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/status.py

@@ -12,6 +12,7 @@ from pathlib import Path
 PROJECT_ROOT = Path(__file__).parent.parent.resolve()
 
 from hermes_cli.colors import Colors, color
+from hermes_cli.config import get_env_path, get_env_value
 from hermes_constants import OPENROUTER_MODELS_URL
 
 def check_mark(ok: bool) -> str:
@@ -65,7 +66,7 @@ def show_status(args):
     print(f"  Project:      {PROJECT_ROOT}")
     print(f"  Python:       {sys.version.split()[0]}")
     
-    env_path = PROJECT_ROOT / '.env'
+    env_path = get_env_path()
     print(f"  .env file:    {check_mark(env_path.exists())} {'exists' if env_path.exists() else 'not found'}")
     
     # =========================================================================
@@ -88,7 +89,7 @@ def show_status(args):
     }
     
     for name, env_var in keys.items():
-        value = os.getenv(env_var, "")
+        value = get_env_value(env_var) or ""
         has_key = bool(value)
         display = redact_key(value) if not show_all else value
         print(f"  {name:<12}  {check_mark(has_key)} {display}")