From 5b4aa6dcb455eb0631498ba68883389fc32be9bc Mon Sep 17 00:00:00 2001
From: Stefan Haubold <stefan@entire.io>
Date: Fri, 27 Mar 2026 15:10:02 +0100
Subject: [PATCH] capture scenario where git hooks are overwritten during a
 running agent prompt

Entire-Checkpoint: 921759ff3b5f
---
 .../integration_test/hook_overwrite_test.go   | 116 ++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100644 cmd/entire/cli/integration_test/hook_overwrite_test.go

diff --git a/cmd/entire/cli/integration_test/hook_overwrite_test.go b/cmd/entire/cli/integration_test/hook_overwrite_test.go
new file mode 100644
index 000000000..656856323
--- /dev/null
+++ b/cmd/entire/cli/integration_test/hook_overwrite_test.go
@@ -0,0 +1,116 @@
+//go:build integration
+
+package integration
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/entireio/cli/cmd/entire/cli/strategy"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// TestHookOverwrite_MidTurnWipe_NextPromptRecovers simulates the scenario from
+// https://github.com/entireio/cli/issues/784:
+//
+// Flow:
+//  1. Prompt 1: agent creates files, commits via hooks → checkpoint trailer ✓
+//  2. Mid-turn: third-party tool (husky/lefthook) overwrites git hooks
+//  3. Agent commits again (no hooks fire) → NO trailer
+//  4. Prompt 2 starts (user-prompt-submit) → EnsureSetup reinstalls hooks
+//  5. Agent commits via hooks → checkpoint trailer ✓ (hooks restored)
+//
+// The key insight: GitCommitWithShadowHooks invokes the binary directly (simulating
+// working hooks), while GitAdd+GitCommit uses go-git without hooks (simulating
+// overwritten hooks where `entire` is never called).
+func TestHookOverwrite_MidTurnWipe_NextPromptRecovers(t *testing.T) {
+	t.Parallel()
+
+	env := NewFeatureBranchEnv(t)
+	hooksDir := filepath.Join(env.RepoDir, ".git", "hooks")
+
+	sess := env.NewSession()
+
+	// === Prompt 1: normal flow, hooks work ===
+	err := env.SimulateUserPromptSubmitWithPromptAndTranscriptPath(
+		sess.ID, "Create files A and B", sess.TranscriptPath)
+	require.NoError(t, err)
+
+	env.WriteFile("fileA.go", "package main\n\nfunc A() {}\n")
+	env.WriteFile("fileB.go", "package main\n\nfunc B() {}\n")
+
+	sess.CreateTranscript("Create files A and B", []FileChange{
+		{Path: "fileA.go", Content: "package main\n\nfunc A() {}\n"},
+		{Path: "fileB.go", Content: "package main\n\nfunc B() {}\n"},
+	})
+
+	// First commit — hooks are intact, binary is invoked → trailer added
+	env.GitCommitWithShadowHooks("Add file A", "fileA.go")
+	cpID1 := env.GetCheckpointIDFromCommitMessage(env.GetHeadHash())
+	require.NotEmpty(t, cpID1, "first commit should have checkpoint trailer")
+
+	// === Simulate husky/lefthook overwriting hooks mid-turn ===
+	// This is what happens when an agent runs `npm install` and husky's
+	// `prepare` lifecycle script reinstalls its own hooks.
+	for _, hookName := range strategy.ManagedGitHookNames() {
+		hookPath := filepath.Join(hooksDir, hookName)
+		huskyContent := "#!/bin/sh\n# husky - do not edit\n. \"$(dirname \"$0\")/_/husky.sh\"\n"
+		err := os.WriteFile(hookPath, []byte(huskyContent), 0o755)
+		require.NoError(t, err)
+	}
+
+	// Verify hooks are overwritten
+	require.False(t, strategy.IsGitHookInstalledInDir(t.Context(), env.RepoDir),
+		"hooks should be detected as overwritten")
+
+	// Second commit — hooks are gone, use plain go-git commit (no binary invoked).
+	// This simulates what happens in the real world: git runs the husky hook script,
+	// which doesn't call `entire`, so no trailer is added.
+	env.GitAdd("fileB.go")
+	env.GitCommit("Add file B")
+	cpID2 := env.GetCheckpointIDFromCommitMessage(env.GetHeadHash())
+	assert.Empty(t, cpID2,
+		"second commit should NOT have trailer (hooks were overwritten, entire never called)")
+
+	// End prompt 1
+	err = env.SimulateStop(sess.ID, sess.TranscriptPath)
+	require.NoError(t, err)
+
+	// === Prompt 2: EnsureSetup should reinstall hooks ===
+	sess2 := env.NewSession()
+
+	env.WriteFile("fileC.go", "package main\n\nfunc C() {}\n")
+
+	sess2.CreateTranscript("Create file C", []FileChange{
+		{Path: "fileC.go", Content: "package main\n\nfunc C() {}\n"},
+	})
+
+	err = env.SimulateUserPromptSubmitWithPromptAndTranscriptPath(
+		sess2.ID, "Create file C", sess2.TranscriptPath)
+	require.NoError(t, err)
+
+	// Verify hooks were reinstalled by EnsureSetup
+	require.True(t, strategy.IsGitHookInstalledInDir(t.Context(), env.RepoDir),
+		"hooks should be reinstalled by EnsureSetup at prompt 2 start")
+
+	// Verify overwritten hooks were backed up (chaining preserved)
+	for _, hookName := range strategy.ManagedGitHookNames() {
+		backupPath := filepath.Join(hooksDir, hookName+".pre-entire")
+		_, err := os.Stat(backupPath)
+		assert.NoError(t, err, "backup %s.pre-entire should exist after reinstall", hookName)
+	}
+
+	// Third commit — hooks restored, binary invoked again → trailer added
+	env.GitCommitWithShadowHooks("Add file C", "fileC.go")
+	cpID3 := env.GetCheckpointIDFromCommitMessage(env.GetHeadHash())
+	assert.NotEmpty(t, cpID3,
+		"third commit should have trailer (hooks reinstalled by prompt 2)")
+
+	// Checkpoint IDs should be distinct
+	if cpID3 != "" {
+		assert.NotEqual(t, cpID1, cpID3,
+			"checkpoint IDs from prompt 1 and prompt 2 should be distinct")
+	}
+}