feat: clean up legacy graphify hooks during install and uninstall

Remove old generated hook scripts and entries when installing or
uninstalling graphify for both Claude and Codex platforms. This
prevents stale legacy hooks from accumulating in user configurations
and ensures a clean migration to the current hook format.

Author: robertmonka

graphify/__main__.py

@@ -1096,27 +1096,47 @@ def _install_codex_hook(project_dir: Path) -> None:
         }
     }
 
-    pre_tool = existing.setdefault("hooks", {}).setdefault("PreToolUse", [])
-    existing["hooks"]["PreToolUse"] = [h for h in pre_tool if "graphify" not in str(h)]
-    existing["hooks"]["PreToolUse"].extend(hook_entry["hooks"]["PreToolUse"])
+    _remove_graphify_hook_entries(existing)
+    hooks = existing.setdefault("hooks", {})
+    hooks.setdefault("PreToolUse", []).extend(hook_entry["hooks"]["PreToolUse"])
     hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
     print(f"  .codex/hooks.json  ->  PreToolUse hook registered ({graphify_exe} hook-check)")
 
 
+def _remove_graphify_hook_entries(settings: dict) -> None:
+    """Remove graphify hook entries while preserving unrelated hooks."""
+    hooks = settings.get("hooks")
+    if not isinstance(hooks, dict):
+        settings["hooks"] = {}
+        return
+
+    for event, event_hooks in list(hooks.items()):
+        if not isinstance(event_hooks, list):
+            if "graphify" in str(event_hooks):
+                hooks.pop(event, None)
+            continue
+        filtered = [h for h in event_hooks if "graphify" not in str(h)]
+        if filtered:
+            hooks[event] = filtered
+        else:
+            hooks.pop(event, None)
+
+    if not hooks:
+        settings.pop("hooks", None)
+
+
 def _uninstall_codex_hook(project_dir: Path) -> None:
-    """Remove graphify PreToolUse hook from .codex/hooks.json."""
+    """Remove graphify hooks from .codex/hooks.json."""
     hooks_path = project_dir / ".codex" / "hooks.json"
     if not hooks_path.exists():
         return
     try:
         existing = json.loads(hooks_path.read_text(encoding="utf-8"))
     except json.JSONDecodeError:
         return
-    pre_tool = existing.get("hooks", {}).get("PreToolUse", [])
-    filtered = [h for h in pre_tool if "graphify" not in str(h)]
-    existing["hooks"]["PreToolUse"] = filtered
+    _remove_graphify_hook_entries(existing)
     hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
-    print(f"  .codex/hooks.json  ->  PreToolUse hook removed")
+    print(f"  .codex/hooks.json  ->  graphify hooks removed")
 
 
 def _agents_install(project_dir: Path, platform: str) -> None:
@@ -1209,24 +1229,18 @@ def claude_install(project_dir: Path | None = None) -> None:
 
 def _remove_graphify_claude_hooks(settings: dict) -> None:
     """Remove graphify Claude hooks while preserving unrelated hooks."""
-    hooks = settings.get("hooks")
-    if not isinstance(hooks, dict):
-        settings["hooks"] = {}
-        return
+    _remove_graphify_hook_entries(settings)
 
-    for event in ("UserPromptSubmit", "PreToolUse"):
-        event_hooks = hooks.get(event)
-        if not isinstance(event_hooks, list):
-            hooks.pop(event, None)
-            continue
-        filtered = [h for h in event_hooks if "graphify" not in str(h)]
-        if filtered:
-            hooks[event] = filtered
-        else:
-            hooks.pop(event, None)
 
-    if not hooks:
-        settings.pop("hooks", None)
+def _remove_graphify_claude_hook_scripts(claude_dir: Path) -> list[Path]:
+    """Remove generated graphify Claude hook scripts."""
+    removed = []
+    for name in ("graphify-guard.py", "graphify-hook.cjs"):
+        hook_path = claude_dir / "hooks" / name
+        if hook_path.exists():
+            hook_path.unlink()
+            removed.append(hook_path)
+    return removed
 
 
 def _load_json_object(path: Path) -> dict:
@@ -1251,6 +1265,7 @@ def _install_claude_hook(project_dir: Path) -> None:
     settings_path = claude_dir / "settings.json"
     hooks_dir = claude_dir / "hooks"
     hooks_dir.mkdir(parents=True, exist_ok=True)
+    _remove_graphify_claude_hook_scripts(claude_dir)
 
     guard_path = hooks_dir / "graphify-guard.py"
     guard_path.write_text(_GRAPHIFY_GUARD_SCRIPT, encoding="utf-8")
@@ -1285,10 +1300,8 @@ def _uninstall_claude_hook(project_dir: Path) -> None:
             settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
             print("  .claude/settings.json  ->  graphify hooks removed")
 
-    guard_path = claude_dir / "hooks" / "graphify-guard.py"
-    if guard_path.exists():
-        guard_path.unlink()
-        print("  .claude/hooks/graphify-guard.py  ->  removed")
+    for hook_path in _remove_graphify_claude_hook_scripts(claude_dir):
+        print(f"  {hook_path.relative_to(claude_dir.parent)}  ->  removed")
 
 def claude_uninstall(project_dir: Path | None = None) -> None:
     """Remove the graphify section from the local CLAUDE.md."""
@@ -1382,7 +1395,7 @@ def main() -> None:
     # Skip during install/uninstall (hook writes trigger a fresh check anyway).
     # Deduplicate paths so platforms sharing the same install dir don't warn twice.
     if not any(arg in ("install", "uninstall") for arg in sys.argv) and (
-        len(sys.argv) < 2 or sys.argv[1] not in ("skill", "setup")
+        len(sys.argv) < 2 or sys.argv[1] not in ("skill", "setup", "hook-check")
     ):
         for skill_dst in {_platform_skill_destination(platform_name) for platform_name in _PLATFORM_CONFIG}:
             _check_skill_version(skill_dst)

tests/test_claude_md.py

@@ -179,13 +179,44 @@ def test_install_preserves_unrelated_settings_hooks(tmp_path):
     assert any("graphify-guard.py" in str(h) for h in pre_tool)
 
 
+def test_install_removes_legacy_claude_hook_script(tmp_path):
+    """Installing graphify removes old generated Claude hook scripts."""
+    hooks_dir = tmp_path / ".claude" / "hooks"
+    hooks_dir.mkdir(parents=True)
+    legacy_hook = hooks_dir / "graphify-hook.cjs"
+    legacy_hook.write_text("console.log('legacy graphify hook')")
+    settings_path = tmp_path / ".claude" / "settings.json"
+    settings_path.write_text(json.dumps({
+        "hooks": {
+            "UserPromptSubmit": [
+                {"hooks": [{"type": "command", "command": f"node {legacy_hook} user-prompt"}]},
+            ],
+            "PreToolUse": [
+                {"matcher": "Bash", "hooks": [{"type": "command", "command": "echo keep"}]},
+                {"matcher": "Bash", "hooks": [{"type": "command", "command": f"node {legacy_hook} pre-tool"}]},
+            ],
+        }
+    }))
+
+    claude_install(tmp_path)
+
+    settings = json.loads(settings_path.read_text())
+    assert not legacy_hook.exists()
+    assert "graphify-hook.cjs" not in str(settings)
+    assert "echo keep" in str(settings)
+    assert (hooks_dir / "graphify-guard.py").exists()
+
+
 def test_uninstall_removes_settings_hook(tmp_path):
     """claude_uninstall removes graphify hooks and guard script."""
     claude_install(tmp_path)
+    legacy_hook = tmp_path / ".claude" / "hooks" / "graphify-hook.cjs"
+    legacy_hook.write_text("console.log('legacy graphify hook')")
     claude_uninstall(tmp_path)
     settings_path = tmp_path / ".claude" / "settings.json"
     guard_path = tmp_path / ".claude" / "hooks" / "graphify-guard.py"
     assert not guard_path.exists()
+    assert not legacy_hook.exists()
     if settings_path.exists():
         settings = json.loads(settings_path.read_text())
         hooks = settings.get("hooks", {})

tests/test_install.py

@@ -1,5 +1,6 @@
 """Tests for graphify install --platform routing."""
 from contextlib import contextmanager
+import json
 import os
 from pathlib import Path
 import sys
@@ -353,6 +354,58 @@ def test_codex_agents_install_writes_agents_md(tmp_path):
     assert "GRAPH_REPORT.md" in agents_md.read_text()
 
 
+def test_codex_agents_install_removes_legacy_prompt_hook(tmp_path):
+    hooks_path = tmp_path / ".codex" / "hooks.json"
+    hooks_path.parent.mkdir(parents=True)
+    hooks_path.write_text(json.dumps({
+        "hooks": {
+            "UserPromptSubmit": [
+                {"hooks": [{"type": "command", "command": "echo graphify legacy prompt"}]},
+                {"hooks": [{"type": "command", "command": "echo keep prompt"}]},
+            ],
+            "PreToolUse": [
+                {"matcher": "Bash", "hooks": [{"type": "command", "command": "graphify hook-check"}]},
+                {"matcher": "Bash", "hooks": [{"type": "command", "command": "echo keep tool"}]},
+            ],
+        }
+    }))
+
+    _agents_install(tmp_path, "codex")
+
+    settings = json.loads(hooks_path.read_text())
+    hooks = settings["hooks"]
+    assert "legacy prompt" not in str(settings)
+    assert "keep prompt" in str(hooks.get("UserPromptSubmit", []))
+    assert "keep tool" in str(hooks.get("PreToolUse", []))
+    graphify_pre_tool = [h for h in hooks["PreToolUse"] if "hook-check" in str(h)]
+    assert len(graphify_pre_tool) == 1
+
+
+def test_codex_uninstall_removes_all_graphify_hooks(tmp_path):
+    from graphify.__main__ import _uninstall_codex_hook
+    hooks_path = tmp_path / ".codex" / "hooks.json"
+    hooks_path.parent.mkdir(parents=True)
+    hooks_path.write_text(json.dumps({
+        "hooks": {
+            "UserPromptSubmit": [
+                {"hooks": [{"type": "command", "command": "echo graphify legacy prompt"}]},
+            ],
+            "PreToolUse": [
+                {"matcher": "Bash", "hooks": [{"type": "command", "command": "graphify hook-check"}]},
+            ],
+            "PostToolUse": [
+                {"matcher": "Bash", "hooks": [{"type": "command", "command": "echo keep"}]},
+            ],
+        }
+    }))
+
+    _uninstall_codex_hook(tmp_path)
+
+    settings = json.loads(hooks_path.read_text())
+    assert "graphify" not in str(settings)
+    assert "keep" in str(settings)
+
+
 def test_opencode_agents_install_writes_agents_md(tmp_path):
     _agents_install(tmp_path, "opencode")
     assert (tmp_path / "AGENTS.md").exists()