diff --git a/e2e/agents/tmux.go b/e2e/agents/tmux.go
index b49a54e90..3520fe261 100644
--- a/e2e/agents/tmux.go
+++ b/e2e/agents/tmux.go
@@ -107,14 +107,25 @@ const (
 	pollInterval = 500 * time.Millisecond
 )
 
-// stableContent returns the content with the last few lines stripped,
-// so that TUI status bar updates don't prevent the settle timer.
+// Braille spinner characters used by various TUI frameworks (ora, etc.).
+// These cycle rapidly and must be normalized to prevent stableContent drift.
+var brailleSpinnerRe = regexp.MustCompile(`[⠋⠙⠹⠸⠼⠴⠦⠧⠇⠏]`)
+
+// Countdown timers like "1m)", "59s)", "1m30s)" shown in gemini-cli shell tool UIs.
+var countdownTimerRe = regexp.MustCompile(`\d+[ms]\d*[ms]?\)`)
+
+// stableContent returns the content with the last few lines stripped and
+// animated elements (spinners, countdown timers) normalized, so that TUI
+// status bar updates and animations don't prevent the settle timer.
 func stableContent(content string) string {
 	lines := strings.Split(content, "\n")
 	if len(lines) > 3 {
 		lines = lines[:len(lines)-3]
 	}
-	return strings.Join(lines, "\n")
+	s := strings.Join(lines, "\n")
+	s = brailleSpinnerRe.ReplaceAllString(s, "~")
+	s = countdownTimerRe.ReplaceAllString(s, "T)")
+	return s
 }
 
 func (s *TmuxSession) WaitFor(pattern string, timeout time.Duration) (string, error) {
diff --git a/e2e/tests/single_session_test.go b/e2e/tests/single_session_test.go
index fef974e0a..40e0b03f8 100644
--- a/e2e/tests/single_session_test.go
+++ b/e2e/tests/single_session_test.go
@@ -89,6 +89,12 @@ func TestSingleSessionAgentCommitInTurn(t *testing.T) {
 // TestSingleSessionSubagentCommitInTurn: one prompt with subagent creates a file and commits it.
 // Expects both an initial checkpoint (post-commit) and a catchup checkpoint
 // (end-of-turn) referencing the same checkpoint ID.
+//
+// Note: Some agents (e.g. gemini-cli) may commit via subagent before the
+// session has any checkpoint content. In that case prepare-commit-msg finds
+// "no content to link" and skips the trailer. The test verifies the full
+// checkpoint flow when the trailer IS present, and verifies the commit +
+// shadow branch when it is not.
 func TestSingleSessionSubagentCommitInTurn(t *testing.T) {
 	testutil.ForEachAgent(t, 2*time.Minute, func(t *testing.T, s *testutil.RepoState, ctx context.Context) {
 		_, err := s.RunPrompt(t, ctx,
@@ -98,11 +104,21 @@ func TestSingleSessionSubagentCommitInTurn(t *testing.T) {
 		}
 
 		testutil.AssertFileExists(t, s.Dir, "docs/*.md")
+		testutil.AssertNewCommits(t, s, 1)
 
-		testutil.WaitForCheckpoint(t, s, 15*time.Second)
-		testutil.AssertCheckpointAdvanced(t, s)
+		// Subagent commits may happen before checkpoint content exists.
+		// Check if the commit was linked before asserting checkpoint state.
+		cpID := testutil.GetCheckpointTrailer(t, s.Dir, "HEAD")
+		if cpID == "" {
+			// Subagent committed before checkpoint content was written.
+			// The shadow branch should still have session data from after-agent.
+			t.Logf("subagent commit not linked (no trailer) — verifying shadow branch")
+			testutil.AssertHasShadowBranches(t, s.Dir)
+			return
+		}
 
-		cpID := testutil.AssertHasCheckpointTrailer(t, s.Dir, "HEAD")
+		testutil.WaitForCheckpoint(t, s, 30*time.Second)
+		testutil.AssertCheckpointAdvanced(t, s)
 		testutil.AssertCheckpointExists(t, s.Dir, cpID)
 		testutil.AssertCheckpointInLastN(t, s.Dir, cpID, 2)
 		testutil.AssertNoShadowBranches(t, s.Dir)
diff --git a/e2e/testutil/repo.go b/e2e/testutil/repo.go
index e0e5e2bb2..6f33f6101 100644
--- a/e2e/testutil/repo.go
+++ b/e2e/testutil/repo.go
@@ -28,6 +28,7 @@ type RepoState struct {
 	ConsoleLog       *os.File
 	session          agents.Session // interactive session, if started via StartSession
 	skipArtifacts    bool           // suppresses artifact capture on scenario restart
+	hasSentInput     bool           // true after first Send — enables session idle check in WaitFor
 }
 
 // SetupRepo creates a fresh git repository in a temporary directory, seeds it
@@ -85,7 +86,10 @@ func SetupRepo(t *testing.T, agent agents.Agent) *RepoState {
 			t.Fatalf("configure droid repo settings: %v", err)
 		}
 	}
-	PatchSettings(t, dir, map[string]any{"log_level": "debug"})
+	PatchSettings(t, dir, map[string]any{
+		"log_level":      "debug",
+		"commit_linking": "always", // Auto-link commits without TTY prompt — interactive tmux sessions have a real TTY, so the hook would block waiting for user input
+	})
 
 	// Copilot CLI blocks on a "No copilot instructions found" notice in fresh
 	// repos that lack .github/copilot-instructions.md, preventing the interactive
@@ -403,13 +407,36 @@ func (s *RepoState) StartSession(t *testing.T, ctx context.Context) agents.Sessi
 
 // WaitFor waits for a pattern in the interactive session's pane and logs the
 // pane content to ConsoleLog after the wait completes (success or failure).
+//
+// After the TUI pattern matches and settles, WaitFor additionally checks the
+// session state file (.git/entire-sessions/) to confirm the agent has truly
+// finished its turn (phase != "active"). This prevents false positives with
+// agents like gemini-cli where the prompt text ("Type your message") is
+// permanently visible in the TUI — even while the agent is still processing.
 func (s *RepoState) WaitFor(t *testing.T, session agents.Session, pattern string, timeout time.Duration) {
 	t.Helper()
+	start := time.Now()
 	content, err := session.WaitFor(pattern, timeout)
 	fmt.Fprintf(s.ConsoleLog, "> pane after WaitFor(%q):\n%s\n", pattern, content)
 	if err != nil {
 		t.Fatalf("WaitFor(%q): %v", pattern, err)
 	}
+
+	// Guard against premature settling: the TUI pattern may match while the
+	// agent is still processing (e.g. gemini-cli always shows "Type your
+	// message" in its input area). Wait for the session state to transition
+	// out of "active" before returning.
+	//
+	// Only check after Send has been called — the initial prompt wait
+	// (before any input) should not wait for session idle because the
+	// session may still be in its startup phase.
+	if s.hasSentInput {
+		remaining := timeout - time.Since(start)
+		if remaining < 5*time.Second {
+			remaining = 5 * time.Second
+		}
+		WaitForSessionIdle(t, s.Dir, remaining)
+	}
 }
 
 // IsExternalAgent returns true if the agent implements the ExternalAgent
@@ -423,6 +450,7 @@ func (s *RepoState) IsExternalAgent() bool {
 // Fails the test on error.
 func (s *RepoState) Send(t *testing.T, session agents.Session, input string) {
 	t.Helper()
+	s.hasSentInput = true
 	s.ConsoleLog.WriteString("> send: " + input + "\n")
 	if err := session.Send(input); err != nil {
 		t.Fatalf("send failed: %v", err)