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:

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
 

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}")

run_agent.py

@@ -37,19 +37,30 @@ import fire
 from datetime import datetime
 from pathlib import Path
 
-# Load environment variables from .env file
+# Load .env from ~/.hermes/.env first, then project root as dev fallback
 from dotenv import load_dotenv
 
-# Load .env file if it exists
-env_path = Path(__file__).parent / '.env'
-if env_path.exists():
+_hermes_home = Path(os.getenv("HERMES_HOME", Path.home() / ".hermes"))
+_user_env = _hermes_home / ".env"
+_project_env = Path(__file__).parent / '.env'
+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")
-    logger.info("Loaded environment variables from %s", env_path)
+        load_dotenv(dotenv_path=_user_env, encoding="latin-1")
+    logger.info("Loaded environment variables from %s", _user_env)
+elif _project_env.exists():
+    try:
+        load_dotenv(dotenv_path=_project_env, encoding="utf-8")
+    except UnicodeDecodeError:
+        load_dotenv(dotenv_path=_project_env, encoding="latin-1")
+    logger.info("Loaded environment variables from %s", _project_env)
 else:
-    logger.info("No .env file found at %s. Using system environment variables.", env_path)
+    logger.info("No .env file found. Using system environment variables.")
+
+# 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")
 
 # Import our tool system
 from model_tools import get_tool_definitions, handle_function_call, check_toolset_requirements