diff --git a/scripts/agent-branch-finish.sh b/scripts/agent-branch-finish.sh
index e97cd7d..d63539c 100755
--- a/scripts/agent-branch-finish.sh
+++ b/scripts/agent-branch-finish.sh
@@ -165,7 +165,11 @@ if ! git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
 fi
 
 repo_root="$(git rev-parse --show-toplevel)"
-current_worktree="$(pwd -P)"
+# The physical cwd may be a subdirectory inside the source worktree. Cleanup
+# decisions need the enclosing worktree root, otherwise finishing from `src/`
+# can delete the caller's cwd and turn a successful merge into a false shell
+# failure.
+current_worktree="$repo_root"
 common_git_dir_raw="$(git -C "$repo_root" rev-parse --git-common-dir)"
 if [[ "$common_git_dir_raw" == /* ]]; then
   common_git_dir="$common_git_dir_raw"
@@ -846,10 +850,12 @@ if [[ "$CLEANUP_AFTER_MERGE" -eq 1 ]]; then
     echo "[agent-branch-finish] You can run manual cleanup: gx cleanup --base ${BASE_BRANCH}" >&2
   fi
 
-  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/worktree."
   if [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${agent_worktree_root}"/* && -d "$source_worktree" ]]; then
+    echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/remote."
     echo "[agent-branch-finish] Current worktree '${source_worktree}' still exists because it is the active shell cwd." >&2
     echo "[agent-branch-finish] Leave this directory, then run: gx cleanup --base ${BASE_BRANCH}" >&2
+  else
+    echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/worktree."
   fi
 else
   pivot_to_repo_root_before_prune
diff --git a/templates/scripts/agent-branch-finish.sh b/templates/scripts/agent-branch-finish.sh
index e97cd7d..d63539c 100755
--- a/templates/scripts/agent-branch-finish.sh
+++ b/templates/scripts/agent-branch-finish.sh
@@ -165,7 +165,11 @@ if ! git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
 fi
 
 repo_root="$(git rev-parse --show-toplevel)"
-current_worktree="$(pwd -P)"
+# The physical cwd may be a subdirectory inside the source worktree. Cleanup
+# decisions need the enclosing worktree root, otherwise finishing from `src/`
+# can delete the caller's cwd and turn a successful merge into a false shell
+# failure.
+current_worktree="$repo_root"
 common_git_dir_raw="$(git -C "$repo_root" rev-parse --git-common-dir)"
 if [[ "$common_git_dir_raw" == /* ]]; then
   common_git_dir="$common_git_dir_raw"
@@ -846,10 +850,12 @@ if [[ "$CLEANUP_AFTER_MERGE" -eq 1 ]]; then
     echo "[agent-branch-finish] You can run manual cleanup: gx cleanup --base ${BASE_BRANCH}" >&2
   fi
 
-  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/worktree."
   if [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${agent_worktree_root}"/* && -d "$source_worktree" ]]; then
+    echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/remote."
     echo "[agent-branch-finish] Current worktree '${source_worktree}' still exists because it is the active shell cwd." >&2
     echo "[agent-branch-finish] Leave this directory, then run: gx cleanup --base ${BASE_BRANCH}" >&2
+  else
+    echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/worktree."
   fi
 else
   pivot_to_repo_root_before_prune
diff --git a/test/finish.test.js b/test/finish.test.js
index 09fb408..0691c30 100644
--- a/test/finish.test.js
+++ b/test/finish.test.js
@@ -734,6 +734,8 @@ test('agent-branch-finish cleanup succeeds from active agent worktree when base
   assert.equal(result.status, 0, result.stderr || result.stdout);
   result = runCmd('git', ['push', '-u', 'origin', 'agent/test-active-worktree-cleanup'], agentWorktreePath);
   assert.equal(result.status, 0, result.stderr || result.stdout);
+  const agentSubdir = path.join(agentWorktreePath, 'nested', 'cwd');
+  fs.mkdirSync(agentSubdir, { recursive: true });
 
   const { fakePath: fakeGhPath } = createFakeGhScript(`
 if [[ "$1" == "pr" && "$2" == "create" ]]; then
@@ -756,13 +758,13 @@ exit 1
 
   const finish = runBranchFinish(
     ['--branch', 'agent/test-active-worktree-cleanup', '--base', 'dev', '--mode', 'pr', '--cleanup'],
-    agentWorktreePath,
+    agentSubdir,
     { GUARDEX_GH_BIN: fakeGhPath },
   );
   assert.equal(finish.status, 0, finish.stderr || finish.stdout);
   assert.match(
     finish.stdout,
-    /Merged 'agent\/test-active-worktree-cleanup' into 'dev' via pr flow and cleaned source branch\/worktree\./,
+    /Merged 'agent\/test-active-worktree-cleanup' into 'dev' via pr flow and cleaned source branch\/remote\./,
   );
   assert.match(finish.stderr, /Current worktree '.+' still exists because it is the active shell cwd/);
 
diff --git a/test/metadata.test.js b/test/metadata.test.js
index 3c04d34..d5de329 100644
--- a/test/metadata.test.js
+++ b/test/metadata.test.js
@@ -235,6 +235,7 @@ test('critical runtime helper scripts and active-agents sources stay in sync wit
 test('agent-branch-finish pivots out of active agent cwd before every prune path', () => {
   const script = fs.readFileSync(path.join(repoRoot, 'scripts', 'agent-branch-finish.sh'), 'utf8');
 
+  assert.match(script, /current_worktree="\$repo_root"/);
   assert.match(script, /pivot_to_repo_root_before_prune\(\) \{\n\s+if \[\[ "\$current_worktree" == "\$source_worktree"/);
   assert.match(script, /cd "\$repo_root" 2>\/dev\/null \|\| true/);
   assert.match(