Merge branch 'refs/heads/main' into cw/agent-details-conflict-1772799979862

# Conflicts:
#	apps/server/drizzle/meta/_journal.json

apps/server/agent/cleanup-manager.ts

@@ -8,7 +8,7 @@
 import { promisify } from 'node:util';
 import { execFile } from 'node:child_process';
 import { readFile, readdir, rm, cp, mkdir } from 'node:fs/promises';
-import { existsSync } from 'node:fs';
+import { existsSync, readdirSync } from 'node:fs';
 import { join } from 'node:path';
 import type { AgentRepository } from '../db/repositories/agent-repository.js';
 import type { ProjectRepository } from '../db/repositories/project-repository.js';
@@ -49,10 +49,35 @@ export class CleanupManager {
    */
   private resolveAgentCwd(worktreeId: string): string {
     const base = this.getAgentWorkdir(worktreeId);
+
+    // Fast path: .cw/output exists at the base level
+    if (existsSync(join(base, '.cw', 'output'))) {
+      return base;
+    }
+
+    // Standalone agents use a workspace/ subdirectory
     const workspaceSub = join(base, 'workspace');
-    if (!existsSync(join(base, '.cw', 'output')) && existsSync(join(workspaceSub, '.cw'))) {
+    if (existsSync(join(workspaceSub, '.cw'))) {
       return workspaceSub;
     }
+
+    // Initiative-based agents may have written .cw/ inside a project
+    // subdirectory (e.g. agent-workdirs/<name>/codewalk-district/.cw/).
+    // Probe immediate children for a .cw/output directory.
+    try {
+      const entries = readdirSync(base, { withFileTypes: true });
+      for (const entry of entries) {
+        if (entry.isDirectory() && entry.name !== '.cw') {
+          const projectSub = join(base, entry.name);
+          if (existsSync(join(projectSub, '.cw', 'output'))) {
+            return projectSub;
+          }
+        }
+      }
+    } catch {
+      // base dir may not exist
+    }
+
     return base;
   }
 

apps/server/agent/file-io.test.ts

@@ -68,6 +68,7 @@ describe('writeInputFiles', () => {
       name: 'Phase One',
       content: 'First phase',
       status: 'pending',
+      mergeBase: null,
       createdAt: new Date(),
       updatedAt: new Date(),
     } as Phase;

apps/server/agent/file-io.ts

@@ -397,6 +397,34 @@ export async function readDecisionFiles(agentWorkdir: string): Promise<ParsedDec
   });
 }
 
+export interface ParsedCommentResponse {
+  commentId: string;
+  body: string;
+  resolved?: boolean;
+}
+
+export async function readCommentResponses(agentWorkdir: string): Promise<ParsedCommentResponse[]> {
+  const filePath = join(agentWorkdir, '.cw', 'output', 'comment-responses.json');
+  try {
+    const raw = await readFile(filePath, 'utf-8');
+    const parsed = JSON.parse(raw);
+    if (!Array.isArray(parsed)) return [];
+    return parsed
+      .filter((entry: unknown) => {
+        if (typeof entry !== 'object' || entry === null) return false;
+        const e = entry as Record<string, unknown>;
+        return typeof e.commentId === 'string' && typeof e.body === 'string';
+      })
+      .map((entry: Record<string, unknown>) => ({
+        commentId: String(entry.commentId),
+        body: String(entry.body),
+        resolved: typeof entry.resolved === 'boolean' ? entry.resolved : undefined,
+      }));
+  } catch {
+    return [];
+  }
+}
+
 export async function readPageFiles(agentWorkdir: string): Promise<ParsedPageFile[]> {
   const dirPath = join(agentWorkdir, '.cw', 'output', 'pages');
   return readFrontmatterDir(dirPath, (data, body, filename) => {

apps/server/agent/manager.ts

@@ -27,6 +27,7 @@ import type { TaskRepository } from '../db/repositories/task-repository.js';
 import type { PageRepository } from '../db/repositories/page-repository.js';
 import type { LogChunkRepository } from '../db/repositories/log-chunk-repository.js';
 import type { ChatSessionRepository } from '../db/repositories/chat-session-repository.js';
+import type { ReviewCommentRepository } from '../db/repositories/review-comment-repository.js';
 import { generateUniqueAlias } from './alias.js';
 import type {
   EventBus,
@@ -42,7 +43,7 @@ import { getProvider } from './providers/registry.js';
 import { createModuleLogger } from '../logger/index.js';
 import { getProjectCloneDir } from '../git/project-clones.js';
 import { join } from 'node:path';
-import { unlink, readFile, writeFile as writeFileAsync } from 'node:fs/promises';
+import { unlink, readFile, writeFile as writeFileAsync, mkdir } from 'node:fs/promises';
 import { existsSync } from 'node:fs';
 import type { AccountCredentialManager } from './credentials/types.js';
 import { ProcessManager } from './process-manager.js';
@@ -84,11 +85,12 @@ export class MultiProviderAgentManager implements AgentManager {
     private debug: boolean = false,
     processManagerOverride?: ProcessManager,
     private chatSessionRepository?: ChatSessionRepository,
+    private reviewCommentRepository?: ReviewCommentRepository,
   ) {
     this.signalManager = new FileSystemSignalManager();
     this.processManager = processManagerOverride ?? new ProcessManager(workspaceRoot, projectRepository);
     this.credentialHandler = new CredentialHandler(workspaceRoot, accountRepository, credentialManager);
-    this.outputHandler = new OutputHandler(repository, eventBus, changeSetRepository, phaseRepository, taskRepository, pageRepository, this.signalManager, chatSessionRepository);
+    this.outputHandler = new OutputHandler(repository, eventBus, changeSetRepository, phaseRepository, taskRepository, pageRepository, this.signalManager, chatSessionRepository, reviewCommentRepository);
     this.cleanupManager = new CleanupManager(workspaceRoot, repository, projectRepository, eventBus, debug, this.signalManager);
     this.lifecycleController = createLifecycleController({
       repository,
@@ -295,6 +297,10 @@ export class MultiProviderAgentManager implements AgentManager {
     if (options.inputContext) {
       await writeInputFiles({ agentWorkdir: agentCwd, ...options.inputContext, agentId, agentName: alias });
       log.debug({ alias }, 'input files written');
+    } else {
+      // Always create .cw/output/ at the agent workdir root so the agent
+      // writes signal.json here rather than in a project subdirectory.
+      await mkdir(join(agentCwd, '.cw', 'output'), { recursive: true });
     }
 
     // 4. Build spawn command
@@ -330,32 +336,10 @@ export class MultiProviderAgentManager implements AgentManager {
 
     await this.repository.update(agentId, { pid, outputFilePath, prompt });
 
-    // Write spawn diagnostic file for post-execution verification
-    const diagnostic = {
-      timestamp: new Date().toISOString(),
-      agentId,
-      alias,
-      intendedCwd: finalCwd,
-      worktreeId: agent.worktreeId,
-      provider: providerName,
-      command,
-      args,
-      env: processEnv,
-      cwdExistsAtSpawn: existsSync(finalCwd),
-      initiativeId: initiativeId || null,
-      customCwdProvided: !!cwd,
-      accountId: accountId || null,
-    };
-
-    await writeFileAsync(
-      join(finalCwd, '.cw', 'spawn-diagnostic.json'),
-      JSON.stringify(diagnostic, null, 2),
-      'utf-8'
-    );
-
+    // Register agent and start polling BEFORE non-critical I/O so that a
+    // diagnostic-write failure can never orphan a running process.
     const activeEntry: ActiveAgent = { agentId, pid, tailer, outputFilePath, agentCwd: finalCwd };
     this.activeAgents.set(agentId, activeEntry);
-    log.info({ agentId, alias, pid, diagnosticWritten: true }, 'detached subprocess started with diagnostic');
 
     // Emit spawned event
     if (this.eventBus) {
@@ -375,6 +359,37 @@ export class MultiProviderAgentManager implements AgentManager {
     );
     activeEntry.cancelPoll = cancel;
 
+    // Write spawn diagnostic file (non-fatal — .cw/ may not exist yet for
+    // agents spawned without inputContext, e.g. conflict-resolution agents)
+    try {
+      const diagnosticDir = join(finalCwd, '.cw');
+      await mkdir(diagnosticDir, { recursive: true });
+      const diagnostic = {
+        timestamp: new Date().toISOString(),
+        agentId,
+        alias,
+        intendedCwd: finalCwd,
+        worktreeId: agent.worktreeId,
+        provider: providerName,
+        command,
+        args,
+        env: processEnv,
+        cwdExistsAtSpawn: existsSync(finalCwd),
+        initiativeId: initiativeId || null,
+        customCwdProvided: !!cwd,
+        accountId: accountId || null,
+      };
+      await writeFileAsync(
+        join(diagnosticDir, 'spawn-diagnostic.json'),
+        JSON.stringify(diagnostic, null, 2),
+        'utf-8'
+      );
+    } catch (err) {
+      log.warn({ agentId, alias, err: err instanceof Error ? err.message : String(err) }, 'failed to write spawn diagnostic');
+    }
+
+    log.info({ agentId, alias, pid }, 'detached subprocess started');
+
     return this.toAgentInfo(agent);
   }
 

apps/server/agent/output-handler.ts

@@ -7,7 +7,7 @@
  */
 
 import { readFile } from 'node:fs/promises';
-import { existsSync } from 'node:fs';
+import { existsSync, readdirSync } from 'node:fs';
 import { join } from 'node:path';
 import type { AgentRepository } from '../db/repositories/agent-repository.js';
 import type { ChangeSetRepository, CreateChangeSetEntryData } from '../db/repositories/change-set-repository.js';
@@ -15,6 +15,7 @@ import type { PhaseRepository } from '../db/repositories/phase-repository.js';
 import type { TaskRepository } from '../db/repositories/task-repository.js';
 import type { PageRepository } from '../db/repositories/page-repository.js';
 import type { ChatSessionRepository } from '../db/repositories/chat-session-repository.js';
+import type { ReviewCommentRepository } from '../db/repositories/review-comment-repository.js';
 import type {
   EventBus,
   AgentStoppedEvent,
@@ -37,6 +38,7 @@ import {
   readDecisionFiles,
   readPageFiles,
   readFrontmatterFile,
+  readCommentResponses,
 } from './file-io.js';
 import { getProvider } from './providers/registry.js';
 import { markdownToTiptapJson } from './markdown-to-tiptap.js';
@@ -92,6 +94,7 @@ export class OutputHandler {
     private pageRepository?: PageRepository,
     private signalManager?: SignalManager,
     private chatSessionRepository?: ChatSessionRepository,
+    private reviewCommentRepository?: ReviewCommentRepository,
   ) {}
 
   /**
@@ -230,10 +233,10 @@ export class OutputHandler {
 
       log.debug({ agentId }, 'detached agent completed');
 
-      // Resolve actual agent working directory — standalone agents run in a
-      // "workspace/" subdirectory inside getAgentWorkdir, so prefer agentCwd
-      // recorded at spawn time when available.
-      const agentWorkdir = active?.agentCwd ?? getAgentWorkdir(agent.worktreeId);
+      // Resolve actual agent working directory.
+      // The recorded agentCwd may be the parent dir (agent-workdirs/<name>/) while
+      // the agent actually writes .cw/output/ inside a project subdirectory.
+      const agentWorkdir = this.resolveAgentWorkdir(active?.agentCwd ?? getAgentWorkdir(agent.worktreeId));
       const outputDir = join(agentWorkdir, '.cw', 'output');
       const expectedPwdFile = join(agentWorkdir, '.cw', 'expected-pwd.txt');
       const diagnosticFile = join(agentWorkdir, '.cw', 'spawn-diagnostic.json');
@@ -851,6 +854,28 @@ export class OutputHandler {
       }
     }
 
+    // Process comment responses from agent (for review/execute tasks)
+    if (this.reviewCommentRepository) {
+      try {
+        const commentResponses = await readCommentResponses(agentWorkdir);
+        for (const resp of commentResponses) {
+          try {
+            await this.reviewCommentRepository.createReply(resp.commentId, resp.body, 'agent');
+            if (resp.resolved) {
+              await this.reviewCommentRepository.resolve(resp.commentId);
+            }
+          } catch (err) {
+            log.warn({ agentId, commentId: resp.commentId, err: err instanceof Error ? err.message : String(err) }, 'failed to process comment response');
+          }
+        }
+        if (commentResponses.length > 0) {
+          log.info({ agentId, count: commentResponses.length }, 'processed agent comment responses');
+        }
+      } catch (err) {
+        log.warn({ agentId, err: err instanceof Error ? err.message : String(err) }, 'failed to read comment responses');
+      }
+    }
+
     const resultPayload: AgentResult = {
       success: true,
       message: resultMessage,
@@ -1133,6 +1158,31 @@ export class OutputHandler {
     }
   }
 
+  /**
+   * Resolve the actual agent working directory. The recorded agentCwd may be
+   * the parent (agent-workdirs/<name>/) but .cw/output/ could be inside a
+   * project subdirectory (e.g. codewalk-district/.cw/output/).
+   */
+  private resolveAgentWorkdir(base: string): string {
+    if (existsSync(join(base, '.cw', 'output'))) return base;
+
+    // Standalone agents: workspace/ subdirectory
+    const workspaceSub = join(base, 'workspace');
+    if (existsSync(join(workspaceSub, '.cw'))) return workspaceSub;
+
+    // Initiative-based agents: probe project subdirectories
+    try {
+      for (const entry of readdirSync(base, { withFileTypes: true })) {
+        if (entry.isDirectory() && entry.name !== '.cw') {
+          const sub = join(base, entry.name);
+          if (existsSync(join(sub, '.cw', 'output'))) return sub;
+        }
+      }
+    } catch { /* base may not exist */ }
+
+    return base;
+  }
+
   private emitCrashed(agent: { id: string; name: string; taskId: string | null }, error: string): void {
     if (this.eventBus) {
       const event: AgentCrashedEvent = {

apps/server/agent/prompts/conflict-resolution.ts

@@ -0,0 +1,77 @@
+/**
+ * Conflict resolution prompt — spawned when initiative branch has merge conflicts
+ * with the target branch.
+ */
+
+import {
+  SIGNAL_FORMAT,
+  SESSION_STARTUP,
+  GIT_WORKFLOW,
+  CONTEXT_MANAGEMENT,
+} from './shared.js';
+
+export function buildConflictResolutionPrompt(
+  sourceBranch: string,
+  targetBranch: string,
+  conflicts: string[],
+): string {
+  const conflictList = conflicts.map(f => `- \`${f}\``).join('\n');
+
+  return `<role>
+You are a Conflict Resolution agent. Your job is to merge \`${targetBranch}\` into the initiative branch \`${sourceBranch}\` and resolve all merge conflicts. You are working on a temporary branch created from \`${sourceBranch}\`. After resolving conflicts and committing, you must advance the initiative branch pointer using \`git update-ref\`.
+</role>
+
+<conflict_details>
+**Source branch (initiative):** \`${sourceBranch}\`
+**Target branch (default):** \`${targetBranch}\`
+
+**Conflicting files:**
+${conflictList}
+</conflict_details>
+${SIGNAL_FORMAT}
+${SESSION_STARTUP}
+
+<resolution_protocol>
+Follow these steps in order:
+
+1. **Inspect divergence**: Run \`git log --oneline ${targetBranch}..${sourceBranch}\` and \`git log --oneline ${sourceBranch}..${targetBranch}\` to understand what each side changed.
+
+2. **Review conflicting files**: For each conflicting file, read both versions:
+   - \`git show ${sourceBranch}:<file>\`
+   - \`git show ${targetBranch}:<file>\`
+
+3. **Merge**: Run \`git merge ${targetBranch} --no-edit\`. This will produce conflict markers.
+
+4. **Resolve each file**: For each conflicting file:
+   - Read the file to see conflict markers (\`<<<<<<<\`, \`=======\`, \`>>>>>>>\`)
+   - Understand both sides' intent from step 1-2
+   - Choose the correct resolution — keep both changes when they don't overlap, prefer the more complete version when they do
+   - If you genuinely cannot determine the correct resolution, signal "questions" explaining the ambiguity
+
+5. **Verify**: Run \`git diff --check\` to confirm no conflict markers remain. Run the test suite to confirm nothing is broken.
+
+6. **Commit**: Stage resolved files with \`git add <file>\` (never \`git add .\`), then \`git commit --no-edit\` to complete the merge commit.
+
+7. **Update initiative branch**: Run \`git update-ref refs/heads/${sourceBranch} HEAD\` to advance the initiative branch to include the merge result. This is necessary because you are working on a temporary branch — this command propagates the merge commit to the actual initiative branch.
+
+8. **Signal done**: Write signal.json with status "done".
+</resolution_protocol>
+${GIT_WORKFLOW}
+${CONTEXT_MANAGEMENT}
+
+<important>
+- You are on a temporary branch created from ${sourceBranch}. You are merging ${targetBranch} INTO this branch — bringing it up to date, NOT the other way around.
+- After committing the merge, you MUST run \`git update-ref refs/heads/${sourceBranch} HEAD\` to advance the initiative branch pointer. Without this step, the initiative branch will not reflect the merge.
+- Do NOT force-push or rebase. A merge commit is the correct approach.
+- If tests fail after resolution, fix the code — don't skip tests.
+- If a conflict is genuinely ambiguous (e.g., both sides rewrote the same function differently), signal "questions" with the specific ambiguity and your proposed resolution.
+</important>`;
+}
+
+export function buildConflictResolutionDescription(
+  sourceBranch: string,
+  targetBranch: string,
+  conflicts: string[],
+): string {
+  return `Resolve ${conflicts.length} merge conflict(s) between ${sourceBranch} and ${targetBranch}: ${conflicts.join(', ')}`;
+}

apps/server/agent/prompts/detail.ts

@@ -13,7 +13,7 @@ ${CODEBASE_EXPLORATION}
 
 <output_format>
 Write one file per task to \`.cw/output/tasks/{id}.md\`:
-- Frontmatter: \`title\`, \`category\` (execute|research|discuss|plan|detail|refine|verify|merge|review), \`type\` (auto|checkpoint:human-verify|checkpoint:decision|checkpoint:human-action), \`dependencies\` (list of task IDs that must complete before this task can start)
+- Frontmatter: \`title\`, \`category\` (execute|research|discuss|plan|detail|refine|verify|merge|review), \`dependencies\` (list of task IDs that must complete before this task can start)
 - Body: Detailed task description
 </output_format>
 
@@ -92,14 +92,6 @@ Each task is handled by a separate agent that must load the full codebase contex
 Bundle related changes into one task. "Add user validation" + "Add user API route" + "Add user route tests" is ONE task ("Add user creation endpoint with validation and tests"), not three.
 </task_sizing>
 
-<checkpoint_tasks>
-- \`checkpoint:human-verify\`: Visual changes, migrations, API contracts
-- \`checkpoint:decision\`: Architecture choices affecting multiple phases
-- \`checkpoint:human-action\`: External setup (DNS, credentials, third-party config)
-
-~90% of tasks should be \`auto\`.
-</checkpoint_tasks>
-
 <existing_context>
 - Read ALL \`context/tasks/\` files before generating output
 - Only create tasks for THIS phase (\`phase.md\`)

apps/server/agent/prompts/execute.ts

@@ -14,13 +14,26 @@ import {
 } from './shared.js';
 
 export function buildExecutePrompt(taskDescription?: string): string {
+  const hasReviewComments = taskDescription?.includes('[comment:');
+  const reviewCommentsSection = hasReviewComments
+    ? `
+<review_comments>
+You are addressing review feedback. Each comment is tagged with [comment:ID].
+For EACH comment you address:
+1. Fix the issue in code, OR explain why no change is needed.
+2. Write \`.cw/output/comment-responses.json\`:
+   [{"commentId": "abc123", "body": "Fixed: added try-catch around token validation", "resolved": true}]
+Set resolved:true when you fixed it, false when you're explaining why you didn't.
+</review_comments>`
+    : '';
+
   const taskSection = taskDescription
     ? `
 <task>
 ${taskDescription}
 
 Read \`.cw/input/task.md\` for the full structured task with metadata, priority, and dependencies.
-</task>`
+</task>${reviewCommentsSection}`
     : '';
 
   return `<role>

apps/server/agent/prompts/index.ts

@@ -15,3 +15,4 @@ export { buildChatPrompt } from './chat.js';
 export type { ChatHistoryEntry } from './chat.js';
 export { buildWorkspaceLayout } from './workspace.js';
 export { buildPreviewInstructions } from './preview.js';
+export { buildConflictResolutionPrompt, buildConflictResolutionDescription } from './conflict-resolution.js';

apps/server/agent/prompts/workspace.ts

@@ -36,5 +36,7 @@ This is an isolated git worktree. Other agents may be working in parallel on sep
 The following project directories contain the source code (git worktrees):
 
 ${lines.join('\n')}
+
+**IMPORTANT**: All \`.cw/output/\` paths (signal.json, progress.md, etc.) are relative to this working directory (\`${agentCwd}\`), NOT to any project subdirectory. Always write to \`${join(agentCwd, '.cw/output/')}\` regardless of your current \`cd\` location.
 </workspace>`;
 }