feat(doctor): surface skill directory health in diagnostics

docs/plans/state.json

@@ -1203,7 +1203,7 @@
     "phases": {
       "phase_1_command_dispatch": {
         "priority": "P0",
-        "status": "in_progress",
+        "status": "completed",
         "description": "flynn skills CLI commands (list/info/install/uninstall/refresh) with doctor enhancement",
         "effort": "2-3 hours",
         "sub_slices": {
@@ -1255,6 +1255,15 @@
               "src/cli/skills.test.ts"
             ],
             "test_status": "typecheck + targeted skills CLI tests + full test suite + lint (warnings only, 0 errors) + build passing"
+          },
+          "doctor_skills_diagnostics": {
+            "status": "completed",
+            "description": "Enhanced `flynn doctor` skills diagnostics to report availability counts and warn on missing configured skill directories",
+            "files_modified": [
+              "src/cli/doctor.ts",
+              "src/cli/doctor.test.ts"
+            ],
+            "test_status": "typecheck + targeted doctor tests + full test suite + lint (warnings only, 0 errors) + build passing"
           }
         }
       },
@@ -1295,7 +1304,7 @@
   },
 
   "overall_progress": {
-    "total_test_count": 1502,
+    "total_test_count": 1504,
     "all_tests_passing": true,
     "p0_completion": "3/3 (100%)",
     "p1_completion": "4/4 (100%)",
@@ -1315,7 +1324,7 @@
     "gmail_auth_cli": "flynn gmail-auth command implemented with OAuth2 flow, doctor check, config routed to Telegram",
     "native_audio_support": "completed — smart routing for native audio (Gemini/OpenAI/GitHub) vs Whisper transcription fallback",
     "remaining_phases_completion": "Phase 1: 3/3 (100%) — context levels, command registry, memory structure. Phase 2: 2/2 (100%) — component registry, confidence routing. Phase 3: 2/2 (100%) — adaptive memory/compaction, truthfulness/autonomy hardening",
-    "next_up": "Skills infrastructure Phase 1: add doctor enhancement for skills diagnostics"
+    "next_up": "Skills infrastructure Phase 2: implement skill auto-reload watcher with configurable debounce"
   },
   "soul_md_and_cron_create": {
     "date": "2026-02-11",