Fix for replaying amended parent commits during rebase (#333)

* Avoid replaying amended parent commits

Preserve a branch's last valid base when its parent is rewritten, and only
use verified ancestor commits as rebase boundaries. Recover previously
corrupted metadata from the parent reflog when possible, otherwise stop
safely instead of replaying superseded parent commits.

* Record adopted branch merge bases

Store the actual common ancestor when adding an existing branch so cascade rebases replay only that branch's unique commits while retaining the amended-parent safety guard.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Copilot-Session: 30bcbf2a-5ef1-4bdb-a0fc-618294ae8ded

---------

Copilot-Session: 30bcbf2a-5ef1-4bdb-a0fc-618294ae8ded

Author: skarim

cmd/add.go

@@ -169,6 +169,14 @@ func runAdd(cfg *config.Config, opts *addOptions, args []string) error {
 	// If the branch already exists in git but is not part of any stack,
 	// adopt it instead of erroring. This mirrors the init command's behavior.
 	adopted := git.BranchExists(branchName)
+	var adoptedBase string
+	if adopted {
+		adoptedBase, err = git.MergeBase(currentBranch, branchName)
+		if err != nil {
+			cfg.Errorf("failed to determine the common base of %s and %s: %s", currentBranch, branchName, err)
+			return ErrSilent
+		}
+	}
 
 	// Stage changes before creating the branch so we can fail early if
 	// there's nothing to commit (avoids leaving an empty orphan branch).
@@ -191,9 +199,12 @@ func runAdd(cfg *config.Config, opts *addOptions, args []string) error {
 		return ErrSilent
 	}
 
-	base, err := git.RevParse(currentBranch)
-	if err != nil {
-		cfg.Warningf("could not resolve base SHA for %s: %s", currentBranch, err)
+	base := adoptedBase
+	if !adopted {
+		base, err = git.RevParse(currentBranch)
+		if err != nil {
+			cfg.Warningf("could not resolve base SHA for %s: %s", currentBranch, err)
+		}
 	}
 	s.Branches = append(s.Branches, stack.BranchRef{Branch: branchName, Base: base})
 

cmd/add_test.go

@@ -446,6 +446,11 @@ func TestAdd_AdoptsExistingBranch(t *testing.T) {
 		GitDirFn:        func() (string, error) { return gitDir, nil },
 		CurrentBranchFn: func() (string, error) { return "b1", nil },
 		BranchExistsFn:  func(name string) bool { return name == "existing-branch" },
+		MergeBaseFn: func(parent, branch string) (string, error) {
+			assert.Equal(t, "b1", parent)
+			assert.Equal(t, "existing-branch", branch)
+			return "common-base", nil
+		},
 		CreateBranchFn: func(name, base string) error {
 			createBranchCalled = true
 			return nil
@@ -472,6 +477,8 @@ func TestAdd_AdoptsExistingBranch(t *testing.T) {
 	require.NoError(t, err)
 	names := sf.Stacks[0].BranchNames()
 	assert.Equal(t, "existing-branch", names[len(names)-1], "adopted branch appended to stack")
+	assert.Equal(t, "common-base", sf.Stacks[0].Branches[len(sf.Stacks[0].Branches)-1].Base,
+		"adopted branch should record the actual common ancestor")
 }
 
 func TestAdd_RejectsExistingBranchInStack(t *testing.T) {
@@ -520,6 +527,7 @@ func TestAdd_AdoptsExistingBranchWithCommit(t *testing.T) {
 		GitDirFn:        func() (string, error) { return gitDir, nil },
 		CurrentBranchFn: func() (string, error) { return "b1", nil },
 		BranchExistsFn:  func(name string) bool { return name == "existing-branch" },
+		MergeBaseFn:     func(string, string) (string, error) { return "common-base", nil },
 		RevParseMultiFn: func(refs []string) ([]string, error) {
 			return []string{"aaa", "bbb"}, nil // different SHAs = branch has commits
 		},
@@ -548,3 +556,36 @@ func TestAdd_AdoptsExistingBranchWithCommit(t *testing.T) {
 	assert.True(t, commitCalled, "Commit should be called on the adopted branch")
 	assert.Contains(t, output, "Adopted")
 }
+
+func TestAdd_AdoptExistingBranchWithoutCommonBaseFails(t *testing.T) {
+	gitDir := t.TempDir()
+	saveStack(t, gitDir, stack.Stack{
+		Trunk:    stack.BranchRef{Branch: "main"},
+		Branches: []stack.BranchRef{{Branch: "b1"}},
+	})
+
+	checkedOut := false
+	restore := git.SetOps(&git.MockOps{
+		GitDirFn:        func() (string, error) { return gitDir, nil },
+		CurrentBranchFn: func() (string, error) { return "b1", nil },
+		BranchExistsFn:  func(name string) bool { return name == "unrelated" },
+		MergeBaseFn:     func(string, string) (string, error) { return "", assert.AnError },
+		CheckoutBranchFn: func(string) error {
+			checkedOut = true
+			return nil
+		},
+	})
+	defer restore()
+
+	cfg, outR, errR := config.NewTestConfig()
+	err := runAdd(cfg, &addOptions{}, []string{"unrelated"})
+	output := collectOutput(cfg, outR, errR)
+
+	assert.ErrorIs(t, err, ErrSilent)
+	assert.False(t, checkedOut)
+	assert.Contains(t, output, "failed to determine the common base")
+
+	sf, loadErr := stack.Load(gitDir)
+	require.NoError(t, loadErr)
+	assert.Equal(t, []string{"b1"}, sf.Stacks[0].BranchNames())
+}