refactor: enhance skills and subagents settings management

- Updated useSkillsSettings and useSubagents hooks to improve state management and error handling.
- Added new settings API methods for skills configuration and agent discovery.
- Refactored app-store to include enableSkills and skillsSources state management.
- Enhanced settings migration to sync skills configuration with the server.

These changes streamline the management of skills and subagents, ensuring better integration and user experience.

apps/ui/src/components/views/settings-view/providers/claude-settings-tab/hooks/use-skills-settings.ts

@@ -11,17 +11,20 @@ import { toast } from 'sonner';
 import { getElectronAPI } from '@/lib/electron';
 
 export function useSkillsSettings() {
-  const { settings } = useAppStore();
+  const enabled = useAppStore((state) => state.enableSkills);
+  const sources = useAppStore((state) => state.skillsSources);
   const [isLoading, setIsLoading] = useState(false);
 
-  const enabled = settings?.enableSkills ?? true;
-  const sources = settings?.skillsSources ?? ['user', 'project'];
-
   const updateEnabled = async (newEnabled: boolean) => {
     setIsLoading(true);
     try {
       const api = getElectronAPI();
+      if (!api.settings) {
+        throw new Error('Settings API not available');
+      }
       await api.settings.updateGlobal({ enableSkills: newEnabled });
+      // Update local store after successful server update
+      useAppStore.setState({ enableSkills: newEnabled });
       toast.success(newEnabled ? 'Skills enabled' : 'Skills disabled');
     } catch (error) {
       toast.error('Failed to update skills settings');
@@ -35,7 +38,12 @@ export function useSkillsSettings() {
     setIsLoading(true);
     try {
       const api = getElectronAPI();
+      if (!api.settings) {
+        throw new Error('Settings API not available');
+      }
       await api.settings.updateGlobal({ skillsSources: newSources });
+      // Update local store after successful server update
+      useAppStore.setState({ skillsSources: newSources });
       toast.success('Skills sources updated');
     } catch (error) {
       toast.error('Failed to update skills sources');

apps/ui/src/components/views/settings-view/providers/claude-settings-tab/hooks/use-subagents.ts

@@ -3,27 +3,28 @@
  *
  * Provides read-only view of custom subagent configurations
  * used for specialized task delegation. Supports:
- * - Programmatic agents (stored in settings JSON) - global and project-level
  * - Filesystem agents (AGENT.md files in .claude/agents/) - user and project-level (read-only)
+ *
+ * Filesystem agents are discovered via the server API and displayed in the UI.
+ * Agent definitions in settings JSON are used server-side only.
  */
 
-import { useState, useEffect } from 'react';
+import { useState, useEffect, useCallback } from 'react';
 import { useAppStore } from '@/store/app-store';
 import type { AgentDefinition } from '@automaker/types';
 import { getElectronAPI } from '@/lib/electron';
 
 export type SubagentScope = 'global' | 'project';
-export type SubagentType = 'programmatic' | 'filesystem';
+export type SubagentType = 'filesystem';
 export type FilesystemSource = 'user' | 'project';
 
 export interface SubagentWithScope {
   name: string;
   definition: AgentDefinition;
-  scope: SubagentScope; // For programmatic agents
+  scope: SubagentScope;
   type: SubagentType;
-  // For filesystem agents:
-  source?: FilesystemSource;
-  filePath?: string;
+  source: FilesystemSource;
+  filePath: string;
 }
 
 interface FilesystemAgent {
@@ -34,71 +35,46 @@ interface FilesystemAgent {
 }
 
 export function useSubagents() {
-  const { settings, currentProject, projectSettings } = useAppStore();
+  const currentProject = useAppStore((state) => state.currentProject);
   const [isLoading, setIsLoading] = useState(false);
   const [subagentsWithScope, setSubagentsWithScope] = useState<SubagentWithScope[]>([]);
-  const [filesystemAgents, setFilesystemAgents] = useState<FilesystemAgent[]>([]);
 
   // Fetch filesystem agents
-  const fetchFilesystemAgents = async () => {
+  const fetchFilesystemAgents = useCallback(async () => {
+    setIsLoading(true);
     try {
       const api = getElectronAPI();
+      if (!api.settings) {
+        console.warn('Settings API not available');
+        return;
+      }
       const data = await api.settings.discoverAgents(currentProject?.path, ['user', 'project']);
 
-      if (data.success) {
-        setFilesystemAgents(data.agents || []);
+      if (data.success && data.agents) {
+        // Transform filesystem agents to SubagentWithScope format
+        const agents: SubagentWithScope[] = data.agents.map(
+          ({ name, definition, source, filePath }: FilesystemAgent) => ({
+            name,
+            definition,
+            scope: source === 'user' ? 'global' : 'project',
+            type: 'filesystem' as const,
+            source,
+            filePath,
+          })
+        );
+        setSubagentsWithScope(agents);
       }
     } catch (error) {
       console.error('Failed to fetch filesystem agents:', error);
+    } finally {
+      setIsLoading(false);
     }
-  };
+  }, [currentProject?.path]);
 
   // Fetch filesystem agents on mount and when project changes
   useEffect(() => {
     fetchFilesystemAgents();
-  }, [currentProject?.path]);
-
-  // Merge programmatic and filesystem agents
-  useEffect(() => {
-    const globalSubagents = settings?.customSubagents || {};
-    const projectSubagents = projectSettings?.customSubagents || {};
-
-    const merged: SubagentWithScope[] = [];
-
-    // Add programmatic global agents
-    Object.entries(globalSubagents).forEach(([name, definition]) => {
-      merged.push({ name, definition, scope: 'global', type: 'programmatic' });
-    });
-
-    // Add programmatic project agents (override globals with same name)
-    Object.entries(projectSubagents).forEach(([name, definition]) => {
-      const globalIndex = merged.findIndex((s) => s.name === name && s.scope === 'global');
-      if (globalIndex !== -1) {
-        merged.splice(globalIndex, 1);
-      }
-      merged.push({ name, definition, scope: 'project', type: 'programmatic' });
-    });
-
-    // Add filesystem agents
-    filesystemAgents.forEach(({ name, definition, source, filePath }) => {
-      // Remove any programmatic agents with the same name (filesystem takes precedence)
-      const programmaticIndex = merged.findIndex((s) => s.name === name);
-      if (programmaticIndex !== -1) {
-        merged.splice(programmaticIndex, 1);
-      }
-
-      merged.push({
-        name,
-        definition,
-        scope: source === 'user' ? 'global' : 'project',
-        type: 'filesystem',
-        source,
-        filePath,
-      });
-    });
-
-    setSubagentsWithScope(merged);
-  }, [settings?.customSubagents, projectSettings?.customSubagents, filesystemAgents]);
+  }, [fetchFilesystemAgents]);
 
   return {
     subagentsWithScope,

apps/ui/src/hooks/use-settings-migration.ts

@@ -234,6 +234,8 @@ export async function syncSettingsToServer(): Promise<boolean> {
       keyboardShortcuts: state.keyboardShortcuts,
       aiProfiles: state.aiProfiles,
       mcpServers: state.mcpServers,
+      enableSkills: state.enableSkills,
+      skillsSources: state.skillsSources,
       promptCustomization: state.promptCustomization,
       projects: state.projects,
       trashedProjects: state.trashedProjects,

apps/ui/src/lib/electron.ts

@@ -758,6 +758,83 @@ export interface ElectronAPI {
     }>;
   };
   ideation?: IdeationAPI;
+  settings?: {
+    getStatus: () => Promise<{
+      success: boolean;
+      hasGlobalSettings: boolean;
+      hasCredentials: boolean;
+      dataDir: string;
+      needsMigration: boolean;
+    }>;
+    getGlobal: () => Promise<{
+      success: boolean;
+      settings?: Record<string, unknown>;
+      error?: string;
+    }>;
+    updateGlobal: (updates: Record<string, unknown>) => Promise<{
+      success: boolean;
+      settings?: Record<string, unknown>;
+      error?: string;
+    }>;
+    getCredentials: () => Promise<{
+      success: boolean;
+      credentials?: {
+        anthropic: { configured: boolean; masked: string };
+        google: { configured: boolean; masked: string };
+        openai: { configured: boolean; masked: string };
+      };
+      error?: string;
+    }>;
+    updateCredentials: (updates: {
+      apiKeys?: { anthropic?: string; google?: string; openai?: string };
+    }) => Promise<{
+      success: boolean;
+      credentials?: {
+        anthropic: { configured: boolean; masked: string };
+        google: { configured: boolean; masked: string };
+        openai: { configured: boolean; masked: string };
+      };
+      error?: string;
+    }>;
+    getProject: (projectPath: string) => Promise<{
+      success: boolean;
+      settings?: Record<string, unknown>;
+      error?: string;
+    }>;
+    updateProject: (
+      projectPath: string,
+      updates: Record<string, unknown>
+    ) => Promise<{
+      success: boolean;
+      settings?: Record<string, unknown>;
+      error?: string;
+    }>;
+    migrate: (data: Record<string, string>) => Promise<{
+      success: boolean;
+      migratedGlobalSettings: boolean;
+      migratedCredentials: boolean;
+      migratedProjectCount: number;
+      errors: string[];
+    }>;
+    discoverAgents: (
+      projectPath?: string,
+      sources?: Array<'user' | 'project'>
+    ) => Promise<{
+      success: boolean;
+      agents?: Array<{
+        name: string;
+        definition: {
+          description: string;
+          prompt: string;
+          tools?: string[];
+          model?: 'sonnet' | 'opus' | 'haiku' | 'inherit';
+        };
+        source: 'user' | 'project';
+        filePath: string;
+      }>;
+      error?: string;
+    }>;
+  };
 }
 
 // Note: Window interface is declared in @/types/electron.d.ts

apps/ui/src/store/app-store.ts

@@ -512,6 +512,10 @@ export interface AppState {
   // MCP Servers
   mcpServers: MCPServerConfig[]; // List of configured MCP servers for agent use
 
+  // Skills Configuration
+  enableSkills: boolean; // Enable Skills functionality (loads from .claude/skills/ directories)
+  skillsSources: Array<'user' | 'project'>; // Which directories to load Skills from
+
   // Prompt Customization
   promptCustomization: PromptCustomization; // Custom prompts for Auto Mode, Agent, Backlog Plan, Enhancement
 
@@ -1022,6 +1026,8 @@ const initialState: AppState = {
   enableSandboxMode: false, // Default to disabled (can be enabled for additional security)
   skipSandboxWarning: false, // Default to disabled (show sandbox warning dialog)
   mcpServers: [], // No MCP servers configured by default
+  enableSkills: true, // Skills enabled by default
+  skillsSources: ['user', 'project'] as Array<'user' | 'project'>, // Load from both sources by default
   promptCustomization: {}, // Empty by default - all prompts use built-in defaults
   aiProfiles: DEFAULT_AI_PROFILES,
   projectAnalysis: null,