@gzoo/cortex 0.5.9

package/packages/mcp/dist/tools/projects.js

@@ -0,0 +1,17 @@
+export async function handleListProjects(store) {
+    const projects = await store.listProjects();
+    return {
+        projects: projects.map((p) => ({
+            id: p.id,
+            name: p.name,
+            rootPath: p.rootPath,
+            privacyLevel: p.privacyLevel,
+            fileCount: p.fileCount,
+            entityCount: p.entityCount,
+            lastIngestedAt: p.lastIngestedAt,
+            createdAt: p.createdAt,
+        })),
+        total: projects.length,
+    };
+}
+//# sourceMappingURL=projects.js.map

package/packages/mcp/dist/tools/projects.js.map

@@ -0,0 +1 @@
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package/packages/mcp/dist/tools/query.d.ts

@@ -0,0 +1,20 @@
+import type { QueryEngine } from '@cortex/graph';
+import type { Router } from '@cortex/llm';
+export interface QueryCortexInput {
+    question: string;
+    projectId?: string;
+}
+export interface QueryCortexResult {
+    answer: string;
+    citations: Array<{
+        entityId: string;
+        entityType: string;
+        entityName: string;
+        sourceFile: string;
+    }>;
+    entityCount: number;
+    provider: string;
+    model: string;
+}
+export declare function handleQueryCortex(input: QueryCortexInput, queryEngine: QueryEngine, router: Router, store: import('@cortex/graph').SQLiteStore): Promise<QueryCortexResult>;
+//# sourceMappingURL=query.d.ts.map

package/packages/mcp/dist/tools/query.d.ts.map

@@ -0,0 +1 @@
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package/packages/mcp/dist/tools/query.js

@@ -0,0 +1,65 @@
+import { LLMTask } from '@cortex/core';
+import { conversationalQueryPrompt } from '@cortex/llm';
+export async function handleQueryCortex(input, queryEngine, router, store) {
+    const [context, graphStats, projects] = await Promise.all([
+        queryEngine.assembleContext(input.question, undefined, input.projectId),
+        store.getStats(),
+        store.listProjects(),
+    ]);
+    const graphSummary = [
+        `${graphStats.entityCount} entities, ${graphStats.relationshipCount} relationships, ${graphStats.fileCount} files indexed`,
+        projects.length > 0
+            ? `Projects: ${projects.map((p) => `${p.name} (${p.rootPath})`).join(', ')}`
+            : 'No projects configured.',
+        projects.some((p) => p.lastIngestedAt)
+            ? `Last ingested: ${projects.map((p) => p.lastIngestedAt).filter(Boolean).sort().pop()}`
+            : '',
+    ].filter(Boolean).join('\n');
+    if (context.entities.length === 0 && graphStats.entityCount === 0) {
+        return {
+            answer: 'No entities found. Make sure `cortex watch` has been run on your project files.',
+            citations: [],
+            entityCount: 0,
+            provider: 'none',
+            model: 'none',
+        };
+    }
+    const contextEntities = context.entities.map((e) => ({
+        id: e.id,
+        type: e.type,
+        name: e.name,
+        content: e.content,
+        sourceFile: e.sourceFile,
+        createdAt: e.createdAt,
+        relationships: context.relationships
+            .filter((r) => r.sourceEntityId === e.id)
+            .map((r) => ({ type: r.type, targetEntityId: r.targetEntityId })),
+    }));
+    const result = await router.complete({
+        systemPrompt: conversationalQueryPrompt.systemPrompt,
+        userPrompt: conversationalQueryPrompt.buildUserPrompt({
+            contextEntities,
+            userQuery: input.question,
+            graphSummary,
+        }),
+        promptId: conversationalQueryPrompt.PROMPT_ID,
+        promptVersion: conversationalQueryPrompt.PROMPT_VERSION,
+        task: LLMTask.CONVERSATIONAL_QUERY,
+        modelPreference: conversationalQueryPrompt.config.model,
+        temperature: conversationalQueryPrompt.config.temperature,
+        maxTokens: conversationalQueryPrompt.config.maxTokens,
+    });
+    return {
+        answer: result.content,
+        citations: context.entities.map((e) => ({
+            entityId: e.id,
+            entityType: e.type,
+            entityName: e.name,
+            sourceFile: e.sourceFile,
+        })),
+        entityCount: context.entities.length,
+        provider: result.provider,
+        model: result.model,
+    };
+}
+//# sourceMappingURL=query.js.map

package/packages/mcp/dist/tools/query.js.map

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package/packages/mcp/dist/tools/status.d.ts

@@ -0,0 +1,15 @@
+import type { SQLiteStore } from '@cortex/graph';
+export interface GetStatusResult {
+    graph: {
+        entityCount: number;
+        relationshipCount: number;
+        fileCount: number;
+        projectCount: number;
+        contradictionCount: number;
+        dbSizeBytes: number;
+    };
+    ready: boolean;
+    hint?: string;
+}
+export declare function handleGetStatus(store: SQLiteStore): Promise<GetStatusResult>;
+//# sourceMappingURL=status.d.ts.map

package/packages/mcp/dist/tools/status.d.ts.map

@@ -0,0 +1 @@
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package/packages/mcp/dist/tools/status.js

@@ -0,0 +1,17 @@
+export async function handleGetStatus(store) {
+    const stats = await store.getStats();
+    const ready = stats.entityCount > 0;
+    return {
+        graph: {
+            entityCount: stats.entityCount,
+            relationshipCount: stats.relationshipCount,
+            fileCount: stats.fileCount,
+            projectCount: stats.projectCount,
+            contradictionCount: stats.contradictionCount,
+            dbSizeBytes: stats.dbSizeBytes,
+        },
+        ready,
+        ...(!ready && { hint: 'No entities yet. Run `cortex watch` in your project directory to ingest files.' }),
+    };
+}
+//# sourceMappingURL=status.js.map

package/packages/mcp/dist/tools/status.js.map

@@ -0,0 +1 @@
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package/packages/mcp/package.json

@@ -0,0 +1,27 @@
+{
+  "name": "@cortex/mcp",
+  "version": "0.1.0",
+  "private": true,
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "cortex-mcp": "dist/index.js"
+  },
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js"
+    }
+  },
+  "scripts": {
+    "build": "tsc --build",
+    "dev": "tsc --build --watch"
+  },
+  "dependencies": {
+    "@cortex/core": "*",
+    "@cortex/graph": "*",
+    "@cortex/llm": "*",
+    "@modelcontextprotocol/sdk": "^1.17.0"
+  }
+}

package/packages/mcp/tsconfig.json

@@ -0,0 +1,14 @@
+{
+  "extends": "../../tsconfig.base.json",
+  "compilerOptions": {
+    "outDir": "dist",
+    "rootDir": "src",
+    "composite": true
+  },
+  "include": ["src/**/*.ts"],
+  "references": [
+    { "path": "../core" },
+    { "path": "../graph" },
+    { "path": "../llm" }
+  ]
+}

package/packages/server/dist/index.d.ts

@@ -0,0 +1,17 @@
+import { type CortexConfig } from '@cortex/core';
+import { SQLiteStore, QueryEngine } from '@cortex/graph';
+import { Router as LLMRouter } from '@cortex/llm';
+export interface ServerOptions {
+    config: CortexConfig;
+    port?: number;
+    host?: string;
+    enableWatch?: boolean;
+    webDistPath?: string;
+}
+export interface ServerBundle {
+    store: SQLiteStore;
+    queryEngine: QueryEngine;
+    router: LLMRouter;
+}
+export declare function startServer(options: ServerOptions): Promise<void>;
+//# sourceMappingURL=index.d.ts.map

package/packages/server/dist/index.d.ts.map

@@ -0,0 +1 @@
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package/packages/server/dist/index.js

@@ -0,0 +1,170 @@
+import express from 'express';
+import { createServer } from 'node:http';
+import { resolve } from 'node:path';
+import cors from 'cors';
+import { createLogger } from '@cortex/core';
+import { SQLiteStore, QueryEngine, VectorStore } from '@cortex/graph';
+import { Router as LLMRouter } from '@cortex/llm';
+import { createEntityRoutes } from './routes/entities.js';
+import { createRelationshipRoutes } from './routes/relationships.js';
+import { createProjectRoutes } from './routes/projects.js';
+import { createQueryRoutes } from './routes/query.js';
+import { createContradictionRoutes } from './routes/contradictions.js';
+import { createStatusRoutes } from './routes/status.js';
+import { createEventRelay } from './ws/event-relay.js';
+import { createAuthMiddleware } from './middleware/auth.js';
+const logger = createLogger('server');
+function createBundle(config) {
+    const store = new SQLiteStore({ dbPath: config.graph.dbPath, backupOnStartup: false });
+    const vectorStore = new VectorStore();
+    const queryEngine = new QueryEngine(store, vectorStore);
+    const router = new LLMRouter({ config });
+    return { store, queryEngine, router };
+}
+export async function startServer(options) {
+    const { config, enableWatch = true } = options;
+    const port = options.port ?? config.server?.port ?? 3710;
+    const host = options.host ?? config.server?.host ?? '127.0.0.1';
+    const bundle = createBundle(config);
+    const app = express();
+    const server = createServer(app);
+    // Middleware — CORS
+    const corsOrigin = config.server?.cors ?? [];
+    app.use(cors({
+        origin: (origin, callback) => {
+            // Allow requests with no origin (curl, server-to-server)
+            if (!origin)
+                return callback(null, true);
+            // Check explicit whitelist first
+            if (corsOrigin.includes(origin))
+                return callback(null, true);
+            // Allow any localhost/127.0.0.1 origin (any port)
+            if (/^https?:\/\/(localhost|127\.0\.0\.1)(:\d+)?$/.test(origin)) {
+                return callback(null, true);
+            }
+            callback(new Error('CORS not allowed'));
+        },
+    }));
+    app.use(express.json());
+    // Warn if non-localhost without auth
+    const isLocal = host === '127.0.0.1' || host === 'localhost' || host === '::1';
+    if (!isLocal && !config.server.auth.enabled) {
+        logger.warn('Server bound to non-localhost without auth enabled. ' +
+            'Set server.auth.enabled=true and server.auth.token in config, ' +
+            'or set CORTEX_SERVER_AUTH_TOKEN env var.');
+    }
+    // Simple in-memory rate limiter for LLM-backed endpoints
+    const rateLimitWindow = 60_000; // 1 minute
+    const rateLimitMax = 30; // max requests per window
+    const rateLimitMap = new Map();
+    const rateLimiter = (req, res, next) => {
+        const key = req.ip ?? 'unknown';
+        const now = Date.now();
+        const entry = rateLimitMap.get(key);
+        if (!entry || now >= entry.resetAt) {
+            rateLimitMap.set(key, { count: 1, resetAt: now + rateLimitWindow });
+            return next();
+        }
+        entry.count++;
+        if (entry.count > rateLimitMax) {
+            res.status(429).json({
+                success: false,
+                error: { code: 'RATE_LIMITED', message: 'Too many requests. Try again later.' },
+            });
+            return;
+        }
+        next();
+    };
+    // API routes
+    const api = express.Router();
+    api.use(createAuthMiddleware({ config, host }));
+    api.use('/entities', createEntityRoutes(bundle));
+    api.use('/relationships', createRelationshipRoutes(bundle));
+    api.use('/projects', createProjectRoutes(bundle));
+    api.use('/query', rateLimiter, createQueryRoutes(bundle));
+    api.use('/contradictions', createContradictionRoutes(bundle));
+    api.use('/', createStatusRoutes(bundle));
+    app.use('/api/v1', api);
+    // WebSocket event relay
+    const relay = createEventRelay(server, config, host);
+    logger.info('WebSocket relay attached', { path: '/ws' });
+    // Serve static web dashboard if available
+    if (options.webDistPath) {
+        const webDist = resolve(options.webDistPath);
+        app.use(express.static(webDist));
+        // SPA fallback: serve index.html for all non-API routes
+        app.get('*', (_req, res) => {
+            res.sendFile(resolve(webDist, 'index.html'));
+        });
+        logger.info('Serving web dashboard', { path: webDist });
+    }
+    // Start file watcher if enabled
+    if (enableWatch) {
+        try {
+            const { FileWatcher, IngestionPipeline } = await import('@cortex/ingest');
+            const projects = await bundle.store.listProjects();
+            if (projects.length > 0) {
+                for (const project of projects) {
+                    const pipeline = new IngestionPipeline(bundle.router, bundle.store, {
+                        projectId: project.id,
+                        projectName: project.name,
+                        projectRoot: project.rootPath,
+                        maxFileSize: config.ingest.maxFileSize,
+                        batchSize: config.ingest.batchSize,
+                        projectPrivacyLevel: project.privacyLevel,
+                        mergeConfidenceThreshold: 0.85,
+                    });
+                    const watcher = new FileWatcher({
+                        dirs: [project.rootPath],
+                        exclude: config.ingest.exclude,
+                        fileTypes: config.ingest.fileTypes,
+                        debounceMs: config.ingest.debounceMs,
+                        followSymlinks: config.ingest.followSymlinks,
+                        maxFileSize: config.ingest.maxFileSize,
+                        ignoreInitial: true, // Don't re-ingest existing files on server start
+                    });
+                    watcher.onFileChange(async (filePath, changeType) => {
+                        if (changeType === 'add' || changeType === 'change') {
+                            await pipeline.ingestFile(filePath);
+                        }
+                    });
+                    watcher.start();
+                    logger.info('Watching project', { name: project.name, path: project.rootPath });
+                }
+            }
+            else {
+                logger.warn('No projects registered — file watcher not started. Run `cortex init` first.');
+            }
+        }
+        catch (err) {
+            logger.warn('File watcher failed to start', {
+                error: err instanceof Error ? err.message : String(err),
+            });
+        }
+    }
+    // Start listening
+    server.listen(port, host, () => {
+        logger.info(`Cortex server running at http://${host}:${port}`);
+        console.log(`\n  Cortex server running at http://${host}:${port}`);
+        console.log(`  API:       http://${host}:${port}/api/v1`);
+        console.log(`  WebSocket: ws://${host}:${port}/ws`);
+        if (options.webDistPath) {
+            console.log(`  Dashboard: http://${host}:${port}/`);
+        }
+        if (enableWatch) {
+            console.log(`  Watcher:   active`);
+        }
+        console.log('');
+    });
+    // Graceful shutdown
+    const shutdown = () => {
+        logger.info('Shutting down...');
+        relay.close();
+        server.close();
+        bundle.store.close();
+        process.exit(0);
+    };
+    process.on('SIGINT', shutdown);
+    process.on('SIGTERM', shutdown);
+}
+//# sourceMappingURL=index.js.map

package/packages/server/dist/index.js.map

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package/packages/server/dist/middleware/auth.d.ts

@@ -0,0 +1,9 @@
+import type { Request, Response, NextFunction } from 'express';
+import { type CortexConfig } from '@cortex/core';
+export interface AuthMiddlewareOptions {
+    config: CortexConfig;
+    host: string;
+}
+export declare function createAuthMiddleware(options: AuthMiddlewareOptions): (req: Request, res: Response, next: NextFunction) => void;
+export declare function validateWsToken(config: CortexConfig, host: string, url: string | undefined): boolean;
+//# sourceMappingURL=auth.d.ts.map

package/packages/server/dist/middleware/auth.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"auth.d.ts","sourceRoot":"","sources":["../../src/middleware/auth.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AAC/D,OAAO,EAAE,KAAK,YAAY,EAAgB,MAAM,cAAc,CAAC;AAiB/D,MAAM,WAAW,qBAAqB;IACpC,MAAM,EAAE,YAAY,CAAC;IACrB,IAAI,EAAE,MAAM,CAAC;CACd;AAED,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,qBAAqB,GAC7B,CAAC,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,IAAI,EAAE,YAAY,KAAK,IAAI,CAoE3D;AAED,wBAAgB,eAAe,CAAC,MAAM,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,OAAO,CAiBpG"}

package/packages/server/dist/middleware/auth.js

@@ -0,0 +1,94 @@
+import { timingSafeEqual } from 'node:crypto';
+import { createLogger } from '@cortex/core';
+const logger = createLogger('server:auth');
+const LOCALHOST_HOSTS = new Set(['127.0.0.1', 'localhost', '::1']);
+function isLocalhost(host) {
+    return LOCALHOST_HOSTS.has(host);
+}
+function safeEqual(a, b) {
+    const bufA = Buffer.from(a, 'utf-8');
+    const bufB = Buffer.from(b, 'utf-8');
+    if (bufA.length !== bufB.length)
+        return false;
+    return timingSafeEqual(bufA, bufB);
+}
+export function createAuthMiddleware(options) {
+    const { config, host } = options;
+    const authEnabled = config.server.auth.enabled;
+    const token = config.server.auth.token;
+    const isLocal = isLocalhost(host);
+    // Auth required if explicitly enabled OR if binding to non-localhost
+    const authRequired = authEnabled || !isLocal;
+    if (!authRequired) {
+        return (_req, _res, next) => next();
+    }
+    if (!token) {
+        logger.error('Auth is required but no token configured. All API requests will be rejected.');
+        return (_req, res, _next) => {
+            res.status(500).json({
+                success: false,
+                error: {
+                    code: 'SERVER_AUTH_REQUIRED',
+                    message: 'Server authentication is required but no token is configured.',
+                },
+            });
+        };
+    }
+    logger.info('API authentication enabled');
+    return (req, res, next) => {
+        const authHeader = req.headers.authorization;
+        if (!authHeader) {
+            res.status(401).json({
+                success: false,
+                error: {
+                    code: 'SERVER_AUTH_REQUIRED',
+                    message: 'Authentication required. Provide an Authorization: Bearer <token> header.',
+                },
+            });
+            return;
+        }
+        if (!authHeader.startsWith('Bearer ')) {
+            res.status(401).json({
+                success: false,
+                error: {
+                    code: 'SERVER_AUTH_INVALID',
+                    message: 'Invalid authorization format. Expected: Bearer <token>',
+                },
+            });
+            return;
+        }
+        const provided = authHeader.slice(7);
+        if (!safeEqual(provided, token)) {
+            res.status(401).json({
+                success: false,
+                error: {
+                    code: 'SERVER_AUTH_INVALID',
+                    message: 'Invalid authentication token.',
+                },
+            });
+            return;
+        }
+        next();
+    };
+}
+export function validateWsToken(config, host, url) {
+    const authEnabled = config.server.auth.enabled;
+    const token = config.server.auth.token;
+    const isLocal = isLocalhost(host);
+    const authRequired = authEnabled || !isLocal;
+    if (!authRequired)
+        return true;
+    if (!token)
+        return false;
+    try {
+        const params = new URL(url ?? '', 'http://localhost').searchParams;
+        const provided = params.get('token');
+        if (!provided)
+            return false;
+        return safeEqual(provided, token);
+    }
+    catch {
+        return false;
+    }
+}
+//# sourceMappingURL=auth.js.map

package/packages/server/dist/middleware/auth.js.map

@@ -0,0 +1 @@
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package/packages/server/dist/routes/contradictions.d.ts

@@ -0,0 +1,4 @@
+import { Router } from 'express';
+import type { ServerBundle } from '../index.js';
+export declare function createContradictionRoutes(bundle: ServerBundle): Router;
+//# sourceMappingURL=contradictions.d.ts.map

package/packages/server/dist/routes/contradictions.d.ts.map

@@ -0,0 +1 @@
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package/packages/server/dist/routes/contradictions.js

@@ -0,0 +1,63 @@
+import { Router } from 'express';
+import { createLogger } from '@cortex/core';
+const logger = createLogger('server:contradictions');
+export function createContradictionRoutes(bundle) {
+    const router = Router();
+    const { store } = bundle;
+    // GET /contradictions
+    router.get('/', async (req, res) => {
+        try {
+            const { status, severity, limit: rawLimit = '50' } = req.query;
+            const parsedLimit = Math.max(1, Math.min(Number(rawLimit) || 50, 500));
+            const contradictions = await store.findContradictions({
+                status: status,
+                limit: parsedLimit,
+            });
+            // Filter by severity client-side (store doesn't support severity filter)
+            const filtered = severity
+                ? contradictions.filter(c => c.severity === severity)
+                : contradictions;
+            // Enrich with entity names
+            const enriched = await Promise.all(filtered.map(async (c) => {
+                const entityA = await store.getEntity(c.entityIds[0]);
+                const entityB = await store.getEntity(c.entityIds[1]);
+                return {
+                    ...c,
+                    entityA: entityA ? { id: entityA.id, name: entityA.name, type: entityA.type, summary: entityA.summary } : null,
+                    entityB: entityB ? { id: entityB.id, name: entityB.name, type: entityB.type, summary: entityB.summary } : null,
+                };
+            }));
+            res.json({ success: true, data: enriched, meta: { total: enriched.length } });
+        }
+        catch (err) {
+            logger.error('Request failed', { error: err instanceof Error ? err.message : String(err) });
+            res.status(500).json({ success: false, error: { code: 'SERVER_ERROR', message: 'Internal server error' } });
+        }
+    });
+    // POST /contradictions/:id/resolve
+    router.post('/:id/resolve', async (req, res) => {
+        try {
+            const { action } = req.body;
+            const validActions = ['supersede', 'dismiss', 'keep_old', 'both_valid'];
+            if (!action || !validActions.includes(action)) {
+                res.status(400).json({
+                    success: false,
+                    error: { code: 'BAD_REQUEST', message: `action must be one of: ${validActions.join(', ')}` },
+                });
+                return;
+            }
+            await store.updateContradiction(req.params.id, {
+                status: 'resolved',
+                resolvedAction: action,
+                resolvedAt: new Date().toISOString(),
+            });
+            res.json({ success: true, data: { id: req.params.id, status: 'resolved', action } });
+        }
+        catch (err) {
+            logger.error('Request failed', { error: err instanceof Error ? err.message : String(err) });
+            res.status(500).json({ success: false, error: { code: 'SERVER_ERROR', message: 'Internal server error' } });
+        }
+    });
+    return router;
+}
+//# sourceMappingURL=contradictions.js.map

package/packages/server/dist/routes/contradictions.js.map

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package/packages/server/dist/routes/entities.d.ts

@@ -0,0 +1,4 @@
+import { Router } from 'express';
+import type { ServerBundle } from '../index.js';
+export declare function createEntityRoutes(bundle: ServerBundle): Router;
+//# sourceMappingURL=entities.d.ts.map

package/packages/server/dist/routes/entities.d.ts.map

@@ -0,0 +1 @@
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