neuronlayer 0.1.7 → 0.1.9

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "neuronlayer",
-  "version": "0.1.7",
-  "description": "Persistent memory layer for AI coding assistants - MCP server that makes AI truly understand your codebase",
+  "version": "0.1.9",
+  "description": "MCP server that gives AI assistants persistent understanding of your codebase",
   "type": "module",
   "main": "dist/index.js",
   "bin": {

package/src/cli/commands.ts

@@ -22,7 +22,7 @@ export function listProjects(): CommandResult {
   if (projects.length === 0) {
     return {
       success: true,
-      message: 'No projects registered. Use "memorylayer projects add <path>" to add one.'
+      message: 'No projects registered. Use "neuronlayer projects add <path>" to add one.'
     };
   }
 
@@ -123,7 +123,7 @@ export function discoverProjects(): CommandResult {
     lines.push(`    ${path}`);
     lines.push('');
   }
-  lines.push('Use "memorylayer projects add <path>" to register a project.');
+  lines.push('Use "neuronlayer projects add <path>" to register a project.');
 
   return {
     success: true,
@@ -144,7 +144,7 @@ export function exportDecisions(
     if (!activeProject) {
       return {
         success: false,
-        message: 'No project specified and no active project. Use "memorylayer projects switch <id>" first.'
+        message: 'No project specified and no active project. Use "neuronlayer projects switch <id>" first.'
       };
     }
     targetPath = activeProject.path;
@@ -155,17 +155,23 @@ export function exportDecisions(
   if (!projectInfo) {
     return {
       success: false,
-      message: `Project not registered: ${targetPath}. Use "memorylayer projects add ${targetPath}" first.`
+      message: `Project not registered: ${targetPath}. Use "neuronlayer projects add ${targetPath}" first.`
     };
   }
 
-  // Open database and get decisions
-  const dbPath = join(projectInfo.dataDir, 'memorylayer.db');
+  // Open database and get decisions (check both new and old names)
+  let dbPath = join(projectInfo.dataDir, 'neuronlayer.db');
   if (!existsSync(dbPath)) {
-    return {
-      success: false,
-      message: `Project database not found. Has the project been indexed?`
-    };
+    // Fall back to old name for backwards compatibility
+    const oldDbPath = join(projectInfo.dataDir, 'memorylayer.db');
+    if (existsSync(oldDbPath)) {
+      dbPath = oldDbPath;
+    } else {
+      return {
+        success: false,
+        message: `Project database not found. Has the project been indexed?`
+      };
+    }
   }
 
   const db = initializeDatabase(dbPath);
@@ -210,7 +216,7 @@ export function showProject(projectId?: string): CommandResult {
       success: false,
       message: projectId
         ? `Project not found: ${projectId}`
-        : 'No active project. Use "memorylayer projects switch <id>" first.'
+        : 'No active project. Use "neuronlayer projects switch <id>" first.'
     };
   }
 
@@ -272,6 +278,40 @@ function configureMCPClient(
   }
 }
 
+// Helper to configure project-local .mcp.json for Claude Code
+function configureProjectMCP(
+  configPath: string,
+  projectPath: string
+): { success: boolean; message: string } {
+  let config: { mcpServers?: Record<string, unknown> } = { mcpServers: {} };
+
+  try {
+    if (existsSync(configPath)) {
+      const content = readFileSync(configPath, 'utf-8');
+      config = JSON.parse(content);
+    }
+  } catch {
+    // Config doesn't exist or is invalid, start fresh
+  }
+
+  if (!config.mcpServers) {
+    config.mcpServers = {};
+  }
+
+  // Use simple name since this is project-specific
+  config.mcpServers['neuronlayer'] = {
+    command: 'npx',
+    args: ['-y', 'neuronlayer', '--project', '.']
+  };
+
+  try {
+    writeFileSync(configPath, JSON.stringify(config, null, 2));
+    return { success: true, message: `Claude Code: ${configPath} (project-local)` };
+  } catch (err) {
+    return { success: false, message: `Claude Code: Failed - ${err instanceof Error ? err.message : String(err)}` };
+  }
+}
+
 // Initialize neuronlayer for current project + auto-configure Claude Desktop & OpenCode
 export function initProject(projectPath?: string): CommandResult {
   const targetPath = projectPath || process.cwd();
@@ -315,14 +355,29 @@ export function initProject(projectPath?: string): CommandResult {
     failedClients.push(openCodeResult.message);
   }
 
-  // 4. Configure Claude Code (CLI) - uses same config location as Claude Desktop on some systems
-  // Also check for .claude.json in home directory
-  const claudeCodeConfigPath = join(homedir(), '.claude.json');
-  const claudeCodeResult = configureMCPClient('Claude Code', claudeCodeConfigPath, serverName, targetPath);
+  // 4. Configure Claude Code (CLI) - use project-local .mcp.json
+  // This ensures only the current project's NeuronLayer connects
+  const claudeCodeConfigPath = join(targetPath, '.mcp.json');
+  const claudeCodeResult = configureProjectMCP(claudeCodeConfigPath, targetPath);
   if (claudeCodeResult.success) {
     configuredClients.push(claudeCodeResult.message);
   }
 
+  // 5. Configure Cursor
+  let cursorConfigPath: string;
+  if (platform === 'win32') {
+    cursorConfigPath = join(homedir(), 'AppData', 'Roaming', 'Cursor', 'User', 'globalStorage', 'cursor.mcp', 'mcp.json');
+  } else if (platform === 'darwin') {
+    cursorConfigPath = join(homedir(), 'Library', 'Application Support', 'Cursor', 'User', 'globalStorage', 'cursor.mcp', 'mcp.json');
+  } else {
+    cursorConfigPath = join(homedir(), '.config', 'Cursor', 'User', 'globalStorage', 'cursor.mcp', 'mcp.json');
+  }
+
+  const cursorResult = configureMCPClient('Cursor', cursorConfigPath, serverName, targetPath);
+  if (cursorResult.success) {
+    configuredClients.push(cursorResult.message);
+  }
+
   // Build result message
   let message = `
 NeuronLayer initialized!
@@ -351,14 +406,15 @@ ${configuredClients.map(c => '  ✓ ' + c).join('\n')}
 // Print help
 export function printHelp(): void {
   console.log(`
-MemoryLayer CLI - Persistent Memory for AI Coding Assistants
+NeuronLayer CLI - Code Intelligence for AI Coding Assistants
 
 USAGE:
-  memorylayer [command] [options]
+  neuronlayer [command] [options]
 
 COMMANDS:
-  init [path]               Initialize project + auto-configure Claude Desktop
-  (no command)              Start MCP server for Claude Desktop
+  init [path]               Initialize project + auto-configure AI tools
+  serve [options]           Start HTTP API server (for non-MCP tools)
+  (no command)              Start MCP server
   projects list             List all registered projects
   projects add <path>       Add a project to the registry
   projects remove <id>      Remove a project from the registry
@@ -370,6 +426,7 @@ COMMANDS:
 
 OPTIONS:
   --project, -p <path>      Path to the project directory
+  --port <number>           Port for HTTP server (default: 3333)
   --output, -o <dir>        Output directory for exports
   --format <type>           ADR format: madr, nygard, simple
 
@@ -382,19 +439,23 @@ EXAMPLES:
   neuronlayer --project /path/to/project
 
   # List all projects
-  memorylayer projects list
+  neuronlayer projects list
 
   # Add a new project
-  memorylayer projects add /path/to/my-project
+  neuronlayer projects add /path/to/my-project
 
   # Switch active project
-  memorylayer projects switch abc123
+  neuronlayer projects switch abc123
 
   # Export decisions to ADR files
-  memorylayer export --format madr
+  neuronlayer export --format madr
 
   # Discover projects
-  memorylayer projects discover
+  neuronlayer projects discover
+
+  # Start HTTP API server (for tools without MCP support)
+  neuronlayer serve --project /path/to/project
+  neuronlayer serve --port 8080
 
 For more information, visit: https://github.com/abhisavakar/neuronlayer
 `);
@@ -429,7 +490,7 @@ export function executeCLI(args: string[]): void {
           const path = args[2];
           if (!path) {
             console.error('Error: Project path required.');
-            console.error('Usage: memorylayer projects add <path>');
+            console.error('Usage: neuronlayer projects add <path>');
             process.exit(1);
           }
           const result = addProject(path);
@@ -441,7 +502,7 @@ export function executeCLI(args: string[]): void {
           const id = args[2];
           if (!id) {
             console.error('Error: Project ID required.');
-            console.error('Usage: memorylayer projects remove <id>');
+            console.error('Usage: neuronlayer projects remove <id>');
             process.exit(1);
           }
           const result = removeProject(id);
@@ -453,7 +514,7 @@ export function executeCLI(args: string[]): void {
           const id = args[2];
           if (!id) {
             console.error('Error: Project ID required.');
-            console.error('Usage: memorylayer projects switch <id>');
+            console.error('Usage: neuronlayer projects switch <id>');
             process.exit(1);
           }
           const result = switchProject(id);

package/src/core/adr-exporter.ts

@@ -107,7 +107,7 @@ export class ADRExporter {
     lines.push('');
     lines.push('---');
     lines.push('');
-    lines.push('*Generated by MemoryLayer*');
+    lines.push('*Generated by NeuronLayer*');
 
     writeFileSync(indexPath, lines.join('\n'));
     return indexPath;
@@ -157,7 +157,7 @@ ${decision.supersededBy ? `## Superseded By
 This decision has been superseded by [ADR ${decision.supersededBy}](./${decision.supersededBy}.md).
 ` : ''}
 ---
-*Exported from MemoryLayer*
+*Exported from NeuronLayer*
 `;
   }
 
@@ -192,7 +192,7 @@ ${decision.files.length > 0 ? `## Related Files
 ${decision.files.map(f => `- ${f}`).join('\n')}
 ` : ''}
 ---
-*Exported from MemoryLayer*
+*Exported from NeuronLayer*
 `;
   }
 
@@ -216,7 +216,7 @@ ${decision.files.length > 0 ? `## Related Files
 ${decision.files.map(f => `- \`${f}\``).join('\n')}
 ` : ''}
 ---
-*Exported from MemoryLayer*
+*Exported from NeuronLayer*
 `;
   }
 

package/src/core/engine.ts

@@ -1,5 +1,5 @@
 import { join, basename } from 'path';
-import { existsSync, mkdirSync, readFileSync, statSync } from 'fs';
+import { existsSync, mkdirSync, readFileSync, statSync, renameSync } from 'fs';
 import { initializeDatabase, closeDatabase } from '../storage/database.js';
 import { Tier1Storage } from '../storage/tier1.js';
 import { Tier2Storage } from '../storage/tier2.js';
@@ -24,15 +24,15 @@ import { DejaVuDetector, type DejaVuMatch } from './deja-vu.js';
 import { CodeVerifier, type VerificationResult, type VerificationCheck, type ImportVerification, type SecurityScanResult, type DependencyCheckResult } from './code-verifier.js';
 import { GitStalenessChecker, ActivityGate } from './refresh/index.js';
 import { detectLanguage, getPreview, countLines } from '../utils/files.js';
-import type { MemoryLayerConfig, AssembledContext, Decision, ProjectSummary, SearchResult, CodeSymbol, SymbolKind, ActiveFeatureContext, HotContext } from '../types/index.js';
+import type { NeuronLayerConfig, AssembledContext, Decision, ProjectSummary, SearchResult, CodeSymbol, SymbolKind, ActiveFeatureContext, HotContext } from '../types/index.js';
 import type { ArchitectureDoc, ComponentDoc, DailyChangelog, ChangelogOptions, ValidationResult, ActivityResult, UndocumentedItem, ContextHealth, CompactionResult, CompactionOptions, CriticalContext, DriftResult, ConfidenceResult, ConfidenceLevel, ConfidenceSources, ConflictResult, ChangeQueryResult, ChangeQueryOptions, Diagnosis, PastBug, FixSuggestion, Change, Pattern, PatternCategory, PatternValidationResult, ExistingFunction, TestInfo, TestFramework, TestValidationResult, TestUpdate, TestCoverage } from '../types/documentation.js';
 import type Database from 'better-sqlite3';
 
 // Re-export types for external use
 export type { GhostInsight, ConflictWarning, DejaVuMatch, ResurrectedContext, VerificationResult, VerificationCheck, ImportVerification, SecurityScanResult, DependencyCheckResult };
 
-export class MemoryLayerEngine {
-  private config: MemoryLayerConfig;
+export class NeuronLayerEngine {
+  private config: NeuronLayerConfig;
   private db: Database.Database;
   private tier1: Tier1Storage;
   private tier2: Tier2Storage;
@@ -60,7 +60,7 @@ export class MemoryLayerEngine {
   private initializationStatus: 'pending' | 'indexing' | 'ready' | 'error' = 'pending';
   private indexingProgress: { indexed: number; total: number } = { indexed: 0, total: 0 };
 
-  constructor(config: MemoryLayerConfig) {
+  constructor(config: NeuronLayerConfig) {
     this.config = config;
 
     // Ensure data directory exists
@@ -68,8 +68,22 @@ export class MemoryLayerEngine {
       mkdirSync(config.dataDir, { recursive: true });
     }
 
-    // Initialize database
-    const dbPath = join(config.dataDir, 'memorylayer.db');
+    // Initialize database (with migration from old name)
+    let dbPath = join(config.dataDir, 'neuronlayer.db');
+    const oldDbPath = join(config.dataDir, 'memorylayer.db');
+
+    // Migrate from old database name if it exists
+    if (!existsSync(dbPath) && existsSync(oldDbPath)) {
+      try {
+        console.error('Migrating database from memorylayer.db to neuronlayer.db...');
+        renameSync(oldDbPath, dbPath);
+      } catch (err) {
+        // If rename fails (file locked), use the old database path
+        console.error('Migration skipped (file in use), using existing database');
+        dbPath = oldDbPath;
+      }
+    }
+
     this.db = initializeDatabase(dbPath);
 
     // Initialize storage tiers
@@ -214,6 +228,16 @@ export class MemoryLayerEngine {
       this.updateProjectStats();
       // Extract decisions from git and comments
       this.extractDecisions().catch(err => console.error('Decision extraction error:', err));
+
+      // Index tests after code indexing is complete
+      try {
+        const testResult = this.testAwareness.refreshIndex();
+        if (testResult.testsIndexed > 0) {
+          console.error(`Test index: ${testResult.testsIndexed} tests (${testResult.framework})`);
+        }
+      } catch (err) {
+        console.error('Test indexing error:', err);
+      }
     });
 
     this.indexer.on('fileIndexed', (path) => {
@@ -224,6 +248,22 @@ export class MemoryLayerEngine {
       this.summarizer.invalidateSummaryByPath(path);
     });
 
+    this.indexer.on('fileImpact', (impact: { file: string; affectedFiles: string[]; affectedCount: number }) => {
+      // Log impact warning for file changes
+      if (impact.affectedCount > 0) {
+        console.error(`[Impact] ${impact.file} changed → ${impact.affectedCount} file(s) may be affected`);
+        if (impact.affectedCount <= 5) {
+          impact.affectedFiles.forEach(f => console.error(`  → ${f}`));
+        } else {
+          impact.affectedFiles.slice(0, 3).forEach(f => console.error(`  → ${f}`));
+          console.error(`  ... and ${impact.affectedCount - 3} more`);
+        }
+
+        // Track impact in ghost mode for proactive warnings
+        this.ghostMode.onFileImpact(impact.file, impact.affectedFiles);
+      }
+    });
+
     this.indexer.on('error', (error) => {
       console.error('Indexer error:', error);
     });
@@ -232,7 +272,7 @@ export class MemoryLayerEngine {
   async initialize(): Promise<void> {
     if (this.initialized) return;
 
-    console.error(`Initializing MemoryLayer for: ${this.config.projectPath}`);
+    console.error(`Initializing NeuronLayer for: ${this.config.projectPath}`);
 
     try {
       // Perform initial indexing
@@ -274,7 +314,7 @@ export class MemoryLayerEngine {
 
       this.initialized = true;
       this.initializationStatus = 'ready';
-      console.error('MemoryLayer initialized');
+      console.error('NeuronLayer initialized');
     } catch (error) {
       this.initializationStatus = 'error';
       throw error;
@@ -727,6 +767,16 @@ export class MemoryLayerEngine {
     return { imports, importedBy, symbols };
   }
 
+  // Find circular dependencies in the project
+  findCircularDependencies(): Array<string[]> {
+    return this.tier2.findCircularDependencies();
+  }
+
+  // Get transitive dependents (all files affected by changing a file)
+  getTransitiveDependents(filePath: string, maxDepth: number = 3): Array<{ file: string; depth: number; imports: string[] }> {
+    return this.tier2.getTransitiveDependents(filePath, maxDepth);
+  }
+
   // Phase 2: Get symbol count
   getSymbolCount(): number {
     return this.tier2.getSymbolCount();
@@ -1586,7 +1636,7 @@ export class MemoryLayerEngine {
   }
 
   shutdown(): void {
-    console.error('Shutting down MemoryLayer...');
+    console.error('Shutting down NeuronLayer...');
     this.indexer.stopWatching();
     this.activityGate.shutdown();
     this.tier1.save();

package/src/core/ghost-mode.ts

@@ -3,7 +3,7 @@
  *
  * Silently tracks what files Claude reads/writes. When code is written that
  * touches a file with recorded decisions, automatically checks for conflicts.
- * Makes MemoryLayer feel "telepathic" by surfacing relevant context proactively.
+ * Makes NeuronLayer feel "telepathic" by surfacing relevant context proactively.
  */
 
 import type { Decision } from '../types/index.js';
@@ -64,9 +64,16 @@ const TECH_PATTERNS = [
   { pattern: /\b(sass|scss|less)\b/i, category: 'styling', term: 'CSS preprocessor' },
 ];
 
+export interface FileImpact {
+  changedFile: string;
+  affectedFiles: string[];
+  timestamp: Date;
+}
+
 export class GhostMode {
   private activeFiles: Map<string, FileContext> = new Map();
   private recentDecisions: Map<string, Decision[]> = new Map();
+  private recentImpacts: Map<string, FileImpact> = new Map(); // Track file impacts
   private tier2: Tier2Storage;
   private embeddingGenerator: EmbeddingGenerator;
 
@@ -74,12 +81,58 @@ export class GhostMode {
   private readonly MAX_ACTIVE_FILES = 20;
   private readonly FILE_TTL_MS = 60 * 60 * 1000; // 1 hour
   private readonly DECISION_CACHE_SIZE = 50;
+  private readonly IMPACT_TTL_MS = 30 * 60 * 1000; // 30 minutes
 
   constructor(tier2: Tier2Storage, embeddingGenerator: EmbeddingGenerator) {
     this.tier2 = tier2;
     this.embeddingGenerator = embeddingGenerator;
   }
 
+  /**
+   * Called when a file change impacts other files
+   */
+  onFileImpact(changedFile: string, affectedFiles: string[]): void {
+    const impact: FileImpact = {
+      changedFile,
+      affectedFiles,
+      timestamp: new Date()
+    };
+
+    // Store impact for each affected file
+    for (const file of affectedFiles) {
+      this.recentImpacts.set(file, impact);
+    }
+
+    // Evict old impacts
+    this.evictStaleImpacts();
+  }
+
+  /**
+   * Check if a file was recently impacted by changes to another file
+   */
+  getImpactWarning(filePath: string): FileImpact | null {
+    const impact = this.recentImpacts.get(filePath);
+    if (!impact) return null;
+
+    // Check if still within TTL
+    const age = Date.now() - impact.timestamp.getTime();
+    if (age > this.IMPACT_TTL_MS) {
+      this.recentImpacts.delete(filePath);
+      return null;
+    }
+
+    return impact;
+  }
+
+  private evictStaleImpacts(): void {
+    const now = Date.now();
+    for (const [file, impact] of this.recentImpacts) {
+      if (now - impact.timestamp.getTime() > this.IMPACT_TTL_MS) {
+        this.recentImpacts.delete(file);
+      }
+    }
+  }
+
   /**
    * Called when any file is read - silently track and pre-fetch decisions
    */

package/src/core/project-manager.ts

@@ -3,7 +3,7 @@ import { join, basename, resolve } from 'path';
 import { createHash } from 'crypto';
 import { homedir } from 'os';
 import Database from 'better-sqlite3';
-import type { MemoryLayerConfig } from '../types/index.js';
+import type { NeuronLayerConfig } from '../types/index.js';
 
 export interface ProjectInfo {
   id: string;
@@ -177,7 +177,7 @@ export class ProjectManager {
   }
 
   // Get config for a project
-  getProjectConfig(projectPath: string): MemoryLayerConfig {
+  getProjectConfig(projectPath: string): NeuronLayerConfig {
     const normalizedPath = resolve(projectPath);
     const dataDir = this.getProjectDataDir(normalizedPath);
 
@@ -269,7 +269,11 @@ export class ProjectManager {
     const result: Array<{ project: ProjectInfo; db: Database.Database }> = [];
 
     for (const project of this.listProjects()) {
-      const dbPath = join(project.dataDir, 'memorylayer.db');
+      // Check both new and old database names
+      let dbPath = join(project.dataDir, 'neuronlayer.db');
+      if (!existsSync(dbPath)) {
+        dbPath = join(project.dataDir, 'memorylayer.db');
+      }
 
       if (existsSync(dbPath)) {
         try {

package/src/core/refresh/index.ts

@@ -1,5 +1,5 @@
 /**
- * Intelligent Refresh System for MemoryLayer
+ * Intelligent Refresh System for NeuronLayer
  *
  * This module provides a tiered refresh architecture:
  *

package/src/index.ts

@@ -1,7 +1,27 @@
 import { MCPServer } from './server/mcp.js';
+import { HTTPServer } from './server/http.js';
 import { getDefaultConfig, parseArgs } from './utils/config.js';
 import { executeCLI, printHelp } from './cli/commands.js';
 
+function parseServeArgs(args: string[]): { projectPath: string; port: number } {
+  let projectPath = process.cwd();
+  let port = 3333;
+
+  for (let i = 0; i < args.length; i++) {
+    const arg = args[i];
+    const nextArg = args[i + 1];
+    if ((arg === '--project' || arg === '-p') && nextArg) {
+      projectPath = nextArg;
+      i++;
+    } else if (arg === '--port' && nextArg) {
+      port = parseInt(nextArg) || 3333;
+      i++;
+    }
+  }
+
+  return { projectPath, port };
+}
+
 async function main(): Promise<void> {
   const args = process.argv.slice(2);
 
@@ -15,10 +35,31 @@ async function main(): Promise<void> {
     return;
   }
 
+  // Handle serve command - start HTTP API server
+  if (firstArg === 'serve') {
+    const { projectPath, port } = parseServeArgs(args.slice(1));
+    const config = getDefaultConfig(projectPath);
+
+    console.log('NeuronLayer HTTP API starting...');
+    console.log(`Project: ${config.projectPath}`);
+    console.log(`Data directory: ${config.dataDir}`);
+    console.log('');
+
+    const server = new HTTPServer(config, port);
+    try {
+      await server.start();
+    } catch (error) {
+      console.error('Failed to start HTTP server:', error);
+      process.exit(1);
+    }
+    return;
+  }
+
   // No arguments and not piped - show help
   if (args.length === 0 && process.stdin.isTTY) {
     printHelp();
-    console.log('\nTo start as MCP server, use: memorylayer --project <path>\n');
+    console.log('\nTo start as MCP server, use: neuronlayer --project <path>');
+    console.log('To start HTTP API, use: neuronlayer serve --project <path>\n');
     return;
   }
 
@@ -28,7 +69,7 @@ async function main(): Promise<void> {
   // Get configuration
   const config = getDefaultConfig(projectPath);
 
-  console.error('MemoryLayer starting...');
+  console.error('NeuronLayer starting...');
   console.error(`Project: ${config.projectPath}`);
   console.error(`Data directory: ${config.dataDir}`);
 
@@ -38,7 +79,7 @@ async function main(): Promise<void> {
   try {
     await server.start();
   } catch (error) {
-    console.error('Failed to start MemoryLayer:', error);
+    console.error('Failed to start NeuronLayer:', error);
     process.exit(1);
   }
 }