@comfanion/workflow 4.36.1 → 4.36.3

package/bin/cli.js

@@ -576,6 +576,12 @@ program
       spinner.text = 'Restoring config.yaml...';
       let mergedConfig = configBackup;
       
+      // Extract user's custom exclude patterns before merge
+      const userExcludeMatch = configBackup.match(/exclude:\s*\n((?:\s+-\s+.+\n?)+)/);
+      const userExcludes = userExcludeMatch 
+        ? userExcludeMatch[1].match(/-\s+(.+)/g)?.map(m => m.replace(/^-\s+/, '').trim()) || []
+        : [];
+      
       // Add vectorizer section if missing
       if (!mergedConfig.includes('vectorizer:')) {
         const newConfigPath = path.join(targetDir, 'config.yaml');
@@ -593,6 +599,30 @@ program
         }
       }
       
+      // Merge user's custom excludes into vectorizer section
+      if (userExcludes.length > 0) {
+        const newConfigPath = path.join(targetDir, 'config.yaml');
+        const newConfig = await fs.readFile(newConfigPath, 'utf8');
+        const defaultExcludeMatch = newConfig.match(/exclude:\s*\n((?:\s+-\s+.+\n?)+)/);
+        const defaultExcludes = defaultExcludeMatch
+          ? defaultExcludeMatch[1].match(/-\s+(.+)/g)?.map(m => m.replace(/^-\s+/, '').trim()) || []
+          : [];
+        
+        // Find excludes that user added (not in defaults)
+        const customExcludes = userExcludes.filter(e => !defaultExcludes.includes(e));
+        
+        if (customExcludes.length > 0) {
+          // Add custom excludes to the merged config
+          const excludeInsertPoint = mergedConfig.match(/exclude:\s*\n((?:\s+-\s+.+\n?)+)/);
+          if (excludeInsertPoint) {
+            const insertAfter = excludeInsertPoint.index + excludeInsertPoint[0].length;
+            const customLines = customExcludes.map(e => `    - ${e}`).join('\n') + '\n';
+            mergedConfig = mergedConfig.slice(0, insertAfter) + customLines + mergedConfig.slice(insertAfter);
+            console.log(chalk.green(`  ✅ Preserved ${customExcludes.length} custom exclude patterns`));
+          }
+        }
+      }
+      
       await fs.writeFile(configPath, mergedConfig);
       
       // Install plugin dependencies

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@comfanion/workflow",
-  "version": "4.36.1",
+  "version": "4.36.3",
   "description": "Initialize OpenCode Workflow system for AI-assisted development with semantic code search",
   "type": "module",
   "bin": {

package/src/build-info.json

@@ -1,6 +1,6 @@
 {
   "version": "3.0.0",
-  "buildDate": "2026-01-24T14:49:34.378Z",
+  "buildDate": "2026-01-24T14:58:40.429Z",
   "files": [
     "config.yaml",
     "FLOW.yaml",

package/src/vectorizer/index.js

@@ -22,18 +22,22 @@ if (!DEBUG) {
 const INDEX_PRESETS = {
   code: {
     pattern: '**/*.{js,ts,jsx,tsx,mjs,cjs,py,go,rs,java,kt,swift,c,cpp,h,hpp,cs,rb,php,scala,clj}',
-    description: 'Source code files'
+    ignore: ['**/node_modules/**', '**/.git/**', '**/dist/**', '**/build/**', '**/.opencode/**', '**/docs/**', '**/vendor/**', '**/__pycache__/**'],
+    description: 'Source code files (excludes docs, vendor, node_modules)'
   },
   docs: {
-    pattern: '**/*.{md,mdx,txt,rst,adoc}',
-    description: 'Documentation files'
+    pattern: 'docs/**/*.{md,mdx,txt,rst,adoc}',
+    ignore: [],
+    description: 'Documentation in docs/ folder'
   },
   config: {
     pattern: '**/*.{yaml,yml,json,toml,ini,env,xml}',
+    ignore: ['**/node_modules/**', '**/.git/**', '**/.opencode/**'],
     description: 'Configuration files'
   },
   all: {
     pattern: '**/*.{js,ts,jsx,tsx,mjs,cjs,py,go,rs,java,kt,swift,c,cpp,h,hpp,cs,rb,php,scala,clj,md,mdx,txt,rst,adoc,yaml,yml,json,toml}',
+    ignore: ['**/node_modules/**', '**/.git/**', '**/.opencode/**'],
     description: 'All supported files'
   }
 };
@@ -208,6 +212,43 @@ class CodebaseIndexer {
     return results;
   }
 
+  /**
+   * Check if index needs full reindex (files don't match current patterns)
+   * @param {string[]} extraIgnore - Additional patterns to ignore
+   * Returns { needsReindex, reason, currentCount, expectedCount }
+   */
+  async checkHealth(extraIgnore = []) {
+    const { glob } = await import('glob');
+    const preset = INDEX_PRESETS[this.indexName] || INDEX_PRESETS.code;
+    
+    // Combine preset ignore with extra ignore patterns
+    const ignore = [...(preset.ignore || []), ...extraIgnore.map(p => `**/${p}/**`)];
+    
+    const expectedFiles = await glob(preset.pattern, { 
+      cwd: this.root, 
+      nodir: true,
+      ignore
+    });
+    
+    const indexedFiles = Object.keys(this.hashes);
+    const currentCount = indexedFiles.length;
+    const expectedCount = expectedFiles.length;
+    
+    // Check if counts differ significantly (>20% difference or index is empty)
+    const diff = Math.abs(currentCount - expectedCount);
+    const threshold = Math.max(5, expectedCount * 0.2); // 20% or at least 5 files
+    
+    if (currentCount === 0 && expectedCount > 0) {
+      return { needsReindex: true, reason: 'empty', currentCount, expectedCount };
+    }
+    
+    if (diff > threshold) {
+      return { needsReindex: true, reason: 'mismatch', currentCount, expectedCount };
+    }
+    
+    return { needsReindex: false, reason: 'ok', currentCount, expectedCount };
+  }
+
   /**
    * Freshen index - check for stale files and reindex only changed ones
    * Returns { checked, updated, deleted } counts
@@ -246,6 +287,46 @@ class CodebaseIndexer {
     return { checked, updated, deleted };
   }
 
+  /**
+   * Index all files matching the preset pattern
+   * @param {function} onProgress - Optional callback(indexed, total, currentFile)
+   * @param {string[]} extraIgnore - Additional patterns to ignore
+   * Returns { indexed, skipped } counts
+   */
+  async indexAll(onProgress = null, extraIgnore = []) {
+    const { glob } = await import('glob');
+    const preset = INDEX_PRESETS[this.indexName] || INDEX_PRESETS.code;
+    
+    // Combine preset ignore with extra ignore patterns
+    const ignore = [...(preset.ignore || []), ...extraIgnore.map(p => `**/${p}/**`)];
+    
+    const files = await glob(preset.pattern, { 
+      cwd: this.root, 
+      nodir: true,
+      ignore
+    });
+    
+    let indexed = 0;
+    let skipped = 0;
+    
+    for (const relPath of files) {
+      const filePath = path.join(this.root, relPath);
+      try {
+        const wasIndexed = await this.indexFile(filePath);
+        if (wasIndexed) {
+          indexed++;
+          if (onProgress) onProgress(indexed, files.length, relPath);
+        } else {
+          skipped++;
+        }
+      } catch (e) {
+        skipped++;
+      }
+    }
+    
+    return { indexed, skipped, total: files.length };
+  }
+
   /**
    * Index a single file by path (convenience method)
    */