diff --git a/apps/server/agent/manager.ts b/apps/server/agent/manager.ts
index d567fcc..ac36b83 100644
--- a/apps/server/agent/manager.ts
+++ b/apps/server/agent/manager.ts
@@ -297,6 +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
diff --git a/apps/server/agent/prompts/workspace.ts b/apps/server/agent/prompts/workspace.ts
index 846850a..f01c6d3 100644
--- a/apps/server/agent/prompts/workspace.ts
+++ b/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>`;
 }