fix: add missing packages to setuptools config for non-editable installs

- Add `agent`, `tools.*`, `gateway.*` to packages.find include
- Add `hermes_state`, `hermes_time`, `mini_swe_runner`, `rl_cli`, `utils` to py-modules
- Move rl_training_tool LOGS_DIR to ~/.hermes/logs/rl_training/ (was writing
  into the package source tree, which fails on read-only installs)

These were masked in development (editable installs see the whole source tree)
but broke any non-editable install like `pip install .` or wheel builds.

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

pyproject.toml

@@ -71,10 +71,10 @@ 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"]

tools/rl_training_tool.py

@@ -52,10 +52,10 @@ 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"
 
 # Ensure logs directory exists
-LOGS_DIR.mkdir(exist_ok=True)
+LOGS_DIR.mkdir(parents=True, exist_ok=True)
 
 
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