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/core/cache-manager.ts

@@ -1,5 +1,6 @@
 import { existsSync, mkdirSync, readFileSync, writeFileSync, statSync } from 'fs';
 import { join, dirname } from 'path';
+import { StoragePaths, ensureStorageDir } from '../config/storage-paths.js';
 
 interface CacheEntry<T> {
   data: T;
@@ -265,6 +266,16 @@ export class CacheManager<T> {
   }
 }
 
+/**
+ * Extract project path from workflow directory
+ * @param workflowDir - Path to .workflow directory (e.g., /project/.workflow)
+ * @returns Project root path
+ */
+function extractProjectPath(workflowDir: string): string {
+  // workflowDir is typically {projectPath}/.workflow
+  return workflowDir.replace(/[\/\\]\.workflow$/, '') || workflowDir;
+}
+
 /**
  * Create a cache manager for dashboard data
  * @param workflowDir - Path to .workflow directory
@@ -272,6 +283,9 @@ export class CacheManager<T> {
  * @returns CacheManager instance
  */
 export function createDashboardCache(workflowDir: string, ttl?: number): CacheManager<any> {
-  const cacheDir = join(workflowDir, '.ccw-cache');
+  // Use centralized storage path
+  const projectPath = extractProjectPath(workflowDir);
+  const cacheDir = StoragePaths.project(projectPath).cache;
+  ensureStorageDir(cacheDir);
   return new CacheManager('dashboard-data', { cacheDir, ttl });
 }