@posthog/agent 1.10.0 → 1.12.0

package/dist/src/agent.js

@@ -6,11 +6,9 @@ import { GitManager } from './git-manager.js';
 import { TemplateManager } from './template-manager.js';
 import { ClaudeAdapter } from './adapters/claude/claude-adapter.js';
 import { Logger } from './utils/logger.js';
-import { AgentRegistry } from './agent-registry.js';
-import { WorkflowRegistry } from './workflow-registry.js';
-import { StageExecutor } from './stage-executor.js';
 import { PromptBuilder } from './prompt-builder.js';
 import { TaskProgressReporter } from './task-progress-reporter.js';
+import { OpenAIExtractor } from './structured-extraction.js';
 export { PermissionMode } from './types.js';
 
 class Agent {
@@ -23,10 +21,9 @@ class Agent {
     templateManager;
     adapter;
     logger;
-    agentRegistry;
-    workflowRegistry;
-    stageExecutor;
     progressReporter;
+    promptBuilder;
+    extractor;
     mcpServers;
     debug;
     constructor(config = {}) {
@@ -65,24 +62,23 @@ class Agent {
             // TODO: Add author config from environment or config
         });
         this.templateManager = new TemplateManager();
-        this.agentRegistry = new AgentRegistry();
         if (config.posthogApiUrl && config.posthogApiKey) {
             this.posthogAPI = new PostHogAPIClient({
                 apiUrl: config.posthogApiUrl,
                 apiKey: config.posthogApiKey,
             });
         }
-        this.workflowRegistry = new WorkflowRegistry(this.posthogAPI);
-        const promptBuilder = new PromptBuilder({
+        this.promptBuilder = new PromptBuilder({
             getTaskFiles: (taskId) => this.getTaskFiles(taskId),
             generatePlanTemplate: (vars) => this.templateManager.generatePlan(vars),
             posthogClient: this.posthogAPI,
             logger: this.logger.child('PromptBuilder')
         });
-        this.stageExecutor = new StageExecutor(this.agentRegistry, this.logger, promptBuilder, undefined, // eventHandler set via setEventHandler below
-        this.mcpServers);
-        this.stageExecutor.setEventHandler((event) => this.emitEvent(event));
         this.progressReporter = new TaskProgressReporter(this.posthogAPI, this.logger);
+        // Initialize OpenAI extractor if API key is available
+        if (process.env.OPENAI_API_KEY) {
+            this.extractor = new OpenAIExtractor(this.logger.child('OpenAIExtractor'));
+        }
     }
     /**
      * Enable or disable debug logging
@@ -113,206 +109,307 @@ class Agent {
             throw error;
         }
     }
-    // Workflow-based execution
-    async runWorkflow(taskOrId, workflowId, options = {}) {
+    // Adaptive task execution - 3 phases (research → plan → build)
+    async runTask(taskOrId, options = {}) {
         await this._configureLlmGateway();
         const task = typeof taskOrId === 'string' ? await this.fetchTask(taskOrId) : taskOrId;
-        await this.workflowRegistry.loadWorkflows();
-        const workflow = this.workflowRegistry.getWorkflow(workflowId);
-        if (!workflow) {
-            throw new Error(`Workflow ${workflowId} not found`);
+        const cwd = options.repositoryPath || this.workingDirectory;
+        const isCloudMode = options.isCloudMode ?? false;
+        const taskSlug = task.slug || task.id;
+        this.logger.info('Starting adaptive task execution', { taskId: task.id, taskSlug, isCloudMode });
+        // Initialize progress reporter for task run tracking (needed for PR attachment)
+        await this.progressReporter.start(task.id, { totalSteps: 3 }); // 3 phases: research, plan, build
+        this.emitEvent(this.adapter.createStatusEvent('run_started', { runId: this.progressReporter.runId }));
+        // Phase 1: Branch check
+        const existingBranch = await this.gitManager.getTaskBranch(taskSlug);
+        if (!existingBranch) {
+            this.logger.info('Creating task branch', { taskSlug });
+            const branchName = `posthog/task-${taskSlug}`;
+            await this.gitManager.createOrSwitchToBranch(branchName);
+            this.emitEvent(this.adapter.createStatusEvent('branch_created', { branch: branchName }));
+            // Initial commit
+            await this.fileManager.ensureGitignore();
+            await this.gitManager.addAllPostHogFiles();
+            if (isCloudMode) {
+                await this.gitManager.commitAndPush(`Initialize task ${taskSlug}`, { allowEmpty: true });
+            }
+            else {
+                await this.gitManager.commitChanges(`Initialize task ${taskSlug}`);
+            }
         }
-        const orderedStages = [...workflow.stages].sort((a, b) => a.position - b.position);
-        // Ensure task is assigned to workflow and positioned at first stage
-        if (this.posthogAPI) {
-            try {
-                if (task.workflow !== workflowId) {
-                    await this.posthogAPI.updateTask(task.id, { workflow: workflowId });
-                    task.workflow = workflowId;
+        else {
+            this.logger.info('Switching to existing task branch', { branch: existingBranch });
+            await this.gitManager.switchToBranch(existingBranch);
+        }
+        // Phase 2: Research
+        const researchExists = await this.fileManager.readResearch(task.id);
+        if (!researchExists) {
+            this.logger.info('Starting research phase', { taskId: task.id });
+            this.emitEvent(this.adapter.createStatusEvent('phase_start', { phase: 'research' }));
+            // Run research agent
+            const researchPrompt = await this.promptBuilder.buildResearchPrompt(task, cwd);
+            const { RESEARCH_SYSTEM_PROMPT } = await import('./agents/research.js');
+            const fullPrompt = RESEARCH_SYSTEM_PROMPT + '\n\n' + researchPrompt;
+            const baseOptions = {
+                model: 'claude-sonnet-4-5-20250929',
+                cwd,
+                permissionMode: 'plan',
+                settingSources: ['local'],
+                mcpServers: this.mcpServers,
+            };
+            const response = query({
+                prompt: fullPrompt,
+                options: { ...baseOptions, ...(options.queryOverrides || {}) },
+            });
+            let researchContent = '';
+            for await (const message of response) {
+                this.emitEvent(this.adapter.createRawSDKEvent(message));
+                const transformed = this.adapter.transform(message);
+                if (transformed) {
+                    this.emitEvent(transformed);
+                }
+                if (message.type === 'assistant' && message.message?.content) {
+                    for (const c of message.message.content) {
+                        if (c.type === 'text' && c.text)
+                            researchContent += c.text + '\n';
+                    }
                 }
             }
-            catch (e) {
-                this.logger.warn('Failed to sync task workflow before execution', { error: e.message });
+            // Write research.md
+            if (researchContent.trim()) {
+                await this.fileManager.writeResearch(task.id, researchContent.trim());
+                this.logger.info('Research completed', { taskId: task.id });
             }
-        }
-        const executionId = this.taskManager.generateExecutionId();
-        this.logger.info('Starting workflow execution', { taskId: task.id, workflowId, executionId });
-        this.taskManager.startExecution(task.id, 'plan_and_build', executionId);
-        await this.progressReporter.start(task.id, {
-            totalSteps: orderedStages.length,
-        });
-        // Set initial stage on the newly created run
-        const firstStage = orderedStages[0];
-        if (this.posthogAPI && this.progressReporter.runId && firstStage) {
-            try {
-                await this.posthogAPI.updateTaskRun(task.id, this.progressReporter.runId, {
-                    current_stage: firstStage.id
+            // Commit research
+            await this.gitManager.addAllPostHogFiles();
+            // Extract questions using structured output and save to questions.json
+            if (this.extractor) {
+                try {
+                    this.logger.info('Extracting questions from research.md', { taskId: task.id });
+                    const questions = await this.extractQuestionsFromResearch(task.id, false);
+                    this.logger.info('Questions extracted successfully', { taskId: task.id, count: questions.length });
+                    // Save questions.json
+                    await this.fileManager.writeQuestions(task.id, {
+                        questions,
+                        answered: false,
+                        answers: null,
+                    });
+                    this.logger.info('Questions saved to questions.json', { taskId: task.id });
+                    // Emit event for Array to pick up (local mode)
+                    if (!isCloudMode) {
+                        this.emitEvent({
+                            type: 'artifact',
+                            ts: Date.now(),
+                            kind: 'research_questions',
+                            content: questions,
+                        });
+                        this.logger.info('Emitted research_questions artifact event', { taskId: task.id });
+                    }
+                }
+                catch (error) {
+                    this.logger.error('Failed to extract questions', { error: error instanceof Error ? error.message : String(error) });
+                    this.emitEvent({
+                        type: 'error',
+                        ts: Date.now(),
+                        message: `Failed to extract questions: ${error instanceof Error ? error.message : String(error)}`,
+                    });
+                }
+            }
+            else {
+                this.logger.warn('OpenAI extractor not available (OPENAI_API_KEY not set), skipping question extraction');
+                this.emitEvent({
+                    type: 'status',
+                    ts: Date.now(),
+                    phase: 'extraction_skipped',
+                    message: 'Question extraction skipped - OPENAI_API_KEY not configured',
                 });
             }
-            catch (e) {
-                this.logger.warn('Failed to set initial stage on run', { error: e.message });
+            if (isCloudMode) {
+                await this.gitManager.commitAndPush(`Research phase for ${task.title}`);
+            }
+            else {
+                await this.gitManager.commitChanges(`Research phase for ${task.title}`);
+                this.emitEvent(this.adapter.createStatusEvent('phase_complete', { phase: 'research' }));
+                return; // Local mode: return to user
             }
         }
-        try {
-            let startIndex = 0;
-            const currentStageId = task.current_stage;
-            // If task is already at the last stage, fail gracefully without progressing
-            if (currentStageId) {
-                const currIdx = orderedStages.findIndex(s => s.id === currentStageId);
-                const atLastStage = currIdx >= 0 && currIdx === orderedStages.length - 1;
-                if (atLastStage) {
-                    const finalStageKey = orderedStages[currIdx]?.key;
-                    this.emitEvent(this.adapter.createStatusEvent('no_next_stage', { stage: finalStageKey }));
-                    await this.progressReporter.noNextStage(finalStageKey);
-                    await this.progressReporter.complete();
-                    this.taskManager.completeExecution(executionId, { task, workflow });
-                    return { task, workflow };
+        // Phase 3: Auto-answer questions (cloud mode only)
+        if (isCloudMode) {
+            const questionsData = await this.fileManager.readQuestions(task.id);
+            if (questionsData && !questionsData.answered) {
+                this.logger.info('Auto-answering research questions', { taskId: task.id });
+                // Extract questions with recommended answers using structured output
+                if (this.extractor) {
+                    const questionsWithAnswers = await this.extractQuestionsFromResearch(task.id, true);
+                    // Save answers to questions.json
+                    await this.fileManager.writeQuestions(task.id, {
+                        questions: questionsWithAnswers.map(qa => ({
+                            id: qa.id,
+                            question: qa.question,
+                            options: qa.options,
+                        })),
+                        answered: true,
+                        answers: questionsWithAnswers.map(qa => ({
+                            questionId: qa.id,
+                            selectedOption: qa.recommendedAnswer,
+                            customInput: qa.justification,
+                        })),
+                    });
+                    this.logger.info('Auto-answers saved to questions.json', { taskId: task.id });
+                    await this.gitManager.addAllPostHogFiles();
+                    await this.gitManager.commitAndPush(`Answer research questions for ${task.title}`);
+                }
+                else {
+                    this.logger.warn('OpenAI extractor not available, skipping auto-answer');
                 }
             }
-            if (options.resumeFromCurrentStage && currentStageId) {
-                const idx = orderedStages.findIndex(s => s.id === currentStageId);
-                if (idx >= 0)
-                    startIndex = idx;
+        }
+        // Phase 4: Plan
+        const planExists = await this.readPlan(task.id);
+        if (!planExists) {
+            // Check if questions have been answered
+            const questionsData = await this.fileManager.readQuestions(task.id);
+            if (!questionsData || !questionsData.answered) {
+                this.logger.info('Waiting for user answers to research questions');
+                this.emitEvent(this.adapter.createStatusEvent('phase_complete', { phase: 'research_questions' }));
+                return; // Wait for user to answer questions
             }
-            // Align server-side stage when restarting from a different stage
-            if (this.posthogAPI && this.progressReporter.runId) {
-                const targetStage = orderedStages[startIndex];
-                if (targetStage && targetStage.id !== currentStageId) {
-                    try {
-                        await this.posthogAPI.updateTaskRun(task.id, this.progressReporter.runId, {
-                            current_stage: targetStage.id
-                        });
-                    }
-                    catch (e) {
-                        this.logger.warn('Failed to update run stage', { error: e.message });
+            this.logger.info('Starting planning phase', { taskId: task.id });
+            this.emitEvent(this.adapter.createStatusEvent('phase_start', { phase: 'planning' }));
+            // Build context with research + questions + answers
+            const research = await this.fileManager.readResearch(task.id);
+            let researchContext = '';
+            if (research) {
+                researchContext += `## Research Analysis\n\n${research}\n\n`;
+            }
+            // Add questions and answers
+            researchContext += `## Implementation Decisions\n\n`;
+            const answers = questionsData.answers || [];
+            for (const question of questionsData.questions) {
+                const answer = answers.find((a) => a.questionId === question.id);
+                researchContext += `### ${question.question}\n\n`;
+                if (answer) {
+                    researchContext += `**Selected:** ${answer.selectedOption}\n`;
+                    if (answer.customInput) {
+                        researchContext += `**Details:** ${answer.customInput}\n`;
                     }
                 }
+                else {
+                    this.logger.warn('No answer found for question', { questionId: question.id });
+                    researchContext += `**Selected:** Not answered\n`;
+                }
+                researchContext += '\n';
             }
-            for (let i = startIndex; i < orderedStages.length; i++) {
-                const stage = orderedStages[i];
-                await this.progressReporter.stageStarted(stage.key, i);
-                await this.executeStage(task, stage, options);
-                await this.progressReporter.stageCompleted(stage.key, i + 1);
-                if (options.autoProgress) {
-                    const hasNext = i < orderedStages.length - 1;
-                    if (hasNext) {
-                        await this.progressToNextStage(task.id, stage.key);
+            // Run planning agent with full context
+            const planningPrompt = await this.promptBuilder.buildPlanningPrompt(task, cwd);
+            const { PLANNING_SYSTEM_PROMPT } = await import('./agents/planning.js');
+            const fullPrompt = PLANNING_SYSTEM_PROMPT + '\n\n' + planningPrompt + '\n\n' + researchContext;
+            const baseOptions = {
+                model: 'claude-sonnet-4-5-20250929',
+                cwd,
+                permissionMode: 'plan',
+                settingSources: ['local'],
+                mcpServers: this.mcpServers,
+            };
+            const response = query({
+                prompt: fullPrompt,
+                options: { ...baseOptions, ...(options.queryOverrides || {}) },
+            });
+            let planContent = '';
+            for await (const message of response) {
+                this.emitEvent(this.adapter.createRawSDKEvent(message));
+                const transformed = this.adapter.transform(message);
+                if (transformed) {
+                    this.emitEvent(transformed);
+                }
+                if (message.type === 'assistant' && message.message?.content) {
+                    for (const c of message.message.content) {
+                        if (c.type === 'text' && c.text)
+                            planContent += c.text + '\n';
                     }
                 }
             }
-            await this.progressReporter.complete();
-            this.taskManager.completeExecution(executionId, { task, workflow });
-            return { task, workflow };
-        }
-        catch (error) {
-            await this.progressReporter.fail(error);
-            this.taskManager.failExecution(executionId, error);
-            throw error;
-        }
-    }
-    async executeStage(task, stage, options = {}) {
-        this.emitEvent(this.adapter.createStatusEvent('stage_start', { stage: stage.key }));
-        const overrides = options.stageOverrides?.[stage.key];
-        const agentName = stage.agent_name || 'code_generation';
-        const agentDef = this.agentRegistry.getAgent(agentName);
-        const isManual = stage.is_manual_only === true;
-        const stageKeyLower = (stage.key || '').toLowerCase().trim();
-        const isPlanningByKey = stageKeyLower === 'plan' || stageKeyLower.includes('plan');
-        const isPlanning = !isManual && ((agentDef?.agent_type === 'planning') || isPlanningByKey);
-        const shouldCreatePlanningBranch = overrides?.createPlanningBranch !== false; // default true
-        const shouldCreateImplBranch = overrides?.createImplementationBranch !== false; // default true
-        if (isPlanning && shouldCreatePlanningBranch) {
-            const planningBranch = await this.createPlanningBranch(task.id);
-            await this.updateTaskBranch(task.id, planningBranch);
-            this.emitEvent(this.adapter.createStatusEvent('branch_created', { stage: stage.key, branch: planningBranch }));
-            await this.progressReporter.branchCreated(stage.key, planningBranch);
-        }
-        else if (!isPlanning && !isManual && shouldCreateImplBranch) {
-            const implBranch = await this.createImplementationBranch(task.id);
-            await this.updateTaskBranch(task.id, implBranch);
-            this.emitEvent(this.adapter.createStatusEvent('branch_created', { stage: stage.key, branch: implBranch }));
-            await this.progressReporter.branchCreated(stage.key, implBranch);
-        }
-        const result = await this.stageExecutor.execute(task, stage, options);
-        if (result.plan) {
-            await this.writePlan(task.id, result.plan);
-            await this.commitPlan(task.id, task.title);
-            this.emitEvent(this.adapter.createStatusEvent('commit_made', { stage: stage.key, kind: 'plan' }));
-            await this.progressReporter.commitMade(stage.key, 'plan');
+            // Write plan.md
+            if (planContent.trim()) {
+                await this.writePlan(task.id, planContent.trim());
+                this.logger.info('Plan completed', { taskId: task.id });
+            }
+            // Commit plan
+            await this.gitManager.addAllPostHogFiles();
+            if (isCloudMode) {
+                await this.gitManager.commitAndPush(`Planning phase for ${task.title}`);
+            }
+            else {
+                await this.gitManager.commitChanges(`Planning phase for ${task.title}`);
+                this.emitEvent(this.adapter.createStatusEvent('phase_complete', { phase: 'planning' }));
+                return; // Local mode: return to user
+            }
         }
-        if (isManual) {
-            const defaultOpenPR = true; // manual stages default to PR for review
-            const openPR = overrides?.openPullRequest ?? defaultOpenPR;
-            if (openPR) {
-                // Ensure we're on an implementation branch for PRs
-                let branchName = await this.gitManager.getCurrentBranch();
-                const onTaskBranch = branchName.includes(`posthog/task-${task.id}`);
-                if (!onTaskBranch && (overrides?.createImplementationBranch !== false)) {
-                    const implBranch = await this.createImplementationBranch(task.id);
-                    await this.updateTaskBranch(task.id, implBranch);
-                    branchName = implBranch;
-                    this.emitEvent(this.adapter.createStatusEvent('branch_created', { stage: stage.key, branch: implBranch }));
-                    await this.progressReporter.branchCreated(stage.key, implBranch);
-                }
-                try {
-                    const prUrl = await this.createPullRequest(task.id, branchName, task.title, task.description);
-                    await this.updateTaskBranch(task.id, branchName);
-                    await this.attachPullRequestToTask(task.id, prUrl, branchName);
-                    this.emitEvent(this.adapter.createStatusEvent('pr_created', { stage: stage.key, prUrl }));
-                    await this.progressReporter.pullRequestCreated(stage.key, prUrl);
+        // Phase 5: Build
+        const latestRun = task.latest_run;
+        const prExists = latestRun?.output && latestRun.output.pr_url;
+        if (!prExists) {
+            this.logger.info('Starting build phase', { taskId: task.id });
+            this.emitEvent(this.adapter.createStatusEvent('phase_start', { phase: 'build' }));
+            // Run execution agent
+            const executionPrompt = await this.promptBuilder.buildExecutionPrompt(task, cwd);
+            const { EXECUTION_SYSTEM_PROMPT } = await import('./agents/execution.js');
+            const fullPrompt = EXECUTION_SYSTEM_PROMPT + '\n\n' + executionPrompt;
+            const { PermissionMode } = await import('./types.js');
+            const permissionMode = options.permissionMode || PermissionMode.ACCEPT_EDITS;
+            const baseOptions = {
+                model: 'claude-sonnet-4-5-20250929',
+                cwd,
+                permissionMode,
+                settingSources: ['local'],
+                mcpServers: this.mcpServers,
+            };
+            const response = query({
+                prompt: fullPrompt,
+                options: { ...baseOptions, ...(options.queryOverrides || {}) },
+            });
+            for await (const message of response) {
+                this.emitEvent(this.adapter.createRawSDKEvent(message));
+                const transformed = this.adapter.transform(message);
+                if (transformed) {
+                    this.emitEvent(transformed);
                 }
-                catch { }
             }
-            // Do not auto-progress on manual stages
-            this.emitEvent(this.adapter.createStatusEvent('stage_complete', { stage: stage.key }));
-            return;
-        }
-        if (result.results) {
-            const existingPlan = await this.readPlan(task.id);
-            const planSummary = existingPlan ? existingPlan.split('\n')[0] : undefined;
-            await this.commitImplementation(task.id, task.title, planSummary);
-            this.emitEvent(this.adapter.createStatusEvent('commit_made', { stage: stage.key, kind: 'implementation' }));
-            await this.progressReporter.commitMade(stage.key, 'implementation');
-        }
-        // PR creation on complete stage (or if explicitly requested), regardless of whether edits occurred
-        {
-            const defaultOpenPR = stage.key.toLowerCase().includes('complete');
-            const openPR = overrides?.openPullRequest ?? defaultOpenPR;
-            if (openPR) {
+            // Commit and push implementation
+            // Stage ALL changes (not just .posthog/)
+            const hasChanges = await this.gitManager.hasChanges();
+            if (hasChanges) {
+                await this.gitManager.addFiles(['.']); // Stage all changes
+                await this.gitManager.commitChanges(`Implementation for ${task.title}`);
+                // Push to origin
                 const branchName = await this.gitManager.getCurrentBranch();
-                try {
-                    const prUrl = await this.createPullRequest(task.id, branchName, task.title, task.description);
-                    await this.updateTaskBranch(task.id, branchName);
-                    await this.attachPullRequestToTask(task.id, prUrl, branchName);
-                    this.emitEvent(this.adapter.createStatusEvent('pr_created', { stage: stage.key, prUrl }));
-                    await this.progressReporter.pullRequestCreated(stage.key, prUrl);
-                }
-                catch { }
+                await this.gitManager.pushBranch(branchName);
+                this.logger.info('Implementation committed and pushed', { taskId: task.id });
             }
-        }
-        this.emitEvent(this.adapter.createStatusEvent('stage_complete', { stage: stage.key }));
-    }
-    async progressToNextStage(taskId, currentStageKey) {
-        if (!this.posthogAPI || !this.progressReporter.runId) {
-            throw new Error('PostHog API not configured or no active run. Cannot progress stage.');
-        }
-        try {
-            await this.posthogAPI.progressTaskRun(taskId, this.progressReporter.runId);
-        }
-        catch (error) {
-            if (error instanceof Error && error.message.includes('No next stage available')) {
-                this.logger.warn('No next stage available when attempting to progress run', {
-                    taskId,
-                    runId: this.progressReporter.runId,
-                    stage: currentStageKey,
-                    error: error.message,
-                });
-                this.emitEvent(this.adapter.createStatusEvent('no_next_stage', { stage: currentStageKey }));
-                await this.progressReporter.noNextStage(currentStageKey);
-                return;
+            else {
+                this.logger.warn('No changes to commit in build phase', { taskId: task.id });
             }
-            throw error;
+            // Create PR
+            const branchName = await this.gitManager.getCurrentBranch();
+            const prUrl = await this.createPullRequest(task.id, branchName, task.title, task.description);
+            this.logger.info('Pull request created', { taskId: task.id, prUrl });
+            this.emitEvent(this.adapter.createStatusEvent('pr_created', { prUrl }));
+            // Attach PR to task run
+            try {
+                await this.attachPullRequestToTask(task.id, prUrl, branchName);
+                this.logger.info('PR attached to task successfully', { taskId: task.id, prUrl });
+            }
+            catch (error) {
+                this.logger.warn('Could not attach PR to task', { error: error instanceof Error ? error.message : String(error) });
+            }
+        }
+        else {
+            this.logger.info('PR already exists, skipping build phase', { taskId: task.id });
         }
+        // Phase 6: Complete
+        await this.progressReporter.complete();
+        this.logger.info('Task execution complete', { taskId: task.id });
+        this.emitEvent(this.adapter.createStatusEvent('task_complete', { taskId: task.id }));
     }
     // Direct prompt execution - still supported for low-level usage
     async run(prompt, options = {}) {
@@ -384,7 +481,23 @@ class Agent {
         this.logger.debug('Reading plan', { taskId });
         return await this.fileManager.readPlan(taskId);
     }
-    // Git operations for task workflow
+    async extractQuestionsFromResearch(taskId, includeAnswers = false) {
+        this.logger.info('Extracting questions from research.md', { taskId, includeAnswers });
+        if (!this.extractor) {
+            throw new Error('OpenAI extractor not initialized. Set OPENAI_API_KEY environment variable.');
+        }
+        const researchContent = await this.fileManager.readResearch(taskId);
+        if (!researchContent) {
+            throw new Error('research.md not found for task ' + taskId);
+        }
+        if (includeAnswers) {
+            return await this.extractor.extractQuestionsWithAnswers(researchContent);
+        }
+        else {
+            return await this.extractor.extractQuestions(researchContent);
+        }
+    }
+    // Git operations for task execution
     async createPlanningBranch(taskId) {
         this.logger.info('Creating planning branch', { taskId });
         const branchName = await this.gitManager.createTaskPlanningBranch(taskId);