fix(install): scope uninstall to project_dir instead of always deleting the global skill (#2215)

claude_uninstall/gemini_uninstall/codebuddy_uninstall accepted project_dir
but, with the default project=False, still deleted the user-global skill
tree, so a library/test caller passing a project_dir nuked ~/.claude et al
(the API trap behind #2168). They now take remove_user_skill and treat a
passed project_dir as authoritative; uninstall_all opts in explicitly to
preserve 'graphify uninstall' behavior. Also fixes a live CLI bug where
'uninstall --project' deleted the global codebuddy skill.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

graphify/install.py

@@ -792,10 +792,22 @@ def _uninstall_gemini_hook(project_dir: Path) -> None:
     settings["hooks"]["BeforeTool"] = filtered
     settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
     print("  .gemini/settings.json  ->  BeforeTool hook removed")
-def gemini_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
-    """Remove the graphify section from GEMINI.md, uninstall hook, and remove skill file."""
+def gemini_uninstall(project_dir: Path | None = None, *, project: bool = False, remove_user_skill: bool | None = None) -> None:
+    """Remove the graphify section from GEMINI.md, uninstall hook, and remove skill file.
+
+    Scope rules (#2215): a bare call removes the user-global skill; passing
+    ``project_dir`` (or ``project=True``) scopes skill removal to that project
+    and leaves the global tree untouched, unless ``remove_user_skill=True``
+    explicitly opts back into the global delete (as ``uninstall_all`` does).
+    """
+    explicit_dir = project_dir is not None
     project_dir = project_dir or Path(".")
-    _remove_skill_file("gemini", project=project, project_dir=project_dir)
+    if remove_user_skill is None:
+        remove_user_skill = not project and not explicit_dir
+    if project or (explicit_dir and not remove_user_skill):
+        _remove_skill_file("gemini", project=True, project_dir=project_dir)
+    if remove_user_skill:
+        _remove_skill_file("gemini", project=False)
 
     target = project_dir / "GEMINI.md"
     if not target.exists():
@@ -1600,7 +1612,9 @@ def _project_uninstall(platform_name: str, project_dir: Path | None = None) -> N
         if not removed:
             print("nothing to remove")
     elif platform_name == "codebuddy":
-        codebuddy_uninstall(project_dir)
+        # project=True keeps `uninstall --project` project-scoped; previously
+        # this deleted the user-global codebuddy skill (#2215).
+        codebuddy_uninstall(project_dir, project=True)
     else:
         _remove_skill_file(platform_name, project=True, project_dir=project_dir)
 def _project_uninstall_all(project_dir: Path | None = None) -> None:
@@ -1760,10 +1774,12 @@ def uninstall_all(project_dir: Path | None = None, purge: bool = False) -> None:
     pd = project_dir or Path(".")
     print("Uninstalling graphify from all detected platforms...\n")
 
-    # Skill-file / config-section uninstallers
-    claude_uninstall(pd)
-    codebuddy_uninstall(pd)
-    gemini_uninstall(pd)
+    # Skill-file / config-section uninstallers. remove_user_skill=True keeps the
+    # historical `graphify uninstall` behavior: global skill delete plus md/hook
+    # cleanup at the project dir (#2215).
+    claude_uninstall(pd, remove_user_skill=True)
+    codebuddy_uninstall(pd, remove_user_skill=True)
+    gemini_uninstall(pd, remove_user_skill=True)
     vscode_uninstall(pd)
     _cursor_uninstall(pd)
     _kiro_uninstall(pd)
@@ -1798,7 +1814,7 @@ def uninstall_all(project_dir: Path | None = None, purge: bool = False) -> None:
             print(f"\n  {_GRAPHIFY_OUT}/  ->  not found (nothing to purge)")
 
     print("\nDone. Run 'pip uninstall graphifyy' to remove the package itself.")
-def claude_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
+def claude_uninstall(project_dir: Path | None = None, *, project: bool = False, remove_user_skill: bool | None = None) -> None:
     """Remove the graphify skill tree (SKILL.md + references/) and the graphify
     section from CLAUDE.md and its local-only variants, plus the PreToolUse hook.
 
@@ -1809,9 +1825,20 @@ def claude_uninstall(project_dir: Path | None = None, *, project: bool = False)
     A user may relocate the section/hook into the local-only files Claude Code
     supports so they are not committed to a shared repo, so uninstall also cleans
     CLAUDE.local.md, .claude/CLAUDE.local.md and .claude/settings.local.json (#1731).
+
+    Scope rules (#2215): a bare call removes the user-global skill; passing
+    ``project_dir`` (or ``project=True``) scopes skill removal to that project
+    and leaves the global tree untouched, unless ``remove_user_skill=True``
+    explicitly opts back into the global delete (as ``uninstall_all`` does).
     """
+    explicit_dir = project_dir is not None
     project_dir = project_dir or Path(".")
-    _remove_skill_file("claude", project=project, project_dir=project_dir)
+    if remove_user_skill is None:
+        remove_user_skill = not project and not explicit_dir
+    if project or (explicit_dir and not remove_user_skill):
+        _remove_skill_file("claude", project=True, project_dir=project_dir)
+    if remove_user_skill:
+        _remove_skill_file("claude", project=False)
 
     md_targets = [
         project_dir / "CLAUDE.md",
@@ -1914,10 +1941,22 @@ def _uninstall_codebuddy_hook(project_dir: Path) -> None:
     settings["hooks"]["PreToolUse"] = filtered
     settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
     print(f"  .codebuddy/settings.json  ->  PreToolUse hook removed")
-def codebuddy_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
-    """Remove the graphify skill tree (SKILL.md + references/) and the CODEBUDDY.md section."""
+def codebuddy_uninstall(project_dir: Path | None = None, *, project: bool = False, remove_user_skill: bool | None = None) -> None:
+    """Remove the graphify skill tree (SKILL.md + references/) and the CODEBUDDY.md section.
+
+    Scope rules (#2215): a bare call removes the user-global skill; passing
+    ``project_dir`` (or ``project=True``) scopes skill removal to that project
+    and leaves the global tree untouched, unless ``remove_user_skill=True``
+    explicitly opts back into the global delete (as ``uninstall_all`` does).
+    """
+    explicit_dir = project_dir is not None
     project_dir = project_dir or Path(".")
-    _remove_skill_file("codebuddy", project=project, project_dir=project_dir)
+    if remove_user_skill is None:
+        remove_user_skill = not project and not explicit_dir
+    if project or (explicit_dir and not remove_user_skill):
+        _remove_skill_file("codebuddy", project=True, project_dir=project_dir)
+    if remove_user_skill:
+        _remove_skill_file("codebuddy", project=False)
     target = project_dir / "CODEBUDDY.md"
 
     if not target.exists():

tests/test_home_sandbox.py

@@ -39,11 +39,12 @@ def test_claude_config_dir_escape_hatch_is_cleared():
 
 
 def test_global_uninstall_is_captured_by_sandbox(tmp_path, tmp_path_factory):
-    """claude_uninstall deletes the *global* ~/.claude/skills/graphify tree.
+    """Global skill deletes land inside the sandbox home, never the real one.
 
-    Plant that tree inside the sandbox home, run uninstall against an
-    unrelated project dir, and prove the delete landed in the sandbox
-    (and therefore not in the developer's real home).
+    Since #2215, `claude_uninstall(project_dir)` is project-scoped and must NOT
+    touch the global tree; the global delete now requires either a bare call or
+    an explicit `remove_user_skill=True`. Both scopes are exercised here so the
+    sandbox (#2168) is still proven to capture the global delete.
     """
     skill = Path.home() / ".claude" / "skills" / "graphify" / "SKILL.md"
     skill.parent.mkdir(parents=True)
@@ -51,8 +52,13 @@ def test_global_uninstall_is_captured_by_sandbox(tmp_path, tmp_path_factory):
 
     project_dir = tmp_path / "some-project"
     project_dir.mkdir()
-    claude_uninstall(project_dir)
 
+    # Project-scoped call: the global tree in the sandbox home must survive.
+    claude_uninstall(project_dir)
+    assert skill.exists(), "project-scoped uninstall deleted the global skill (#2215 trap)"
+
+    # Explicit global opt-in: the delete happens, and lands in the sandbox.
+    claude_uninstall(project_dir, remove_user_skill=True)
     assert not skill.exists(), "global skill delete was not captured by the sandbox"
     # And the sandbox home itself is still inside pytest's tmp area.
     assert Path.home().is_relative_to(tmp_path_factory.getbasetemp())

tests/test_uninstall_scope.py

@@ -0,0 +1,113 @@
+"""Scope regression tests for the uninstall API trap (issue #2215).
+
+`X_uninstall(project_dir)` used to delete the USER-GLOBAL skill tree because
+`_platform_skill_destination` honors ``project_dir`` only when ``project=True``.
+These tests pin the fixed contract:
+
+- bare call            -> global skill removed (CLI behavior unchanged)
+- fn(pd)               -> project-scoped, global untouched (trap closed)
+- fn(pd, project=True) -> project only
+- fn(pd, remove_user_skill=True) -> global removed, project tree untouched
+- `graphify uninstall --project` for codebuddy no longer nukes the global skill
+"""
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+
+from graphify.install import (
+    _project_uninstall,
+    claude_uninstall,
+    codebuddy_uninstall,
+    gemini_uninstall,
+)
+
+PLATFORMS = [
+    pytest.param(claude_uninstall, "claude", ".claude", id="claude"),
+    pytest.param(gemini_uninstall, "gemini", ".gemini", id="gemini"),
+    pytest.param(codebuddy_uninstall, "codebuddy", ".codebuddy", id="codebuddy"),
+]
+
+
+def _plant_skill_tree(root: Path, dot_dir: str) -> Path:
+    """Create <root>/<dot_dir>/skills/graphify/{SKILL.md, references/x.md, .graphify_version}."""
+    skill_dir = root / dot_dir / "skills" / "graphify"
+    (skill_dir / "references").mkdir(parents=True)
+    (skill_dir / "SKILL.md").write_text("# graphify skill\n", encoding="utf-8")
+    (skill_dir / "references" / "x.md").write_text("ref\n", encoding="utf-8")
+    (skill_dir / ".graphify_version").write_text("0.0.0-test", encoding="utf-8")
+    return skill_dir
+
+
+@pytest.mark.parametrize("uninstall_fn,platform,dot_dir", PLATFORMS)
+def test_project_dir_call_never_touches_global(uninstall_fn, platform, dot_dir, tmp_path):
+    """fn(project_dir) removes only the project skill tree (#2215 trap closed)."""
+    global_tree = _plant_skill_tree(Path.home(), dot_dir)
+    proj_dir = tmp_path / "proj"
+    project_tree = _plant_skill_tree(proj_dir, dot_dir)
+
+    uninstall_fn(proj_dir)
+
+    assert (global_tree / "SKILL.md").exists(), "global skill deleted by project-scoped uninstall"
+    assert (global_tree / "references" / "x.md").exists()
+    assert (global_tree / ".graphify_version").exists()
+    assert not (project_tree / "SKILL.md").exists()
+    assert not project_tree.exists()
+
+
+@pytest.mark.parametrize("uninstall_fn,platform,dot_dir", PLATFORMS)
+def test_bare_call_still_removes_global(uninstall_fn, platform, dot_dir, tmp_path, monkeypatch):
+    """fn() with no args keeps the historical CLI behavior: global skill removed."""
+    global_tree = _plant_skill_tree(Path.home(), dot_dir)
+    cwd = tmp_path / "empty-cwd"
+    cwd.mkdir()
+    monkeypatch.chdir(cwd)
+
+    uninstall_fn()
+
+    assert not (global_tree / "SKILL.md").exists()
+    assert not global_tree.exists()
+
+
+@pytest.mark.parametrize("uninstall_fn,platform,dot_dir", PLATFORMS)
+def test_remove_user_skill_opt_in_with_project_dir(uninstall_fn, platform, dot_dir, tmp_path):
+    """fn(pd, remove_user_skill=True) removes the global skill, leaves the project tree."""
+    global_tree = _plant_skill_tree(Path.home(), dot_dir)
+    proj_dir = tmp_path / "proj"
+    project_tree = _plant_skill_tree(proj_dir, dot_dir)
+
+    uninstall_fn(proj_dir, remove_user_skill=True)
+
+    assert not (global_tree / "SKILL.md").exists()
+    assert not global_tree.exists()
+    assert (project_tree / "SKILL.md").exists()
+    assert (project_tree / "references" / "x.md").exists()
+
+
+@pytest.mark.parametrize("uninstall_fn,platform,dot_dir", PLATFORMS)
+def test_project_true_removes_only_project_tree(uninstall_fn, platform, dot_dir, tmp_path):
+    """fn(pd, project=True) removes only the project skill tree."""
+    global_tree = _plant_skill_tree(Path.home(), dot_dir)
+    proj_dir = tmp_path / "proj"
+    project_tree = _plant_skill_tree(proj_dir, dot_dir)
+
+    uninstall_fn(proj_dir, project=True)
+
+    assert (global_tree / "SKILL.md").exists()
+    assert not (project_tree / "SKILL.md").exists()
+    assert not project_tree.exists()
+
+
+def test_project_uninstall_codebuddy_spares_global(tmp_path):
+    """`graphify uninstall --project` (codebuddy branch) must not delete ~/.codebuddy (#2215)."""
+    global_tree = _plant_skill_tree(Path.home(), ".codebuddy")
+    proj_dir = tmp_path / "proj"
+    project_tree = _plant_skill_tree(proj_dir, ".codebuddy")
+
+    _project_uninstall("codebuddy", proj_dir)
+
+    assert (global_tree / "SKILL.md").exists(), "CLI --project uninstall deleted the global codebuddy skill"
+    assert (global_tree / ".graphify_version").exists()
+    assert not (project_tree / "SKILL.md").exists()
+    assert not project_tree.exists()