feat: preserve session linkage after git rewrites

CLAUDE.md

@@ -351,6 +351,7 @@ The manual-commit strategy (`manual_commit*.go`) does not modify the active bran
 - **Worktree-specific branches** - each git worktree gets its own shadow branch namespace, preventing conflicts
 - **Supports multiple concurrent sessions** - checkpoints from different sessions in the same directory interleave on the same shadow branch
 - Condenses session logs to permanent `entire/checkpoints/v1` branch on user commits
+- Uses the `post-rewrite` Git hook to keep local session linkage aligned after amend/rebase rewrites
 - Builds git trees in-memory using go-git plumbing APIs
 - Rewind restores files from shadow branch commit tree (does not use `git reset`)
 - **Location-independent transcript resolution** - transcript paths are always computed dynamically from the current repo location (via `agent.GetSessionDir` + `agent.ResolveSessionFile`), never stored in checkpoint metadata. This ensures restore/rewind works after repo relocation or across machines.
@@ -374,7 +375,7 @@ The manual-commit strategy (`manual_commit*.go`) does not modify the active bran
 - `manual_commit_rewind.go` - Rewind implementation: file restoration from checkpoint trees
 - `manual_commit_git.go` - Git operations: checkpoint commits, tree building
 - `manual_commit_logs.go` - Session log retrieval and session listing
-- `manual_commit_hooks.go` - Git hook handlers (prepare-commit-msg, post-commit, pre-push)
+- `manual_commit_hooks.go` - Git hook handlers (prepare-commit-msg, post-commit, post-rewrite, pre-push)
 - `manual_commit_reset.go` - Shadow branch reset/cleanup functionality
 - `session_state.go` - Package-level session state functions (`LoadSessionState`, `SaveSessionState`, `ListSessionStates`, `FindMostRecentSession`)
 - `hooks.go` - Git hook installation

cmd/entire/cli/hooks_git_cmd.go

@@ -124,6 +124,7 @@ func newHooksGitCmd() *cobra.Command {
 	cmd.AddCommand(newHooksGitPrepareCommitMsgCmd())
 	cmd.AddCommand(newHooksGitCommitMsgCmd())
 	cmd.AddCommand(newHooksGitPostCommitCmd())
+	cmd.AddCommand(newHooksGitPostRewriteCmd())
 	cmd.AddCommand(newHooksGitPrePushCmd())
 
 	return cmd
@@ -202,6 +203,28 @@ func newHooksGitPostCommitCmd() *cobra.Command {
 	}
 }
 
+func newHooksGitPostRewriteCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:   "post-rewrite <rewrite-type>",
+		Short: "Handle post-rewrite git hook",
+		Args:  cobra.ExactArgs(1),
+		RunE: func(cmd *cobra.Command, args []string) error {
+			if gitHooksDisabled {
+				return nil
+			}
+
+			g := newGitHookContext(cmd.Context(), "post-rewrite")
+			defer g.span.End()
+			g.logInvoked(slog.String("rewrite_type", args[0]))
+
+			hookErr := g.strategy.PostRewrite(g.ctx, args[0], cmd.InOrStdin())
+			g.logCompleted(hookErr)
+
+			return nil
+		},
+	}
+}
+
 func newHooksGitPrePushCmd() *cobra.Command {
 	return &cobra.Command{
 		Use:   "pre-push <remote>",

cmd/entire/cli/hooks_git_cmd_test.go

@@ -245,3 +245,19 @@ func TestHooksGitCmd_DiscoverExternalAgents_WhenEnabled(t *testing.T) {
 		t.Errorf("expected external agent %q to be registered after hook pre-run, got: %v", agentName, err)
 	}
 }
+
+func TestHooksGitCmd_ExposesPostRewriteSubcommand(t *testing.T) {
+	t.Parallel()
+
+	cmd := newHooksGitCmd()
+	found, _, err := cmd.Find([]string{"post-rewrite"})
+	if err != nil {
+		t.Fatalf("could not find post-rewrite subcommand: %v", err)
+	}
+	if found == nil {
+		t.Fatal("expected post-rewrite subcommand, got nil")
+	}
+	if found.Use != "post-rewrite <rewrite-type>" {
+		t.Fatalf("post-rewrite Use = %q, want %q", found.Use, "post-rewrite <rewrite-type>")
+	}
+}

cmd/entire/cli/integration_test/phase_transitions_test.go

@@ -3,6 +3,7 @@
 package integration
 
 import (
+	"os/exec"
 	"testing"
 
 	"github.com/entireio/cli/cmd/entire/cli/paths"
@@ -305,3 +306,222 @@ func TestShadow_AmendPreservesTrailer(t *testing.T) {
 
 	t.Log("AmendPreservesTrailer test completed successfully")
 }
+
+// TestShadow_PostRewriteAmendRemapsSessionState verifies that the git
+// post-rewrite hook updates local session linkage after an amend rewrites the
+// commit SHA.
+func TestShadow_PostRewriteAmendRemapsSessionState(t *testing.T) {
+	t.Parallel()
+
+	env := NewFeatureBranchEnv(t)
+
+	sess := env.NewSession()
+	if err := env.SimulateUserPromptSubmit(sess.ID); err != nil {
+		t.Fatalf("SimulateUserPromptSubmit failed: %v", err)
+	}
+
+	env.WriteFile("main.go", "package main\n\nfunc main() {}\n")
+	sess.CreateTranscript("Create main.go", []FileChange{
+		{Path: "main.go", Content: "package main\n\nfunc main() {}\n"},
+	})
+	if err := env.SimulateStop(sess.ID, sess.TranscriptPath); err != nil {
+		t.Fatalf("SimulateStop failed: %v", err)
+	}
+
+	env.GitCommitWithShadowHooks("Initial implementation", "main.go")
+
+	originalCommitHash := env.GetHeadHash()
+	originalCheckpointID := env.GetCheckpointIDFromCommitMessage(originalCommitHash)
+	if originalCheckpointID == "" {
+		t.Fatal("Original commit should have a checkpoint trailer")
+	}
+
+	stateBeforeAmend, err := env.GetSessionState(sess.ID)
+	if err != nil {
+		t.Fatalf("GetSessionState failed: %v", err)
+	}
+	if stateBeforeAmend == nil {
+		t.Fatal("Session state should exist")
+	}
+	if stateBeforeAmend.BaseCommit != originalCommitHash {
+		t.Fatalf("BaseCommit before amend = %q, want %q", stateBeforeAmend.BaseCommit, originalCommitHash)
+	}
+
+	env.GitCommitAmendWithShadowHooks("Initial implementation (amended)")
+	amendedCommitHash := env.GetHeadHash()
+	if amendedCommitHash == originalCommitHash {
+		t.Fatal("Amended commit should have a different hash")
+	}
+
+	stateAfterAmend, err := env.GetSessionState(sess.ID)
+	if err != nil {
+		t.Fatalf("GetSessionState after amend failed: %v", err)
+	}
+	if stateAfterAmend == nil {
+		t.Fatal("Session state should exist after amend")
+	}
+	if stateAfterAmend.BaseCommit != originalCommitHash {
+		t.Fatalf("BaseCommit after amend = %q, want original %q before post-rewrite", stateAfterAmend.BaseCommit, originalCommitHash)
+	}
+
+	env.GitPostRewriteWithShadowHooks("amend", [2]string{originalCommitHash, amendedCommitHash})
+
+	stateAfterRewrite, err := env.GetSessionState(sess.ID)
+	if err != nil {
+		t.Fatalf("GetSessionState after post-rewrite failed: %v", err)
+	}
+	if stateAfterRewrite == nil {
+		t.Fatal("Session state should exist after post-rewrite")
+	}
+	if stateAfterRewrite.BaseCommit != amendedCommitHash {
+		t.Fatalf("BaseCommit after post-rewrite = %q, want %q", stateAfterRewrite.BaseCommit, amendedCommitHash)
+	}
+	if stateAfterRewrite.AttributionBaseCommit != amendedCommitHash {
+		t.Fatalf("AttributionBaseCommit after post-rewrite = %q, want %q", stateAfterRewrite.AttributionBaseCommit, amendedCommitHash)
+	}
+	if stateAfterRewrite.LastCheckpointID.String() != originalCheckpointID {
+		t.Fatalf("LastCheckpointID after post-rewrite = %q, want %q", stateAfterRewrite.LastCheckpointID.String(), originalCheckpointID)
+	}
+}
+
+func TestShadow_PostRewriteAmendMigratesExistingShadowBranch(t *testing.T) {
+	t.Parallel()
+
+	env := NewFeatureBranchEnv(t)
+
+	sess := env.NewSession()
+	if err := env.SimulateUserPromptSubmit(sess.ID); err != nil {
+		t.Fatalf("SimulateUserPromptSubmit failed: %v", err)
+	}
+
+	env.WriteFile("main.go", "package main\n\nfunc main() {}\n")
+	sess.CreateTranscript("Create main.go", []FileChange{
+		{Path: "main.go", Content: "package main\n\nfunc main() {}\n"},
+	})
+	if err := env.SimulateStop(sess.ID, sess.TranscriptPath); err != nil {
+		t.Fatalf("SimulateStop failed: %v", err)
+	}
+
+	originalCommitHash := env.GetHeadHash()
+	originalShadowBranch := env.GetShadowBranchNameForCommit(originalCommitHash)
+	if !env.BranchExists(originalShadowBranch) {
+		t.Fatalf("expected original shadow branch %q to exist", originalShadowBranch)
+	}
+
+	env.GitCommitAmendWithShadowHooks("Initial commit (amended)")
+
+	amendedCommitHash := env.GetHeadHash()
+	if amendedCommitHash == originalCommitHash {
+		t.Fatal("Amended commit should have a different hash")
+	}
+
+	env.GitPostRewriteWithShadowHooks("amend", [2]string{originalCommitHash, amendedCommitHash})
+
+	newShadowBranch := env.GetShadowBranchNameForCommit(amendedCommitHash)
+	if !env.BranchExists(newShadowBranch) {
+		t.Fatalf("expected migrated shadow branch %q to exist", newShadowBranch)
+	}
+	if env.BranchExists(originalShadowBranch) {
+		t.Fatalf("expected original shadow branch %q to be removed", originalShadowBranch)
+	}
+
+	stateAfterRewrite, err := env.GetSessionState(sess.ID)
+	if err != nil {
+		t.Fatalf("GetSessionState after post-rewrite failed: %v", err)
+	}
+	if stateAfterRewrite == nil {
+		t.Fatal("Session state should exist after post-rewrite")
+	}
+	if stateAfterRewrite.BaseCommit != amendedCommitHash {
+		t.Fatalf("BaseCommit after post-rewrite = %q, want %q", stateAfterRewrite.BaseCommit, amendedCommitHash)
+	}
+	if stateAfterRewrite.AttributionBaseCommit != originalCommitHash {
+		t.Fatalf("AttributionBaseCommit after post-rewrite = %q, want original %q when shadow branch migrates", stateAfterRewrite.AttributionBaseCommit, originalCommitHash)
+	}
+}
+
+func TestShadow_PostRewriteRebaseRemapsSessionState(t *testing.T) {
+	t.Parallel()
+
+	env := NewTestEnv(t)
+	defer env.Cleanup()
+
+	env.InitRepo()
+	env.WriteFile("README.md", "base\n")
+	env.GitAdd("README.md")
+	env.GitCommit("Initial commit")
+
+	env.GitCheckoutNewBranch("feature/post-rewrite-rebase")
+	env.InitEntire()
+
+	sess := env.NewSession()
+	if err := env.SimulateUserPromptSubmit(sess.ID); err != nil {
+		t.Fatalf("SimulateUserPromptSubmit failed: %v", err)
+	}
+
+	env.WriteFile("feature.txt", "feature work\n")
+	sess.CreateTranscript("Add feature file", []FileChange{
+		{Path: "feature.txt", Content: "feature work\n"},
+	})
+	if err := env.SimulateStop(sess.ID, sess.TranscriptPath); err != nil {
+		t.Fatalf("SimulateStop failed: %v", err)
+	}
+
+	env.GitCommitWithShadowHooks("Feature work", "feature.txt")
+	originalFeatureCommit := env.GetHeadHash()
+
+	stateBeforeRebase, err := env.GetSessionState(sess.ID)
+	if err != nil {
+		t.Fatalf("GetSessionState failed: %v", err)
+	}
+	if stateBeforeRebase == nil {
+		t.Fatal("Session state should exist")
+	}
+	if stateBeforeRebase.BaseCommit != originalFeatureCommit {
+		t.Fatalf("BaseCommit before rebase = %q, want %q", stateBeforeRebase.BaseCommit, originalFeatureCommit)
+	}
+
+	env.gitCheckout("master")
+	env.WriteFile("upstream.txt", "upstream\n")
+	env.GitAdd("upstream.txt")
+	env.GitCommit("Upstream change")
+	env.gitCheckout("feature/post-rewrite-rebase")
+
+	cmd := exec.Command("git", "rebase", "master")
+	cmd.Dir = env.RepoDir
+	if output, err := cmd.CombinedOutput(); err != nil {
+		t.Fatalf("git rebase failed: %v\nOutput: %s", err, output)
+	}
+
+	rebasedFeatureCommit := env.GetHeadHash()
+	if rebasedFeatureCommit == originalFeatureCommit {
+		t.Fatal("Rebased commit should have a different hash")
+	}
+
+	stateAfterRebase, err := env.GetSessionState(sess.ID)
+	if err != nil {
+		t.Fatalf("GetSessionState after rebase failed: %v", err)
+	}
+	if stateAfterRebase == nil {
+		t.Fatal("Session state should exist after rebase")
+	}
+	if stateAfterRebase.BaseCommit != originalFeatureCommit {
+		t.Fatalf("BaseCommit after rebase = %q, want original %q before post-rewrite", stateAfterRebase.BaseCommit, originalFeatureCommit)
+	}
+
+	env.GitPostRewriteWithShadowHooks("rebase", [2]string{originalFeatureCommit, rebasedFeatureCommit})
+
+	stateAfterRewrite, err := env.GetSessionState(sess.ID)
+	if err != nil {
+		t.Fatalf("GetSessionState after post-rewrite failed: %v", err)
+	}
+	if stateAfterRewrite == nil {
+		t.Fatal("Session state should exist after post-rewrite")
+	}
+	if stateAfterRewrite.BaseCommit != rebasedFeatureCommit {
+		t.Fatalf("BaseCommit after post-rewrite = %q, want %q", stateAfterRewrite.BaseCommit, rebasedFeatureCommit)
+	}
+	if stateAfterRewrite.AttributionBaseCommit != rebasedFeatureCommit {
+		t.Fatalf("AttributionBaseCommit after post-rewrite = %q, want %q", stateAfterRewrite.AttributionBaseCommit, rebasedFeatureCommit)
+	}
+}

cmd/entire/cli/integration_test/testenv.go

@@ -1240,6 +1240,28 @@ func (env *TestEnv) GitCommitAmendWithShadowHooks(message string, files ...strin
 	}
 }
 
+// GitPostRewriteWithShadowHooks runs the git post-rewrite hook with the provided
+// old->new commit mappings. Each mapping is a pair of commit SHAs.
+func (env *TestEnv) GitPostRewriteWithShadowHooks(rewriteType string, mappings ...[2]string) {
+	env.T.Helper()
+
+	var input strings.Builder
+	for _, mapping := range mappings {
+		input.WriteString(mapping[0])
+		input.WriteByte(' ')
+		input.WriteString(mapping[1])
+		input.WriteByte('\n')
+	}
+
+	cmd := exec.Command(getTestBinary(), "hooks", "git", "post-rewrite", rewriteType)
+	cmd.Dir = env.RepoDir
+	cmd.Env = env.gitHookEnv()
+	cmd.Stdin = strings.NewReader(input.String())
+	if output, err := cmd.CombinedOutput(); err != nil {
+		env.T.Fatalf("post-rewrite hook failed: %v\nOutput: %s", err, output)
+	}
+}
+
 // GitCommitWithTrailerRemoved stages and commits files, simulating what happens when
 // a user removes the Entire-Checkpoint trailer during commit message editing.
 // This tests the opt-out behavior where removing the trailer skips condensation.

cmd/entire/cli/root_test.go

@@ -73,11 +73,11 @@ func TestPersistentPostRun_SkipsHiddenParent(t *testing.T) {
 
 	root := NewRootCmd()
 
-	// Find the leaf command: entire hooks git post-commit
+	// Find the leaf command: entire hooks git post-rewrite
 	// This exercises the real command tree where "hooks" is Hidden but its descendants are not.
-	leaf, _, err := root.Find([]string{"hooks", "git", "post-commit"})
+	leaf, _, err := root.Find([]string{"hooks", "git", "post-rewrite"})
 	if err != nil {
-		t.Fatalf("could not find hooks git post-commit command: %v", err)
+		t.Fatalf("could not find hooks git post-rewrite command: %v", err)
 	}
 
 	if leaf.Hidden {

cmd/entire/cli/strategy/hooks.go

@@ -20,7 +20,7 @@ const backupSuffix = ".pre-entire"
 const chainComment = "# Chain: run pre-existing hook"
 
 // gitHookNames are the git hooks managed by Entire CLI
-var gitHookNames = []string{"prepare-commit-msg", "commit-msg", "post-commit", "pre-push"}
+var gitHookNames = []string{"prepare-commit-msg", "commit-msg", "post-commit", "post-rewrite", "pre-push"}
 
 // ManagedGitHookNames returns the list of git hooks managed by Entire CLI.
 // This is useful for tests that need to manipulate hooks.
@@ -188,6 +188,14 @@ func buildHookSpecs(cmdPrefix string) []hookSpec {
 # %s
 # Post-commit hook: condense session data if commit has Entire-Checkpoint trailer
 %s hooks git post-commit 2>/dev/null || true
+`, entireHookMarker, cmdPrefix),
+		},
+		{
+			name: "post-rewrite",
+			content: fmt.Sprintf(`#!/bin/sh
+# %s
+# Post-rewrite hook: remap session linkage after amend/rebase rewrites
+%s hooks git post-rewrite "$1" 2>/dev/null || true
 `, entireHookMarker, cmdPrefix),
 		},
 		{