diff --git a/apps/server/agent/cleanup-manager.ts b/apps/server/agent/cleanup-manager.ts
index f93c5c4..e35d406 100644
--- a/apps/server/agent/cleanup-manager.ts
+++ b/apps/server/agent/cleanup-manager.ts
@@ -222,7 +222,7 @@ export class CleanupManager {
    * Get the relative subdirectory names of dirty worktrees for an agent.
    * Returns an empty array if all worktrees are clean or the workdir doesn't exist.
    */
-  async getDirtyWorktreePaths(alias: string, initiativeId: string | null): Promise<string[]> {
+  async getDirtyWorktreePaths(alias: string, initiativeId: string | null): Promise<{ name: string; absPath: string }[]> {
     const agentWorkdir = this.getAgentWorkdir(alias);
 
     try {
@@ -242,13 +242,13 @@ export class CleanupManager {
       worktreePaths.push({ absPath: join(agentWorkdir, 'workspace'), name: 'workspace' });
     }
 
-    const dirty: string[] = [];
+    const dirty: { name: string; absPath: string }[] = [];
     for (const { absPath, name } of worktreePaths) {
       try {
         const { stdout } = await execFileAsync('git', ['status', '--porcelain'], { cwd: absPath });
-        if (stdout.trim().length > 0) dirty.push(name);
+        if (stdout.trim().length > 0) dirty.push({ name, absPath });
       } catch {
-        dirty.push(name);
+        dirty.push({ name, absPath });
       }
     }
     return dirty;
diff --git a/apps/server/agent/manager.ts b/apps/server/agent/manager.ts
index dde6b9b..3bde16a 100644
--- a/apps/server/agent/manager.ts
+++ b/apps/server/agent/manager.ts
@@ -453,12 +453,16 @@ export class MultiProviderAgentManager implements AgentManager {
     const dirtyPaths = await this.cleanupManager.getDirtyWorktreePaths(agent.name, agent.initiativeId);
     if (dirtyPaths.length === 0) return false;
 
-    const dirtyList = dirtyPaths.map(p => `- \`${p}/\``).join('\n');
+    // Use absolute paths so the agent can't accidentally commit in the main repo
+    // Use `git add -u` (tracked files only) instead of `git add -A` to avoid staging unrelated files
+    const dirtyList = dirtyPaths.map(p => `- \`${p.absPath}\``).join('\n');
     const commitPrompt =
-      'You have uncommitted changes in the following project directories:\n' +
+      'You have uncommitted changes in the following directories:\n' +
       dirtyList + '\n\n' +
-      'For each directory listed above, `cd` into it, then run `git add -A && git commit -m "<message>"` ' +
-      'with an appropriate commit message describing the work. Do not make any other changes.';
+      'For each directory listed above, `cd` into the EXACT absolute path shown, then run:\n' +
+      '1. `git add -u` to stage only tracked modified files\n' +
+      '2. `git commit -m "<message>"` with a message describing the work\n' +
+      'Do not use `git add -A` or `git add .`. Do not stage untracked files. Do not make any other changes.';
 
     await this.repository.update(agentId, { status: 'running', pendingQuestions: null, result: null });
 
diff --git a/docs/agent.md b/docs/agent.md
index 9e1cf8e..560ca1a 100644
--- a/docs/agent.md
+++ b/docs/agent.md
@@ -138,10 +138,10 @@ When Agent A asks Agent B a question via `cw ask` and Agent B is idle, the conve
 
 After an agent completes (status → `idle`), `tryAutoCleanup` checks if its project worktrees have uncommitted changes:
 
-1. `CleanupManager.getDirtyWorktreePaths()` runs `git status --porcelain` in each project subdirectory (not the parent `agent-workdirs/<alias>/` dir)
+1. `CleanupManager.getDirtyWorktreePaths()` runs `git status --porcelain` in each project subdirectory (not the parent `agent-workdirs/<alias>/` dir), returns `{ name, absPath }[]`
 2. If all clean → worktrees and logs removed immediately
-3. If dirty → `resumeForCommit()` resumes the agent's session with a prompt listing the specific dirty subdirectories (e.g. `- \`my-project/\``)
-4. The agent `cd`s into each listed directory and commits
+3. If dirty → `resumeForCommit()` resumes the agent's session with a prompt listing **absolute paths** to dirty subdirectories, using `git add -u` (tracked files only) to avoid staging unrelated files
+4. The agent `cd`s into each listed absolute path and commits tracked changes only
 5. On next completion, cleanup runs again. `MAX_COMMIT_RETRIES` (1) limits retries — after that the workdir is left in place with a warning
 
 The retry counter is cleaned up on: successful removal, max retries exceeded, or unexpected error. It is **not** cleaned up when a commit retry is successfully launched (so the counter persists across the retry cycle).