Cleanup/remove update enhance doctor

README.md

@@ -85,7 +85,6 @@ agent-notes <command> [options]
 |---------|-------------|
 | `install [--local] [--copy]` | Interactive wizard or direct install |
 | `uninstall [--local]` | Remove installed components |
-| `update` | Pull latest, rebuild, reinstall |
 | `doctor [--local] [--fix]` | Check installation health |
 | `info` | Show status and component counts |
 | `list [clis\|models\|roles\|agents\|skills\|rules\|all]` | List engine components or installed |

agent_notes/cli.py

@@ -237,15 +237,6 @@ def main():
     p_uninstall = subparsers.add_parser("uninstall", help="Remove installed components")
     p_uninstall.add_argument("--local", action="store_true", help="Remove from current project")
 
-    # update
-    p_update = subparsers.add_parser("update", help="Pull latest, show diff, reinstall")
-    p_update.add_argument("--dry-run", action="store_true", help="Show diff only, do not reinstall")
-    p_update.add_argument("-y", "--yes", action="store_true", help="Skip confirmation prompt")
-    p_update.add_argument("--only", action="append", choices=["agents","skills","rules","commands","config","settings"],
-        help="Filter diff to these component types (repeatable)")
-    p_update.add_argument("--since", help="Override 'before' commit label (cosmetic only for now)")
-    p_update.add_argument("--skip-pull", action="store_true", help="Skip git pull")
-
     # doctor
     p_doctor = subparsers.add_parser("doctor", help="Check installation health")
     p_doctor.add_argument("--local", action="store_true", help="Check local installation")
@@ -325,15 +316,6 @@ def main():
     elif args.command == "uninstall":
         from .commands.install import uninstall
         uninstall(local=args.local)
-    elif args.command == "update":
-        from .commands.update import update
-        update(
-            dry_run=args.dry_run,
-            yes=args.yes,
-            only=args.only,
-            since=args.since,
-            skip_pull=args.skip_pull,
-        )
     elif args.command == "doctor":
         from .commands.doctor import doctor
         doctor(local=args.local, fix=args.fix)

agent_notes/commands/__init__.py

@@ -14,14 +14,13 @@
 from . import build
 from . import doctor
 from . import validate
-from . import update
 from . import regenerate
 from . import list as list_cmd
 from . import memory as memory_cmd
 
 __all__ = [
     "install", "uninstall", "show_info",
-    "build", "doctor", "validate", "update",
+    "build", "doctor", "validate",
     "regenerate", "set_role", "interactive_install",
     "list_cmd", "memory_cmd",
 ]

agent_notes/commands/doctor.py

@@ -62,25 +62,60 @@ def _check_session_hook(scope: str, issues: list) -> None:
         ))
 
 
+def check_version_drift(scope: str, issues: list, fix_actions: list) -> None:
+    """Check if the installed package version matches the current running version."""
+    from .. import install_state
+    from ..config import get_version
+    from ..domain.diagnostics import Issue, FixAction
+    from ..services.state_store import get_scope
+    from pathlib import Path
+
+    state = install_state.load_current_state()
+    if state is None:
+        return
+
+    project_path = Path.cwd() if scope == "local" else None
+    scope_state = get_scope(state, scope, project_path)
+    if scope_state is None:
+        return
+
+    installed_version = scope_state.installed_version
+    if not installed_version:
+        return
+
+    current_version = get_version()
+    if installed_version != current_version:
+        issues.append(Issue(
+            "version_drift",
+            "state.json",
+            f"Installed with v{installed_version} but running v{current_version}. "
+            "Run `agent-notes doctor --fix` or `agent-notes install` to update.",
+        ))
+        fix_actions.append(FixAction("_TRIGGER_INSTALL", "state.json", "reinstall to update"))
+
+
 def diagnose(scope: str, fix: bool = False) -> bool:
     """Run all diagnostic checks and optionally apply fixes."""
     from .. import install_state
-    
+
     print_summary(scope)
-    
+
     issues = []
     fix_actions = []
-    
+
     # Run checks
     check_stale_files(scope, issues, fix_actions)
-    check_broken_symlinks(scope, issues, fix_actions) 
+    check_broken_symlinks(scope, issues, fix_actions)
     check_shadowed_files(scope, issues, fix_actions)
     check_missing_files(scope, issues, fix_actions)
     check_content_drift(scope, issues, fix_actions)
-    
+
     # Build freshness check (scope-independent)
     check_build_freshness(issues, fix_actions)
 
+    # Version drift check
+    check_version_drift(scope, issues, fix_actions)
+
     # SessionStart hook check (Claude Code only)
     _check_session_hook(scope, issues)
 

agent_notes/commands/wizard.py

@@ -8,6 +8,7 @@
 from ._install_helpers import (
     count_agents, count_global, count_skills
 )
+from ..services.counts import count_rules_total as _count_rules_total
 from ..services.fs import place_file, place_dir_contents
 from ..services.ui import (
     _can_interactive, _safe_input, _checkbox_select, _radio_select,
@@ -79,22 +80,7 @@ def _get_skill_groups() -> Dict[str, List[str]]:
 
 def _count_rules() -> int:
     """Count rule files."""
-    # For testing, allow bypassing the registry
-    import os
-    if os.environ.get('_WIZARD_TEST_MODE'):
-        if not DIST_RULES_DIR.exists():
-            return 0
-        return len(list(DIST_RULES_DIR.glob("*.md")))
-    else:
-        try:
-            from ..registries import default_rule_registry
-            registry = default_rule_registry()
-            return len(registry.all())
-        except Exception:
-            # Fallback to old behavior if registry fails
-            if not DIST_RULES_DIR.exists():
-                return 0
-            return len(list(DIST_RULES_DIR.glob("*.md")))
+    return _count_rules_total()
 
 
 def _select_cli(step: int = 0, total: int = 0, version: str = '') -> Set[str]:
@@ -629,7 +615,27 @@ def _interactive_install() -> None:
         print(f"{Color.RED}Build failed: {e}{Color.NC}")
         return
 
-    # Execute installation
+    _execute_install(
+        clis=clis,
+        scope=scope,
+        copy_mode=copy_mode,
+        selected_skills=selected_skills,
+        role_models=role_models,
+        memory_backend=memory_backend,
+        memory_path=memory_path,
+    )
+
+
+def _execute_install(
+    clis: Set[str],
+    scope: str,
+    copy_mode: bool,
+    selected_skills: List[str],
+    role_models: Dict[str, Dict[str, str]],
+    memory_backend: str,
+    memory_path: str,
+) -> None:
+    """Run all installation steps after parameters have been collected and the build is done."""
     print(f"\nInstalling ({scope}, {'copy' if copy_mode else 'symlink'}) ...\n")
 
     from ..services import fs as _fs