Don't offer adding a trailer in a rebase or a cherry-pick or reverts

cmd/entire/cli/strategy/hooks_test.go

@@ -137,6 +137,195 @@ func TestGetGitDirInPath_NotARepo(t *testing.T) {
 	}
 }
 
+func TestIsGitSequenceOperation_NoOperation(t *testing.T) {
+	// Create a temp directory and initialize a real git repo
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	ctx := context.Background()
+	cmd := exec.CommandContext(ctx, "git", "init")
+	cmd.Dir = tmpDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init git repo: %v", err)
+	}
+
+	// No sequence operation in progress
+	if isGitSequenceOperation() {
+		t.Error("isGitSequenceOperation() = true, want false for clean repo")
+	}
+}
+
+func TestIsGitSequenceOperation_RebaseMerge(t *testing.T) {
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	ctx := context.Background()
+	cmd := exec.CommandContext(ctx, "git", "init")
+	cmd.Dir = tmpDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init git repo: %v", err)
+	}
+
+	// Simulate rebase-merge state
+	rebaseMergeDir := filepath.Join(tmpDir, ".git", "rebase-merge")
+	if err := os.MkdirAll(rebaseMergeDir, 0o755); err != nil {
+		t.Fatalf("failed to create rebase-merge dir: %v", err)
+	}
+
+	if !isGitSequenceOperation() {
+		t.Error("isGitSequenceOperation() = false, want true during rebase-merge")
+	}
+}
+
+func TestIsGitSequenceOperation_RebaseApply(t *testing.T) {
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	ctx := context.Background()
+	cmd := exec.CommandContext(ctx, "git", "init")
+	cmd.Dir = tmpDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init git repo: %v", err)
+	}
+
+	// Simulate rebase-apply state
+	rebaseApplyDir := filepath.Join(tmpDir, ".git", "rebase-apply")
+	if err := os.MkdirAll(rebaseApplyDir, 0o755); err != nil {
+		t.Fatalf("failed to create rebase-apply dir: %v", err)
+	}
+
+	if !isGitSequenceOperation() {
+		t.Error("isGitSequenceOperation() = false, want true during rebase-apply")
+	}
+}
+
+func TestIsGitSequenceOperation_CherryPick(t *testing.T) {
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	ctx := context.Background()
+	cmd := exec.CommandContext(ctx, "git", "init")
+	cmd.Dir = tmpDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init git repo: %v", err)
+	}
+
+	// Simulate cherry-pick state
+	cherryPickHead := filepath.Join(tmpDir, ".git", "CHERRY_PICK_HEAD")
+	if err := os.WriteFile(cherryPickHead, []byte("abc123"), 0o644); err != nil {
+		t.Fatalf("failed to create CHERRY_PICK_HEAD: %v", err)
+	}
+
+	if !isGitSequenceOperation() {
+		t.Error("isGitSequenceOperation() = false, want true during cherry-pick")
+	}
+}
+
+func TestIsGitSequenceOperation_Revert(t *testing.T) {
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	ctx := context.Background()
+	cmd := exec.CommandContext(ctx, "git", "init")
+	cmd.Dir = tmpDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init git repo: %v", err)
+	}
+
+	// Simulate revert state
+	revertHead := filepath.Join(tmpDir, ".git", "REVERT_HEAD")
+	if err := os.WriteFile(revertHead, []byte("abc123"), 0o644); err != nil {
+		t.Fatalf("failed to create REVERT_HEAD: %v", err)
+	}
+
+	if !isGitSequenceOperation() {
+		t.Error("isGitSequenceOperation() = false, want true during revert")
+	}
+}
+
+func TestIsGitSequenceOperation_Worktree(t *testing.T) {
+	// Test that detection works in a worktree (git dir is different)
+	tmpDir := t.TempDir()
+	mainRepo := filepath.Join(tmpDir, "main")
+	worktreeDir := filepath.Join(tmpDir, "worktree")
+
+	if err := os.MkdirAll(mainRepo, 0o755); err != nil {
+		t.Fatalf("failed to create main repo dir: %v", err)
+	}
+
+	ctx := context.Background()
+
+	// Initialize main repo with a commit
+	cmd := exec.CommandContext(ctx, "git", "init")
+	cmd.Dir = mainRepo
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init main repo: %v", err)
+	}
+
+	cmd = exec.CommandContext(ctx, "git", "config", "user.email", "test@test.com")
+	cmd.Dir = mainRepo
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to configure git email: %v", err)
+	}
+
+	cmd = exec.CommandContext(ctx, "git", "config", "user.name", "Test User")
+	cmd.Dir = mainRepo
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to configure git name: %v", err)
+	}
+
+	testFile := filepath.Join(mainRepo, "test.txt")
+	if err := os.WriteFile(testFile, []byte("test"), 0o644); err != nil {
+		t.Fatalf("failed to create test file: %v", err)
+	}
+
+	cmd = exec.CommandContext(ctx, "git", "add", ".")
+	cmd.Dir = mainRepo
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to git add: %v", err)
+	}
+
+	cmd = exec.CommandContext(ctx, "git", "commit", "-m", "initial")
+	cmd.Dir = mainRepo
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to git commit: %v", err)
+	}
+
+	// Create a worktree
+	cmd = exec.CommandContext(ctx, "git", "worktree", "add", worktreeDir, "-b", "feature")
+	cmd.Dir = mainRepo
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to create worktree: %v", err)
+	}
+
+	// Change to worktree
+	t.Chdir(worktreeDir)
+
+	// Should not detect sequence operation in clean worktree
+	if isGitSequenceOperation() {
+		t.Error("isGitSequenceOperation() = true in clean worktree, want false")
+	}
+
+	// Get the worktree's git dir and simulate rebase state there
+	cmd = exec.CommandContext(ctx, "git", "rev-parse", "--git-dir")
+	cmd.Dir = worktreeDir
+	output, err := cmd.Output()
+	if err != nil {
+		t.Fatalf("failed to get git dir: %v", err)
+	}
+	gitDir := strings.TrimSpace(string(output))
+
+	rebaseMergeDir := filepath.Join(gitDir, "rebase-merge")
+	if err := os.MkdirAll(rebaseMergeDir, 0o755); err != nil {
+		t.Fatalf("failed to create rebase-merge dir in worktree: %v", err)
+	}
+
+	// Now should detect sequence operation
+	if !isGitSequenceOperation() {
+		t.Error("isGitSequenceOperation() = false in worktree during rebase, want true")
+	}
+}
+
 func TestInstallGitHook_Idempotent(t *testing.T) {
 	// Create a temp directory and initialize a real git repo
 	tmpDir := t.TempDir()

cmd/entire/cli/strategy/manual_commit_hooks.go

@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"log/slog"
 	"os"
+	"path/filepath"
 	"strings"
 
 	"entire.io/cli/cmd/entire/cli/agent"
@@ -133,6 +134,40 @@ func stripCheckpointTrailer(message string) string {
 	return strings.Join(result, "\n")
 }
 
+// isGitSequenceOperation checks if git is currently in the middle of a rebase,
+// cherry-pick, or revert operation. During these operations, commits are being
+// replayed and should not be linked to agent sessions.
+//
+// Detects:
+//   - rebase: .git/rebase-merge/ or .git/rebase-apply/ directories
+//   - cherry-pick: .git/CHERRY_PICK_HEAD file
+//   - revert: .git/REVERT_HEAD file
+func isGitSequenceOperation() bool {
+	// Get git directory (handles worktrees and relative paths correctly)
+	gitDir, err := GetGitDir()
+	if err != nil {
+		return false // Can't determine, assume not in sequence operation
+	}
+
+	// Check for rebase state directories
+	if _, err := os.Stat(filepath.Join(gitDir, "rebase-merge")); err == nil {
+		return true
+	}
+	if _, err := os.Stat(filepath.Join(gitDir, "rebase-apply")); err == nil {
+		return true
+	}
+
+	// Check for cherry-pick and revert state files
+	if _, err := os.Stat(filepath.Join(gitDir, "CHERRY_PICK_HEAD")); err == nil {
+		return true
+	}
+	if _, err := os.Stat(filepath.Join(gitDir, "REVERT_HEAD")); err == nil {
+		return true
+	}
+
+	return false
+}
+
 // PrepareCommitMsg is called by the git prepare-commit-msg hook.
 // Adds an Entire-Checkpoint trailer to the commit message with a stable checkpoint ID.
 // Only adds a trailer if there's actually new session content to condense.
@@ -149,6 +184,16 @@ func stripCheckpointTrailer(message string) string {
 func (s *ManualCommitStrategy) PrepareCommitMsg(commitMsgFile string, source string) error {
 	logCtx := logging.WithComponent(context.Background(), "checkpoint")
 
+	// Skip during rebase, cherry-pick, or revert operations
+	// These are replaying existing commits and should not be linked to agent sessions
+	if isGitSequenceOperation() {
+		logging.Debug(logCtx, "prepare-commit-msg: skipped during git sequence operation",
+			slog.String("strategy", "manual-commit"),
+			slog.String("source", source),
+		)
+		return nil
+	}
+
 	// Skip for merge, squash, and commit (amend) sources
 	// These are auto-generated or reusing existing messages - not from Claude sessions
 	switch source {