@magic-ingredients/tiny-brain-local 0.13.0 → 0.14.10

package/dist/services/repo-service.js

@@ -572,13 +572,12 @@ export class RepoService {
             section += '**Product Requirements Documents (PRDs):**\n';
             section += `- Location: \`docs/prd/{prd-id}/prd.md\`\n`;
             section += `- Features: \`docs/prd/{prd-id}/features/{feature-id}.md\`\n`;
-            section += `- Templates: \`docs/prd/_template/\`\n\n`;
+            section += `- Skills: \`.claude/skills/plan/\`, \`.claude/skills/feature/\`, \`.claude/skills/fix/\`\n\n`;
         }
         if (hasADR) {
             section += '**Architecture Decision Records (ADRs):**\n';
             section += `- Location: \`docs/adr/NNNN-decision-title.md\`\n`;
-            section += `- Templates: \`docs/adr/_template/\`\n`;
-            section += `- Example: \`docs/adr/_template/0001-record-architecture-decisions.md\`\n\n`;
+            section += `- Skill: \`.claude/skills/adr/\`\n\n`;
         }
         // Add PRD commit workflow with ADR checking if both exist
         if (hasPRD && hasADR) {
@@ -611,29 +610,24 @@ export class RepoService {
             return '';
         }
         let section = '\n### Documentation Templates\n\n';
+        const skillsPath = path.join(repoRoot, '.claude', 'skills');
         // Add PRD instructions if directory exists
         if (hasPRD) {
-            const instructionsPath = path.join(prdPath, 'PRD_CREATION_INSTRUCTIONS.md');
-            const templatePath = path.join(prdPath, '_template');
-            const schemaPath = path.join(prdPath, '*.json');
-            const examplePath = path.join(prdPath, 'example-task-management');
-            section += '**PRD Creation:**\n';
-            section += `- ALWAYS read \`${instructionsPath}\` before creating PRDs\n`;
-            section += `- Use templates in \`${templatePath}/\`\n`;
-            section += `- Validate against schemas in \`${schemaPath}\`\n`;
-            section += `- Reference example: \`${examplePath}/\`\n\n`;
+            section += '**PRD & Feature Creation (Model-Invoked Skills):**\n';
+            section += `- Skills are automatically triggered based on your intent - describe what you want to do\n`;
+            section += `- "I want to plan a new feature" → triggers plan skill\n`;
+            section += `- "I want to add a feature to the PRD" → triggers feature skill\n`;
+            section += `- "I want to track a bug fix" → triggers fix skill\n`;
+            section += `- Skills: \`.claude/skills/plan/\`, \`.claude/skills/feature/\`, \`.claude/skills/fix/\`\n`;
+            section += `- Check available skills: ask "What Skills are available?"\n\n`;
         }
         // Add ADR instructions if directory exists
         if (hasADR) {
-            const instructionsPath = path.join(adrPath, '_template', 'ADR_CREATION_INSTRUCTIONS.md');
-            const templatePath = path.join(adrPath, '_template', 'adr-template.md');
-            const schemaPath = path.join(adrPath, '_template', 'adr-schema.json');
-            const examplePath = path.join(adrPath, '_template', '0001-record-architecture-decisions.md');
+            const adrSkillPath = path.join(skillsPath, 'adr');
             section += '**ADR Creation:**\n';
-            section += `- ALWAYS read \`${instructionsPath}\` before creating ADRs\n`;
-            section += `- Use template: \`${templatePath}\`\n`;
-            section += `- Validate against schema: \`${schemaPath}\`\n`;
-            section += `- Reference example: \`${examplePath}\`\n`;
+            section += `- Use \`/adr\` skill to create Architecture Decision Records\n`;
+            section += `- Skill located at \`${adrSkillPath}/\`\n`;
+            section += `- Template at \`${adrSkillPath}/templates/adr-template.md\`\n`;
         }
         return section;
     }
@@ -1211,18 +1205,22 @@ export class RepoService {
             return '';
         }
         let section = '## PRD Workflow\n\n';
-        section += 'IMPORTANT: Before starting work, read and understand all template files in `docs/prd/_template/` and `docs/adr/_template/` to understand the structure and requirements.\n\n';
+        section += 'IMPORTANT: Skills at `.claude/skills/` are **model-invoked** - describe your intent and Claude will use them automatically.\n';
+        section += 'Examples: "I want to plan a new feature", "track this bug fix", "add a feature to the PRD"\n';
+        section += 'Check available skills: ask "What Skills are available?"\n\n';
+        section += '**First-time Setup:** Run `npx tiny-brain analyse` from terminal before starting Claude Code to install skills.\n';
+        section += 'If skills were installed mid-session, restart Claude Code to activate them.\n\n';
         section += '**Product Requirements Documents (PRDs):**\n';
         section += `- Location: \`docs/prd/{prd-id}/prd.md\`\n`;
         section += `- Features: \`docs/prd/{prd-id}/features/{feature-id}.md\`\n`;
-        section += `- Templates: \`docs/prd/_template/\` - READ ALL FILES to understand structure\n\n`;
+        section += `- Skills: plan (create PRDs), feature (add features), fix (track fixes)\n\n`;
         // Check if ADR is enabled before showing ADR-related content
         const enableADR = await this.configService.isADREnabled();
         if (hasADR && enableADR) {
             section += '**Architecture Decision Records (ADRs):**\n';
             section += `- Location: \`docs/adr/NNNN-decision-title.md\`\n`;
-            section += `- Templates: \`docs/adr/_template/\` - READ ALL FILES to understand structure\n`;
-            section += `- Example: \`docs/adr/_template/0001-record-architecture-decisions.md\`\n\n`;
+            section += `- Use \`/adr\` skill to create ADRs\n`;
+            section += `- Skill and template at \`.claude/skills/adr/\`\n\n`;
             section += '**PRD Commit Workflow:**\n\n';
             section += 'After committing PRD-tracked code, ALWAYS check for ADR suggestions:\n\n';
             section += '1. After successful git commit (via Bash tool)\n';
@@ -1277,6 +1275,15 @@ export class RepoService {
             // Add TDD Workflow section
             section += '## TDD Workflow\n\n';
             section += '**MANDATORY:** This repository follows strict Test-Driven Development (TDD) with a 3-phase commit workflow.\n\n';
+            section += '### ⚠️ CRITICAL RULE: One Task = One Commit Cycle\n\n';
+            section += '**NEVER implement multiple tasks in a single commit.**\n\n';
+            section += 'Each PRD task MUST have its own complete TDD cycle:\n';
+            section += '- **1 task** = **1 test commit** (RED phase) + **1 feat commit** (GREEN phase) + optionally **1 refactor commit**\n';
+            section += '- Multiple tasks cannot share commits - even if the implementation is related\n';
+            section += '- This ensures accurate progress tracking and proper task completion detection\n';
+            section += '- Violation of this rule will cause incorrect task tracking in progress.json\n\n';
+            section += '❌ **WRONG**: One commit implements tasks 1-1, 1-4, 1-5, and 1-6\n';
+            section += '✅ **CORRECT**: Four separate commit cycles, one for each task\n\n';
             section += '**CRITICAL RULES - NO EXCEPTIONS:**\n';
             section += '1. **NEVER** commit test files and implementation files together\n';
             section += '2. **ALWAYS** commit in this exact order: Red → Green → (optional) Refactor\n';
@@ -1374,4 +1381,3 @@ export class RepoService {
         return section;
     }
 }
-//# sourceMappingURL=repo-service.js.map

package/dist/services/versioning-service.js

@@ -188,4 +188,3 @@ export class VersioningService {
         return false;
     }
 }
-//# sourceMappingURL=versioning-service.js.map

package/dist/storage/local-filesystem-adapter.js

@@ -251,4 +251,3 @@ export class LocalFilesystemStorageAdapter {
         return this.pathBuilder.buildUserBasePath();
     }
 }
-//# sourceMappingURL=local-filesystem-adapter.js.map

package/dist/storage/platform-config-adapter.js

@@ -179,4 +179,3 @@ export class PlatformConfigAdapter extends LocalFilesystemStorageAdapter {
         return 'unknown';
     }
 }
-//# sourceMappingURL=platform-config-adapter.js.map

package/dist/storage/platform-path-builder.js

@@ -90,4 +90,3 @@ export class PlatformPathBuilder {
         return path.join(os.homedir(), '.tiny-brain', 'backups');
     }
 }
-//# sourceMappingURL=platform-path-builder.js.map

package/dist/storage/storage-path-builder.js

@@ -40,4 +40,3 @@ export class LocalStoragePathBuilder {
         return null;
     }
 }
-//# sourceMappingURL=storage-path-builder.js.map

package/dist/tools/analyse-request/analyse-request.tool.js

@@ -117,4 +117,3 @@ export class AnalyseRequestTool {
         }
     }
 }
-//# sourceMappingURL=analyse-request.tool.js.map

package/dist/tools/analyse.tool.d.ts

@@ -9,6 +9,10 @@ import { Tool as MCPTool } from '@modelcontextprotocol/sdk/types.js';
  */
 export declare class AnalyseTool {
     static getToolDefinition(): MCPTool;
+    /**
+     * Generate pre-analysis feedback showing enabled/disabled features
+     */
+    private static getPreAnalysisFeedback;
     /**
      * Execute repository analysis
      */

package/dist/tools/analyse.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"analyse.tool.d.ts","sourceRoot":"","sources":["../../src/tools/analyse.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAAqB,KAAK,aAAa,EAAE,KAAK,UAAU,EAAE,MAAM,YAAY,CAAC;AACpF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAGlE,OAAO,EAAE,IAAI,IAAI,OAAO,EAAE,MAAM,oCAAoC,CAAC;AAOrE;;;;;GAKG;AACH,qBAAa,WAAW;IACtB,MAAM,CAAC,iBAAiB,IAAI,OAAO;IAwBnC;;OAEG;WACU,OAAO,CAAC,IAAI,EAAE,aAAa,EAAE,OAAO,EAAE,cAAc,GAAG,OAAO,CAAC,UAAU,CAAC;CAiGxF"}
+{"version":3,"file":"analyse.tool.d.ts","sourceRoot":"","sources":["../../src/tools/analyse.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAAqB,KAAK,aAAa,EAAE,KAAK,UAAU,EAAE,MAAM,YAAY,CAAC;AACpF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAGlE,OAAO,EAAE,IAAI,IAAI,OAAO,EAAE,MAAM,oCAAoC,CAAC;AAQrE;;;;;GAKG;AACH,qBAAa,WAAW;IACtB,MAAM,CAAC,iBAAiB,IAAI,OAAO;IAwBnC;;OAEG;mBACkB,sBAAsB;IA4B3C;;OAEG;WACU,OAAO,CAAC,IAAI,EAAE,aAAa,EAAE,OAAO,EAAE,cAAc,GAAG,OAAO,CAAC,UAAU,CAAC;CAsGxF"}

package/dist/tools/analyse.tool.js

@@ -2,6 +2,7 @@ import { z } from 'zod';
 import { createErrorResult } from './index.js';
 import { AnalyseService } from '../services/analyse-service.js';
 import { AgentManager } from '../services/agent-manager.js';
+import { ConfigService } from '@magic-ingredients/tiny-brain-core';
 const AnalyseArgsSchema = z.object({
     dryRun: z.boolean().optional().default(false),
     confirmInstall: z.boolean().optional().default(false),
@@ -16,7 +17,7 @@ export class AnalyseTool {
     static getToolDefinition() {
         return {
             name: 'analyse',
-            description: "🔍 REPOSITORY ANALYSIS 🔍\n\n⚡ ANALYZE & UPDATE: Analyze repository tech stack and manage agents.\n\n✅ FEATURES:\n  • Detect languages, frameworks, and tools\n  • Prompt to install recommended agents\n  • Check for agent updates\n  • Show tech stack changes\n  • Dry-run mode for preview\n\n💡 USAGE:\n  • analyse - Analyze and prompt for installation\n  • analyse --dry-run - Preview changes without prompting\n\n🤖 AGENTS:\n  • Recommends agents based on tech stack\n  • Updates agents to latest versions\n  • Removes deprecated agents\n\n📊 OUTPUT:\n  • Tech stack summary\n  • Agent recommendations\n  • Installation results",
+            description: "🔍 REPOSITORY ANALYSIS 🔍\n\n⚡ ANALYZE & UPDATE: Analyze repository tech stack and manage agents.\n\n✅ FEATURES:\n  • Detect languages, frameworks, and tools\n  • Prompt to install recommended agents\n  • Check for agent updates\n  • Show tech stack changes\n  • Show installed skills with versions\n  • Dry-run mode for preview\n\n💡 USAGE:\n  • analyse - Analyze and prompt for installation\n  • analyse --dry-run - Preview changes without prompting\n\n🤖 AGENTS:\n  • Recommends agents based on tech stack\n  • Updates agents to latest versions\n  • Removes deprecated agents\n\n📜 SKILLS:\n  • Shows installed skills (/plan, /feature, /fix, /adr)\n  • Displays skill versions\n\n📊 OUTPUT:\n  • Tech stack summary\n  • Agent recommendations\n  • Installed skills list\n  • Installation results",
             inputSchema: {
                 type: 'object',
                 properties: {
@@ -35,17 +36,47 @@ export class AnalyseTool {
             },
         };
     }
+    /**
+     * Generate pre-analysis feedback showing enabled/disabled features
+     */
+    static async getPreAnalysisFeedback(context) {
+        try {
+            const configService = new ConfigService(context);
+            const preferences = await configService.getPreferences();
+            const repo = preferences.repo;
+            const featureStatus = (enabled) => enabled ? '✅ enabled' : '❌ disabled';
+            const lines = [
+                '# Analysis Plan',
+                '',
+                '## Feature Flags',
+                `- **enableSDD**: ${featureStatus(repo.enableSDD)}`,
+                `- **enableTDD**: ${featureStatus(repo.enableTDD)}`,
+                `- **enableADR**: ${featureStatus(repo.enableADR)}`,
+                `- **enableAgenticCoding**: ${featureStatus(repo.enableAgenticCoding)}`,
+                '',
+                '---',
+                '',
+            ];
+            return lines.join('\n');
+        }
+        catch {
+            // If config fails, continue without pre-analysis feedback
+            return null;
+        }
+    }
     /**
      * Execute repository analysis
      */
     static async execute(args, context) {
         try {
             const validatedArgs = AnalyseArgsSchema.parse(args);
+            // Get pre-analysis feedback
+            const preAnalysisFeedback = await AnalyseTool.getPreAnalysisFeedback(context);
             // Create service and perform analysis
             const service = new AnalyseService(context);
             const result = await service.performAnalysis(validatedArgs);
             // Format output for display
-            let output = service.formatAnalysisOutput(result);
+            let output = preAnalysisFeedback ? preAnalysisFeedback + service.formatAnalysisOutput(result) : service.formatAnalysisOutput(result);
             // Handle agent installation
             if (!validatedArgs.dryRun && result.recommendations) {
                 const hasRecommendations = (result.recommendations.install?.length || 0) > 0 ||
@@ -105,6 +136,7 @@ export class AnalyseTool {
                     output += '\n✅ Agent management completed!';
                 }
             }
+            // Note: Repository registration now happens in AnalyseService.performAnalysis()
             return {
                 content: [{
                         type: 'text',
@@ -121,4 +153,3 @@ export class AnalyseTool {
         }
     }
 }
-//# sourceMappingURL=analyse.tool.js.map

package/dist/tools/config/config.tool.d.ts

@@ -6,5 +6,8 @@ export declare class ConfigTool {
     static execute(args: Record<string, unknown>, context: RequestContext): Promise<ToolResult>;
     private static handleList;
     private static handleGet;
+    private static handleShowSources;
+    private static handleSet;
+    private static handleReset;
 }
 //# sourceMappingURL=config.tool.d.ts.map

package/dist/tools/config/config.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.tool.d.ts","sourceRoot":"","sources":["../../../src/tools/config/config.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAA0C,KAAK,UAAU,EAAE,MAAM,aAAa,CAAC;AACtF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,EAAE,IAAI,IAAI,OAAO,EAAE,MAAM,oCAAoC,CAAC;AASrE,qBAAa,UAAU;IACrB,MAAM,CAAC,iBAAiB,IAAI,OAAO;WAsDtB,OAAO,CAClB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,UAAU,CAAC;mBA+BD,UAAU;mBAwCV,SAAS;CAqF/B"}
+{"version":3,"file":"config.tool.d.ts","sourceRoot":"","sources":["../../../src/tools/config/config.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAA0C,KAAK,UAAU,EAAE,MAAM,aAAa,CAAC;AACtF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,EAAE,IAAI,IAAI,OAAO,EAAE,MAAM,oCAAoC,CAAC;AAUrE,qBAAa,UAAU;IACrB,MAAM,CAAC,iBAAiB,IAAI,OAAO;WA4DtB,OAAO,CAClB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,UAAU,CAAC;mBA6BD,UAAU;mBAwCV,SAAS;mBAoCT,iBAAiB;mBAgEjB,SAAS;mBA8CT,WAAW;CAqBjC"}

package/dist/tools/config/config.tool.js

@@ -2,26 +2,25 @@ import { z } from 'zod';
 import { createSuccessResult, createErrorResult } from '../index.js';
 import { ConfigService } from '@magic-ingredients/tiny-brain-core';
 const ConfigArgsSchema = z.object({
-    operation: z.enum(['list', 'get', 'set', 'reset']),
+    operation: z.enum(['list', 'get', 'show-sources', 'set', 'reset']),
     key: z.string().optional(),
-    value: z.union([z.string(), z.boolean(), z.array(z.string())]).optional(),
+    value: z.string().optional(),
+    scope: z.enum(['global', 'repo']).optional(),
 });
 export class ConfigTool {
     static getToolDefinition() {
         return {
             name: 'config',
-            description: `⚙️ CONFIGURATION VIEWER ⚙️
+            description: `⚙️ CONFIGURATION MANAGER ⚙️
 
-📋 READ-ONLY CONFIG ACCESS: View user preferences through MCP.
+📋 MANAGE USER PREFERENCES: View and modify preferences through MCP.
 
 ✅ OPERATIONS:
   • list: Display all current preferences
   • get: Get a specific preference value
-
-❌ WRITE OPERATIONS (CLI ONLY):
-  • set/reset require command line access
-  • Use: npx tiny-brain config preferences set <key> <value>
-  • Use: npx tiny-brain config preferences reset
+  • show-sources: Display preferences with their source (repo/global/default)
+  • set: Set a preference value (requires key, value, and optional scope)
+  • reset: Reset all preferences to defaults
 
 📊 PREFERENCES:
   • autoCommitProgress - Auto-commit progress.json changes
@@ -34,26 +33,34 @@ export class ConfigTool {
   • prdDirectory - PRD directory path
   • testPatterns - Test file patterns array
 
-🎯 HIERARCHY:
-  Repository config > Global config > Hardcoded defaults
+🎯 SCOPE:
+  • repo (default): Save to repository config ([repo]/.tiny-brain/config.json)
+  • global: Save to user config (~/.tiny-brain/config/preferences.json)
 
 💡 EXAMPLES:
   • config operation=list - Show all preferences
-  • config operation=get key=enableTDD - Get specific preference`,
+  • config operation=get key=enableTDD - Get specific preference
+  • config operation=set key=enableTDD value=false scope=global - Set preference`,
             inputSchema: {
                 type: 'object',
                 properties: {
                     operation: {
                         type: 'string',
-                        enum: ['list', 'get', 'set', 'reset'],
+                        enum: ['list', 'get', 'show-sources', 'set', 'reset'],
                         description: 'The config operation to perform',
                     },
                     key: {
                         type: 'string',
-                        description: 'Preference key (required for get operation)',
+                        description: 'Preference key (required for get and set operations)',
                     },
                     value: {
-                        description: 'Preference value (not supported in MCP - use CLI)',
+                        type: 'string',
+                        description: 'Preference value as string (required for set operation)',
+                    },
+                    scope: {
+                        type: 'string',
+                        enum: ['global', 'repo'],
+                        description: 'Config scope: "global" for user config, "repo" for repository config (default)',
                     },
                 },
                 required: ['operation'],
@@ -69,12 +76,12 @@ export class ConfigTool {
                     return await ConfigTool.handleList(configService);
                 case 'get':
                     return await ConfigTool.handleGet(validatedArgs, configService);
+                case 'show-sources':
+                    return await ConfigTool.handleShowSources(configService);
                 case 'set':
+                    return await ConfigTool.handleSet(validatedArgs, configService);
                 case 'reset':
-                    return createErrorResult(`❌ Write operations (${validatedArgs.operation}) are not supported through MCP.\n\n` +
-                        `Please use the command line interface:\n` +
-                        `  npx tiny-brain config preferences ${validatedArgs.operation}` +
-                        (validatedArgs.operation === 'set' ? ' <key> <value>' : ''));
+                    return await ConfigTool.handleReset(configService);
                 default:
                     return createErrorResult(`Unknown operation: ${validatedArgs.operation}`);
             }
@@ -126,61 +133,15 @@ export class ConfigTool {
         if (!args.key) {
             return createErrorResult('key is required for get operation');
         }
-        // Validate key is a valid preference
-        const validKeys = [
-            'autoCommitProgress',
-            'enableAgenticCoding',
-            'enableSDD',
-            'enableTDD',
-            'enableADR',
-            'docsDirectory',
-            'adrDirectory',
-            'prdDirectory',
-            'testPatterns',
-        ];
-        if (!validKeys.includes(args.key)) {
-            return createErrorResult(`Invalid preference key: ${args.key}\n\nValid keys: ${validKeys.join(', ')}`);
-        }
         try {
-            const preferences = await configService.getPreferences();
-            const repo = preferences.repo;
-            // Map flat keys to nested structure
-            let value;
-            switch (args.key) {
-                case 'docsDirectory':
-                    value = repo.directories.docs;
-                    break;
-                case 'adrDirectory':
-                    value = repo.directories.adr;
-                    break;
-                case 'prdDirectory':
-                    value = repo.directories.prd;
-                    break;
-                case 'autoCommitProgress':
-                    value = repo.autoCommitProgress;
-                    break;
-                case 'enableAgenticCoding':
-                    value = repo.enableAgenticCoding;
-                    break;
-                case 'enableSDD':
-                    value = repo.enableSDD;
-                    break;
-                case 'enableTDD':
-                    value = repo.enableTDD;
-                    break;
-                case 'enableADR':
-                    value = repo.enableADR;
-                    break;
-                case 'testPatterns':
-                    value = repo.testPatterns;
-                    break;
-                default:
-                    return createErrorResult(`Unknown preference key: ${args.key}`);
+            const result = await configService.getPreferenceByKey(args.key);
+            if (!result.isValid) {
+                return createErrorResult(result.error);
             }
             const lines = [
                 `# Preference: ${args.key}`,
                 '',
-                `**Value**: ${typeof value === 'object' ? JSON.stringify(value) : value}`,
+                `**Value**: ${typeof result.value === 'object' ? JSON.stringify(result.value) : result.value}`,
                 '',
                 '---',
                 '',
@@ -195,5 +156,113 @@ export class ConfigTool {
             return createErrorResult(`Failed to get preference: ${error instanceof Error ? error.message : 'Unknown error'}`);
         }
     }
+    static async handleShowSources(configService) {
+        try {
+            const sources = await configService.getPreferenceSources();
+            const { repo: repoConfig, global: globalConfig, merged } = sources;
+            // Helper to determine source of a preference value
+            const getSource = (key) => {
+                if (repoConfig.repo && key in repoConfig.repo && repoConfig.repo[key] !== undefined) {
+                    return 'Repository';
+                }
+                if (globalConfig.repo && key in globalConfig.repo && globalConfig.repo[key] !== undefined) {
+                    return 'Global';
+                }
+                return 'Default';
+            };
+            // Helper for nested directory values
+            const getDirSource = (dirKey) => {
+                if (repoConfig.repo?.directories && dirKey in repoConfig.repo.directories) {
+                    return 'Repository';
+                }
+                if (globalConfig.repo?.directories && dirKey in globalConfig.repo.directories) {
+                    return 'Global';
+                }
+                return 'Default';
+            };
+            // Get testPatterns source
+            const testPatternsSource = repoConfig.repo?.testPatterns ? 'Repository' :
+                globalConfig.repo?.testPatterns ? 'Global' : 'Default';
+            const lines = [
+                '# Preference Sources',
+                '',
+                '## Feature Flags',
+                `- **autoCommitProgress**: ${merged.repo.autoCommitProgress} _(${getSource('autoCommitProgress')})_`,
+                `- **enableAgenticCoding**: ${merged.repo.enableAgenticCoding} _(${getSource('enableAgenticCoding')})_`,
+                `- **enableSDD**: ${merged.repo.enableSDD} _(${getSource('enableSDD')})_`,
+                `- **enableTDD**: ${merged.repo.enableTDD} _(${getSource('enableTDD')})_`,
+                `- **enableADR**: ${merged.repo.enableADR} _(${getSource('enableADR')})_`,
+                '',
+                '## Directory Paths',
+                `- **docsDirectory**: \`${merged.repo.directories.docs}\` _(${getDirSource('docs')})_`,
+                `- **adrDirectory**: \`${merged.repo.directories.adr}\` _(${getDirSource('adr')})_`,
+                `- **prdDirectory**: \`${merged.repo.directories.prd}\` _(${getDirSource('prd')})_`,
+                '',
+                '## Test Configuration',
+                `- **testPatterns**: ${JSON.stringify(merged.repo.testPatterns)} _(${testPatternsSource})_`,
+                '',
+                '---',
+                '',
+                '## Config Files',
+                '- **Global**: `~/.tiny-brain/config/preferences.json`',
+                '- **Repository**: `[repo]/.tiny-brain/config.json`',
+            ];
+            return createSuccessResult(lines.join('\n'));
+        }
+        catch (error) {
+            return createErrorResult(`Failed to show preference sources: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    static async handleSet(args, configService) {
+        if (!args.key) {
+            return createErrorResult('key is required for set operation');
+        }
+        if (args.value === undefined) {
+            return createErrorResult('value is required for set operation');
+        }
+        const scope = args.scope || 'repo';
+        try {
+            const result = await configService.setPreferenceByKey(args.key, args.value, scope);
+            if (!result.success) {
+                return createErrorResult(result.error);
+            }
+            const scopeLabel = scope === 'global' ? 'Global' : 'Repository';
+            const displayValue = args.value === 'true' || args.value === 'false'
+                ? args.value === 'true'
+                : args.value;
+            const lines = [
+                '# Preference Updated',
+                '',
+                `✅ **${args.key}** set to \`${displayValue}\``,
+                '',
+                `📁 **Scope**: ${scopeLabel}`,
+                '',
+                '---',
+                '',
+                '💡 Use `config operation=show-sources` to see all preference sources.',
+            ];
+            return createSuccessResult(lines.join('\n'));
+        }
+        catch (error) {
+            return createErrorResult(`Failed to set preference: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    static async handleReset(configService) {
+        try {
+            await configService.resetPreferences();
+            const lines = [
+                '# Preferences reset',
+                '',
+                '✅ All preferences have been reset to their default values.',
+                '',
+                '---',
+                '',
+                '💡 Use `config operation=list` to see current preference values.',
+            ];
+            return createSuccessResult(lines.join('\n'));
+        }
+        catch (error) {
+            return createErrorResult(`Failed to reset preferences: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
 }
-//# sourceMappingURL=config.tool.js.map

package/dist/tools/config/index.js

@@ -1,2 +1 @@
 export { ConfigTool } from './config.tool.js';
-//# sourceMappingURL=index.js.map

package/dist/tools/index.d.ts

@@ -8,23 +8,23 @@ export declare const ToolResultSchema: z.ZodObject<{
         type: z.ZodLiteral<"text">;
         text: z.ZodString;
     }, "strip", z.ZodTypeAny, {
-        type: "text";
         text: string;
-    }, {
         type: "text";
+    }, {
         text: string;
+        type: "text";
     }>, "many">;
     isError: z.ZodOptional<z.ZodBoolean>;
 }, "strip", z.ZodTypeAny, {
     content: {
-        type: "text";
         text: string;
+        type: "text";
     }[];
     isError?: boolean | undefined;
 }, {
     content: {
-        type: "text";
         text: string;
+        type: "text";
     }[];
     isError?: boolean | undefined;
 }>;

package/dist/tools/index.js

@@ -21,4 +21,3 @@ export const createSuccessResult = (text) => ({
 });
 // Note: Tools should be imported from their individual directories or from all-tools.ts
 // to avoid circular dependencies
-//# sourceMappingURL=index.js.map

package/dist/tools/persona/as.tool.js

@@ -568,4 +568,3 @@ export class AsTool {
         context);
     }
 }
-//# sourceMappingURL=as.tool.js.map

package/dist/tools/persona/persona.tool.js

@@ -202,4 +202,3 @@ export class ManagePersonasTool {
         }
     }
 }
-//# sourceMappingURL=persona.tool.js.map

package/dist/tools/plan/plan.tool.d.ts

@@ -17,5 +17,9 @@ export declare class PlanTool {
     private static handleDashboardStatus;
     private static handleAdr;
     private static handleCreateAdr;
+    /**
+     * Handle sync operation - regenerate progress.json from markdown files
+     */
+    private static handleSync;
 }
 //# sourceMappingURL=plan.tool.d.ts.map

package/dist/tools/plan/plan.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"plan.tool.d.ts","sourceRoot":"","sources":["../../../src/tools/plan/plan.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAA0C,KAAK,UAAU,EAAE,MAAM,aAAa,CAAC;AACtF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,EAAE,IAAI,IAAI,OAAO,EAAE,MAAM,oCAAoC,CAAC;AAuJrE,qBAAa,QAAQ;IACnB,MAAM,CAAC,iBAAiB,IAAI,OAAO;WA4LtB,OAAO,CAClB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,UAAU,CAAC;mBAoED,YAAY;mBAuKZ,aAAa;mBAyCb,eAAe;mBA0Df,YAAY;mBA+CZ,YAAY;mBAsDZ,YAAY;mBAiCZ,UAAU;mBA2DV,aAAa;mBA2Cb,oBAAoB;mBA+CpB,mBAAmB;mBAsBnB,qBAAqB;mBAqCrB,SAAS;mBAgGT,eAAe;CAsFrC"}
+{"version":3,"file":"plan.tool.d.ts","sourceRoot":"","sources":["../../../src/tools/plan/plan.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAA0C,KAAK,UAAU,EAAE,MAAM,aAAa,CAAC;AACtF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,EAAE,IAAI,IAAI,OAAO,EAAE,MAAM,oCAAoC,CAAC;AA2LrE,qBAAa,QAAQ;IACnB,MAAM,CAAC,iBAAiB,IAAI,OAAO;WA4LtB,OAAO,CAClB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,UAAU,CAAC;mBA2ED,YAAY;mBA+LZ,aAAa;mBAyCb,eAAe;mBA0Df,YAAY;mBA+CZ,YAAY;mBAsDZ,YAAY;mBAiCZ,UAAU;mBA2DV,aAAa;mBA2Cb,oBAAoB;mBA+CpB,mBAAmB;mBAsBnB,qBAAqB;mBAqCrB,SAAS;mBAgGT,eAAe;IAuFpC;;OAEG;mBACkB,UAAU;CA2DhC"}