Add comprehensive tests for tokenizer, performance benchmarks, and TreeSitter parser functionality

- Implemented unit tests for the Tokenizer class, covering various text inputs, edge cases, and fallback mechanisms.
- Created performance benchmarks comparing tiktoken and pure Python implementations for token counting.
- Developed extensive tests for TreeSitterSymbolParser across Python, JavaScript, and TypeScript, ensuring accurate symbol extraction and parsing.
- Added configuration documentation for MCP integration and custom prompts, enhancing usability and flexibility.
- Introduced a refactor script for GraphAnalyzer to streamline future improvements.

ccw/src/tools/cli-config-manager.ts

@@ -1,10 +1,11 @@
 /**
  * CLI Configuration Manager
  * Handles loading, saving, and managing CLI tool configurations
- * Stores config in .workflow/cli-config.json
+ * Stores config in centralized storage (~/.ccw/projects/{id}/config/)
  */
 import * as fs from 'fs';
 import * as path from 'path';
+import { StoragePaths, ensureStorageDir } from '../config/storage-paths.js';
 
 // ========== Types ==========
 
@@ -50,20 +51,15 @@ export const DEFAULT_CONFIG: CliConfig = {
   }
 };
 
-const CONFIG_DIR = '.workflow';
-const CONFIG_FILE = 'cli-config.json';
-
 // ========== Helper Functions ==========
 
 function getConfigPath(baseDir: string): string {
-  return path.join(baseDir, CONFIG_DIR, CONFIG_FILE);
+  return StoragePaths.project(baseDir).cliConfig;
 }
 
-function ensureConfigDir(baseDir: string): void {
-  const configDir = path.join(baseDir, CONFIG_DIR);
-  if (!fs.existsSync(configDir)) {
-    fs.mkdirSync(configDir, { recursive: true });
-  }
+function ensureConfigDirForProject(baseDir: string): void {
+  const configDir = StoragePaths.project(baseDir).config;
+  ensureStorageDir(configDir);
 }
 
 function isValidToolName(tool: string): tool is CliToolName {
@@ -145,7 +141,7 @@ export function loadCliConfig(baseDir: string): CliConfig {
  * Save CLI configuration to .workflow/cli-config.json
  */
 export function saveCliConfig(baseDir: string, config: CliConfig): void {
-  ensureConfigDir(baseDir);
+  ensureConfigDirForProject(baseDir);
   const configPath = getConfigPath(baseDir);
 
   try {

ccw/src/tools/cli-executor.ts

@@ -29,9 +29,6 @@ import {
   getPrimaryModel
 } from './cli-config-manager.js';
 
-// CLI History storage path
-const CLI_HISTORY_DIR = join(process.cwd(), '.workflow', '.cli-history');
-
 // Lazy-loaded SQLite store module
 let sqliteStoreModule: typeof import('./cli-history-store.js') | null = null;
 

ccw/src/tools/cli-history-store.ts

@@ -7,6 +7,7 @@ import Database from 'better-sqlite3';
 import { existsSync, mkdirSync, readdirSync, readFileSync, statSync, unlinkSync, rmdirSync } from 'fs';
 import { join } from 'path';
 import { parseSessionFile, formatConversation, extractConversationPairs, type ParsedSession, type ParsedTurn } from './session-content-parser.js';
+import { StoragePaths, ensureStorageDir } from '../config/storage-paths.js';
 
 // Types
 export interface ConversationTurn {
@@ -97,12 +98,12 @@ export class CliHistoryStore {
   private dbPath: string;
 
   constructor(baseDir: string) {
-    const historyDir = join(baseDir, '.workflow', '.cli-history');
-    if (!existsSync(historyDir)) {
-      mkdirSync(historyDir, { recursive: true });
-    }
+    // Use centralized storage path
+    const paths = StoragePaths.project(baseDir);
+    const historyDir = paths.cliHistory;
+    ensureStorageDir(historyDir);
 
-    this.dbPath = join(historyDir, 'history.db');
+    this.dbPath = paths.historyDb;
     this.db = new Database(this.dbPath);
     this.db.pragma('journal_mode = WAL');
     this.db.pragma('synchronous = NORMAL');