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>

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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