feat: JIRA integration, Vault support, and consolidated settings UI

apps/desktop/src/main/ai/agent/worker.ts

@@ -352,6 +352,11 @@ async function runSingleSession(
       oauthTokenFilePath: baseSession.oauthTokenFilePath,
     });
   } catch (error) {
+    // Log the error to task_logs.json before cleanup
+    if (logWriter) {
+      const errorMsg = error instanceof Error ? error.message : String(error);
+      logWriter.logText(errorMsg, phase, 'error');
+    }
     // Ensure log cleanup happens on failure
     if (logWriter && !skipPhaseLogging) logWriter.endPhase(phase, false);
     if (logWriter) logWriter.setSubtask(undefined);
@@ -430,6 +435,10 @@ async function run(): Promise<void> {
   } catch (error: unknown) {
     const message = error instanceof Error ? error.message : String(error);
     postError(`Agent session failed: ${message}`);
+    // Write to task_logs.json so the UI shows the error
+    if (logWriter) {
+      logWriter.logText(`Agent session failed: ${message}`, undefined, 'error');
+    }
   } finally {
     // Cleanup MCP clients
     if (mcpClients.length > 0) {
@@ -668,7 +677,13 @@ async function runBuildOrchestrator(
   });
 
   orchestrator.on('error', (error: Error, phase: string) => {
-    postLog(`Error in ${phase} phase: ${error.message}`);
+    const errorMsg = `Error in ${phase} phase: ${error.message}`;
+    postLog(errorMsg);
+    postError(errorMsg);
+    // Also write to task_logs.json so the UI shows the error detail
+    if (logWriter) {
+      logWriter.logText(error.message, phase as Phase, 'error');
+    }
   });
 
   const outcome = await orchestrator.run();

apps/desktop/src/main/ai/config/agent-configs.ts

@@ -88,6 +88,25 @@ export const MEMORY_MCP_TOOLS = [
 /** @deprecated Use MEMORY_MCP_TOOLS instead */
 export const GRAPHITI_MCP_TOOLS = MEMORY_MCP_TOOLS;
 
+/** JIRA MCP tools for issue tracking (when JIRA is configured) */
+export const JIRA_TOOLS = [
+  'mcp__jira__list_projects',
+  'mcp__jira__get_issue',
+  'mcp__jira__create_issue',
+  'mcp__jira__update_issue',
+  'mcp__jira__search_issues',
+  'mcp__jira__add_comment',
+  'mcp__jira__get_transitions',
+  'mcp__jira__transition_issue',
+] as const;
+
+/** Vault MCP tools for external vault access */
+export const VAULT_TOOLS = [
+  'mcp__vault__read_file',
+  'mcp__vault__list_directory',
+  'mcp__vault__search_files',
+] as const;
+
 // =============================================================================
 // Browser Automation MCP Tools (QA agents only)
 // =============================================================================

apps/desktop/src/main/ai/logging/task-log-writer.ts

@@ -145,11 +145,34 @@ export class TaskLogWriter {
         this.flushPendingText();
         break;
 
-      case 'error':
+      case 'error': {
         this.flushPendingText();
-        this.addEntry(logPhase, 'error', event.error.message);
+        // Extract meaningful error message - AI SDK sometimes just sends 'error' as the message
+        const err = event.error;
+        let errorContent = 'Unknown error';
+        if (err) {
+          const msg = err.message || '';
+          const code = err.code || '';
+          const cause = err.cause;
+          // If message is just 'error' (unhelpful), try to extract from cause or code
+          if (msg && msg !== 'error') {
+            errorContent = msg;
+          } else if (cause instanceof Error) {
+            errorContent = cause.message || String(cause);
+          } else if (cause && typeof cause === 'object') {
+            errorContent = JSON.stringify(cause).slice(0, 500);
+          } else if (cause) {
+            errorContent = String(cause);
+          } else if (code && code !== 'error') {
+            errorContent = `Error code: ${code}`;
+          } else {
+            errorContent = `Error: ${JSON.stringify(err).slice(0, 500)}`;
+          }
+        }
+        this.addEntry(logPhase, 'error', errorContent);
         this.save();
         break;
+      }
 
       default:
         // Ignore thinking-delta, usage-update

apps/desktop/src/main/ai/mcp/registry.ts

@@ -118,6 +118,55 @@ function createAutoClaudeServer(specDir: string): McpServerConfig {
   };
 }
 
+/**
+ * JIRA MCP server - issue tracking integration.
+ * Conditionally enabled when project has JIRA configured.
+ * Requires JIRA_HOST, JIRA_EMAIL, JIRA_TOKEN environment variables.
+ *
+ * Uses the community @modelcontextprotocol/server-atlassian package.
+ * If no suitable MCP server is available, JIRA access is handled
+ * directly via the IPC handlers (jira/issue-handlers.ts) instead.
+ */
+function createJiraServer(env: Record<string, string>): McpServerConfig {
+  return {
+    id: 'jira',
+    name: 'JIRA',
+    description: 'Issue tracking integration for JIRA/Atlassian',
+    enabledByDefault: false,
+    transport: {
+      type: 'stdio',
+      command: 'npx',
+      args: ['-y', '@modelcontextprotocol/server-atlassian'],
+      env: {
+        ATLASSIAN_SITE_URL: env.JIRA_HOST || '',
+        ATLASSIAN_USER_EMAIL: env.JIRA_EMAIL || '',
+        ATLASSIAN_API_TOKEN: env.JIRA_TOKEN || '',
+      },
+    },
+  };
+}
+
+/**
+ * Vault MCP server - external vault/Obsidian integration.
+ * Conditionally enabled when vault path is configured.
+ * Provides read-only file access to vault directory for agent context.
+ *
+ * Uses the official @modelcontextprotocol/server-filesystem package.
+ */
+function createVaultServer(vaultPath: string): McpServerConfig {
+  return {
+    id: 'vault',
+    name: 'Vault',
+    description: 'External vault integration for context and learnings',
+    enabledByDefault: false,
+    transport: {
+      type: 'stdio',
+      command: 'npx',
+      args: ['-y', '@modelcontextprotocol/server-filesystem', vaultPath],
+    },
+  };
+}
+
 // =============================================================================
 // Registry
 // =============================================================================
@@ -132,6 +181,10 @@ export interface McpRegistryOptions {
   linearApiKey?: string;
   /** Environment variables for server processes */
   env?: Record<string, string>;
+  /** JIRA environment variables (JIRA_HOST, JIRA_EMAIL, JIRA_TOKEN) */
+  jiraEnv?: Record<string, string>;
+  /** Vault path (if vault integration is enabled) */
+  vaultPath?: string;
 }
 
 /**
@@ -180,6 +233,23 @@ export function getMcpServerConfig(
       return createAutoClaudeServer(specDir);
     }
 
+    case 'jira': {
+      const jiraHost = options.jiraEnv?.JIRA_HOST ?? options.env?.JIRA_HOST;
+      if (!jiraHost) return null;
+      const jiraEnv = options.jiraEnv ?? {
+        JIRA_HOST: options.env?.JIRA_HOST ?? '',
+        JIRA_EMAIL: options.env?.JIRA_EMAIL ?? '',
+        JIRA_TOKEN: options.env?.JIRA_TOKEN ?? '',
+      };
+      return createJiraServer(jiraEnv);
+    }
+
+    case 'vault': {
+      const vPath = options.vaultPath ?? options.env?.VAULT_PATH;
+      if (!vPath) return null;
+      return createVaultServer(vPath);
+    }
+
     default:
       return null;
   }

apps/desktop/src/main/ai/mcp/types.ts

@@ -49,7 +49,9 @@ export type McpServerId =
   | 'memory'
   | 'electron'
   | 'puppeteer'
-  | 'auto-claude';
+  | 'auto-claude'
+  | 'jira'
+  | 'vault';
 
 /** Configuration for a single MCP server */
 export interface McpServerConfig {

apps/desktop/src/main/ai/session/stream-handler.ts

@@ -266,7 +266,33 @@ export function createStreamHandler(onEvent: SessionEventCallback) {
   }
 
   function handleError(part: ErrorPart): void {
-    const errorMessage = part.error instanceof Error ? part.error.message : String(part.error ?? 'Stream error');
+    // DEBUG: Dump the raw error to console for diagnosis
+    console.warn('[StreamHandler] RAW ERROR:', JSON.stringify(part.error, Object.getOwnPropertyNames(part.error instanceof Error ? part.error : {}), 2).slice(0, 1000));
+    console.warn('[StreamHandler] ERROR TYPE:', typeof part.error, part.error?.constructor?.name);
+    if (part.error instanceof Error) {
+      console.warn('[StreamHandler] ERROR CAUSE:', (part.error as { cause?: unknown }).cause);
+      console.warn('[StreamHandler] ERROR STACK:', part.error.stack?.slice(0, 500));
+    }
+
+    // Extract meaningful error message - AI SDK error objects may have nested cause
+    let errorMessage: string;
+    if (part.error instanceof Error) {
+      errorMessage = part.error.message;
+      // If message is just 'error', try cause
+      if (errorMessage === 'error' && (part.error as { cause?: unknown }).cause) {
+        const cause = (part.error as { cause?: unknown }).cause;
+        errorMessage = cause instanceof Error ? cause.message : String(cause);
+      }
+      // Also check stack for more context if message is unhelpful
+      if (errorMessage === 'error' && part.error.stack) {
+        errorMessage = part.error.stack.split('\n')[0] || 'Stream error';
+      }
+    } else if (typeof part.error === 'object' && part.error !== null) {
+      const errObj = part.error as Record<string, unknown>;
+      errorMessage = (errObj.message as string) || (errObj.text as string) || JSON.stringify(part.error).slice(0, 500);
+    } else {
+      errorMessage = String(part.error ?? 'Stream error');
+    }
     const { sessionError } = classifyError(errorMessage);
     emit({ type: 'error', error: sessionError });
   }

apps/desktop/src/main/ipc-handlers/env-handlers.ts

@@ -89,6 +89,29 @@ export function registerEnvHandlers(
     if (config.gitlabAutoSync !== undefined) {
       existingVars[GITLAB_ENV_KEYS.AUTO_SYNC] = config.gitlabAutoSync ? 'true' : 'false';
     }
+    // Independent issue tracking flags (separate from source control)
+    if (config.githubIssuesEnabled !== undefined) {
+      existingVars['GITHUB_ISSUES_ENABLED'] = config.githubIssuesEnabled ? 'true' : 'false';
+    }
+    if (config.gitlabIssuesEnabled !== undefined) {
+      existingVars['GITLAB_ISSUES_ENABLED'] = config.gitlabIssuesEnabled ? 'true' : 'false';
+    }
+    // JIRA Integration
+    if (config.jiraEnabled !== undefined) {
+      existingVars['JIRA_ENABLED'] = config.jiraEnabled ? 'true' : 'false';
+    }
+    if (config.jiraHost !== undefined) {
+      existingVars['JIRA_HOST'] = config.jiraHost;
+    }
+    if (config.jiraEmail !== undefined) {
+      existingVars['JIRA_EMAIL'] = config.jiraEmail;
+    }
+    if (config.jiraToken !== undefined) {
+      existingVars['JIRA_TOKEN'] = config.jiraToken;
+    }
+    if (config.jiraProjectKey !== undefined) {
+      existingVars['JIRA_PROJECT_KEY'] = config.jiraProjectKey;
+    }
     // Git/Worktree Settings
     if (config.defaultBranch !== undefined) {
       existingVars['DEFAULT_BRANCH'] = config.defaultBranch;
@@ -212,6 +235,16 @@ ${envLine(existingVars, GITLAB_ENV_KEYS.INSTANCE_URL, 'https://gitlab.com')}
 ${envLine(existingVars, GITLAB_ENV_KEYS.TOKEN)}
 ${envLine(existingVars, GITLAB_ENV_KEYS.PROJECT, 'group/project')}
 ${envLine(existingVars, GITLAB_ENV_KEYS.AUTO_SYNC, 'false')}
+${existingVars['GITLAB_ISSUES_ENABLED'] !== undefined ? `GITLAB_ISSUES_ENABLED=${existingVars['GITLAB_ISSUES_ENABLED']}` : '# GITLAB_ISSUES_ENABLED=false'}
+
+# =============================================================================
+# JIRA INTEGRATION (OPTIONAL)
+# =============================================================================
+${existingVars['JIRA_ENABLED'] !== undefined ? `JIRA_ENABLED=${existingVars['JIRA_ENABLED']}` : '# JIRA_ENABLED=false'}
+${envLine(existingVars, 'JIRA_HOST', 'https://your-domain.atlassian.net')}
+${envLine(existingVars, 'JIRA_EMAIL')}
+${envLine(existingVars, 'JIRA_TOKEN')}
+${envLine(existingVars, 'JIRA_PROJECT_KEY', 'PROJ')}
 
 # =============================================================================
 # GIT/WORKTREE SETTINGS (OPTIONAL)
@@ -324,6 +357,7 @@ ${existingVars['GRAPHITI_DB_PATH'] ? `GRAPHITI_DB_PATH=${existingVars['GRAPHITI_
         linearEnabled: false,
         githubEnabled: false,
         gitlabEnabled: false,
+        jiraEnabled: false,
         memoryEnabled: false,
         enableFancyUi: true,
         openaiKeyIsGlobal: false
@@ -386,6 +420,30 @@ ${existingVars['GRAPHITI_DB_PATH'] ? `GRAPHITI_DB_PATH=${existingVars['GRAPHITI_
         config.gitlabAutoSync = true;
       }
 
+      // Independent issue tracking flags
+      if (vars['GITHUB_ISSUES_ENABLED']?.toLowerCase() === 'true') {
+        config.githubIssuesEnabled = true;
+      }
+      if (vars['GITLAB_ISSUES_ENABLED']?.toLowerCase() === 'true') {
+        config.gitlabIssuesEnabled = true;
+      }
+
+      // JIRA config
+      if (vars['JIRA_HOST']) {
+        config.jiraHost = vars['JIRA_HOST'];
+        // Enable by default if host exists and JIRA_ENABLED is not explicitly false
+        config.jiraEnabled = vars['JIRA_ENABLED']?.toLowerCase() !== 'false';
+      }
+      if (vars['JIRA_EMAIL']) {
+        config.jiraEmail = vars['JIRA_EMAIL'];
+      }
+      if (vars['JIRA_TOKEN']) {
+        config.jiraToken = vars['JIRA_TOKEN'];
+      }
+      if (vars['JIRA_PROJECT_KEY']) {
+        config.jiraProjectKey = vars['JIRA_PROJECT_KEY'];
+      }
+
       // Git/Worktree config
       if (vars['DEFAULT_BRANCH']) {
         config.defaultBranch = vars['DEFAULT_BRANCH'];

apps/desktop/src/main/ipc-handlers/index.ts

@@ -34,6 +34,8 @@ import { registerProfileHandlers } from './profile-handlers';
 import { registerScreenshotHandlers } from './screenshot-handlers';
 import { registerTerminalWorktreeIpcHandlers } from './terminal';
 import { registerCodexAuthHandlers } from './codex-auth-handlers';
+import { registerJiraHandlers } from './jira';
+import { registerVaultHandlers } from './vault';
 import { notificationService } from '../notification-service';
 import { setAgentManagerRef } from './utils';
 
@@ -127,6 +129,12 @@ export function setupIpcHandlers(
   // Codex OAuth authentication handlers
   registerCodexAuthHandlers();
 
+  // JIRA integration handlers
+  registerJiraHandlers(agentManager, getMainWindow);
+
+  // Vault integration handlers
+  registerVaultHandlers();
+
   console.warn('[IPC] All handler modules registered successfully');
 }
 
@@ -155,5 +163,7 @@ export {
   registerMcpHandlers,
   registerProfileHandlers,
   registerScreenshotHandlers,
-  registerCodexAuthHandlers
+  registerCodexAuthHandlers,
+  registerJiraHandlers,
+  registerVaultHandlers
 };

apps/desktop/src/main/ipc-handlers/jira/index.ts

@@ -0,0 +1,27 @@
+/**
+ * JIRA IPC Handlers Module
+ *
+ * This module exports the main registration function for all JIRA-related IPC handlers.
+ */
+
+import type { BrowserWindow } from 'electron';
+import type { AgentManager } from '../../agent';
+
+import { registerJiraIssueHandlers } from './issue-handlers';
+import { registerJiraInvestigationHandlers } from './investigation-handlers';
+
+/**
+ * Register all JIRA IPC handlers
+ */
+export function registerJiraHandlers(
+  agentManager: AgentManager,
+  getMainWindow: () => BrowserWindow | null
+): void {
+  console.warn('[JIRA] Registering JIRA handlers');
+  registerJiraIssueHandlers();
+  registerJiraInvestigationHandlers(agentManager, getMainWindow);
+  console.warn('[JIRA] JIRA handlers registered');
+}
+
+// Re-export individual registration functions for custom usage
+export { registerJiraIssueHandlers, registerJiraInvestigationHandlers };