if (c.suggestedResolution) {
+                console.log(chalk.dim(`  Suggested: ${c.suggestedResolution}`));
+            }
+            if (c.status === 'active') {
+                console.log(chalk.dim(`  Resolve: cortex resolve ${c.id.slice(0, 8)} --action <supersede|dismiss|keep-old|both-valid>`));
+            }
+        }
+        console.log('');
+        console.log(chalk.dim(`Total: ${contradictions.length} contradiction(s)`));
+        console.log('');
+    }
+    catch (err) {
+        logger.error('Contradictions listing failed', { error: err instanceof Error ? err.message : String(err) });
+        console.error(chalk.red(`Error: ${err instanceof Error ? err.message : String(err)}`));
+    }
+    store.close();
+}
+async function getContradictions(store, includeResolved, severity) {
+    const results = await store.findContradictions(includeResolved ? {} : { status: 'active' });
+    if (severity)
+        return results.filter((c) => c.severity === severity);
+    return results;
+}
+//# sourceMappingURL=contradictions.js.map

package/packages/cli/dist/commands/contradictions.js.map

@@ -0,0 +1 @@
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package/packages/cli/dist/commands/costs.d.ts

@@ -0,0 +1,3 @@
+import { Command } from 'commander';
+export declare function registerCostsCommand(program: Command): void;
+//# sourceMappingURL=costs.d.ts.map

package/packages/cli/dist/commands/costs.d.ts.map

@@ -0,0 +1 @@
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