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/main.py

@@ -33,14 +33,20 @@ from pathlib import Path
 PROJECT_ROOT = Path(__file__).parent.parent.resolve()
 sys.path.insert(0, str(PROJECT_ROOT))
 
-# Load .env file
+# Load .env from ~/.hermes/.env first, then project root as dev fallback
 from dotenv import load_dotenv
-env_path = PROJECT_ROOT / '.env'
-if env_path.exists():
+from hermes_cli.config import get_env_path, get_hermes_home
+_user_env = get_env_path()
+if _user_env.exists():
     try:
-        load_dotenv(dotenv_path=env_path, encoding="utf-8")
+        load_dotenv(dotenv_path=_user_env, encoding="utf-8")
     except UnicodeDecodeError:
-        load_dotenv(dotenv_path=env_path, encoding="latin-1")
+        load_dotenv(dotenv_path=_user_env, encoding="latin-1")
+load_dotenv(dotenv_path=PROJECT_ROOT / '.env', override=False)
+
+# Point mini-swe-agent at ~/.hermes/ so it shares our config
+os.environ.setdefault("MSWEA_GLOBAL_CONFIG_DIR", str(get_hermes_home()))
+os.environ.setdefault("MSWEA_SILENT_STARTUP", "1")
 
 import logging