diff --git a/pyproject.toml b/pyproject.toml
index 58c5a61e5..dbd0273cd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -82,10 +82,10 @@ hermes = "hermes_cli.main:main"
 hermes-agent = "run_agent:main"
 
 [tool.setuptools]
-py-modules = ["run_agent", "model_tools", "toolsets", "batch_runner", "trajectory_compressor", "toolset_distributions", "cli", "hermes_constants"]
+py-modules = ["run_agent", "model_tools", "toolsets", "batch_runner", "trajectory_compressor", "toolset_distributions", "cli", "hermes_constants", "hermes_state", "hermes_time", "mini_swe_runner", "rl_cli", "utils"]
 
 [tool.setuptools.packages.find]
-include = ["tools", "hermes_cli", "gateway", "cron", "honcho_integration"]
+include = ["agent", "tools", "tools.*", "hermes_cli", "gateway", "gateway.*", "cron", "honcho_integration"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
diff --git a/tools/rl_training_tool.py b/tools/rl_training_tool.py
index aa658bfe6..a1948e21c 100644
--- a/tools/rl_training_tool.py
+++ b/tools/rl_training_tool.py
@@ -52,15 +52,13 @@ HERMES_ROOT = Path(__file__).parent.parent
 TINKER_ATROPOS_ROOT = HERMES_ROOT / "tinker-atropos"
 ENVIRONMENTS_DIR = TINKER_ATROPOS_ROOT / "tinker_atropos" / "environments"
 CONFIGS_DIR = TINKER_ATROPOS_ROOT / "configs"
-LOGS_DIR = TINKER_ATROPOS_ROOT / "logs"
-
+LOGS_DIR = Path(os.getenv("HERMES_HOME", Path.home() / ".hermes")) / "logs" / "rl_training"
 
 def _ensure_logs_dir():
     """Lazily create logs directory on first use (avoid side effects at import time)."""
     if TINKER_ATROPOS_ROOT.exists():
         LOGS_DIR.mkdir(exist_ok=True)
 
-
 # ============================================================================
 # Locked Configuration (Infrastructure Settings)
 # ============================================================================