fix: resolve .env and config paths from HERMES_HOME, not PROJECT_ROOT

The `hermes` CLI entry point (hermes_cli/main.py) and the agent runner
(run_agent.py) only loaded .env from the project installation directory.
After the standard installer, code lives at ~/.hermes/hermes-agent/ but
config lives at ~/.hermes/ — so the .env was never found.

Aligns these entry points with the pattern already used by gateway/run.py
and rl_cli.py: load ~/.hermes/.env first, fall back to project root .env
for dev-mode compatibility.

Also fixes:
- status.py checking .env existence and API keys at PROJECT_ROOT
- doctor.py KeyError on tool availability (missing_vars vs env_vars)
- doctor.py checking logs/ and Skills Hub at PROJECT_ROOT instead of HERMES_HOME
- doctor.py redundant logs/ check (already covered by subdirectory loop)
- mini-swe-agent loading config from platformdirs default instead of ~/.hermes/

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

hermes_cli/doctor.py

@@ -23,9 +23,13 @@ if _env_path.exists():
         load_dotenv(_env_path, encoding="utf-8")
     except UnicodeDecodeError:
         load_dotenv(_env_path, encoding="latin-1")
-# Also try project .env as fallback
+# Also try project .env as dev fallback
 load_dotenv(PROJECT_ROOT / ".env", override=False, encoding="utf-8")
 
+# Point mini-swe-agent at ~/.hermes/ so it shares our config
+os.environ.setdefault("MSWEA_GLOBAL_CONFIG_DIR", str(HERMES_HOME))
+os.environ.setdefault("MSWEA_SILENT_STARTUP", "1")
+
 from hermes_cli.colors import Colors, color
 from hermes_constants import OPENROUTER_MODELS_URL
 
@@ -225,17 +229,6 @@ def run_doctor(args):
             check_ok("Created ~/.hermes/SOUL.md with basic template")
             fixed_count += 1
     
-    logs_dir = PROJECT_ROOT / "logs"
-    if logs_dir.exists():
-        check_ok("logs/ directory exists (project root)")
-    else:
-        if should_fix:
-            logs_dir.mkdir(parents=True, exist_ok=True)
-            check_ok("Created logs/ directory")
-            fixed_count += 1
-        else:
-            check_warn("logs/ not found", "(will be created on first use)")
-    
     # Check memory directory
     memories_dir = hermes_home / "memories"
     if memories_dir.exists():
@@ -447,14 +440,15 @@ def run_doctor(args):
             check_ok(info.get("name", tid))
         
         for item in unavailable:
-            if item["missing_vars"]:
-                vars_str = ", ".join(item["missing_vars"])
+            env_vars = item.get("missing_vars") or item.get("env_vars") or []
+            if env_vars:
+                vars_str = ", ".join(env_vars)
                 check_warn(item["name"], f"(missing {vars_str})")
             else:
                 check_warn(item["name"], "(system dependency not met)")
-        
+
         # Count disabled tools with API key requirements
-        api_disabled = [u for u in unavailable if u["missing_vars"]]
+        api_disabled = [u for u in unavailable if (u.get("missing_vars") or u.get("env_vars"))]
         if api_disabled:
             issues.append("Run 'hermes setup' to configure missing API keys for full tool access")
     except Exception as e:
@@ -466,7 +460,7 @@ def run_doctor(args):
     print()
     print(color("◆ Skills Hub", Colors.CYAN, Colors.BOLD))
 
-    hub_dir = PROJECT_ROOT / "skills" / ".hub"
+    hub_dir = HERMES_HOME / "skills" / ".hub"
     if hub_dir.exists():
         check_ok("Skills Hub directory exists")
         lock_file = hub_dir / "lock.json"
@@ -485,7 +479,8 @@ def run_doctor(args):
     else:
         check_warn("Skills Hub directory not initialized", "(run: hermes skills list)")
 
-    github_token = os.environ.get("GITHUB_TOKEN") or os.environ.get("GH_TOKEN")
+    from hermes_cli.config import get_env_value
+    github_token = get_env_value("GITHUB_TOKEN") or get_env_value("GH_TOKEN")
     if github_token:
         check_ok("GitHub token configured (authenticated API access)")
     else: