test: reorganize test structure and add missing unit tests

Reorganize flat tests/ directory to mirror source code structure
(tools/, gateway/, hermes_cli/, integration/). Add 11 new test files
covering previously untested modules: registry, patch_parser,
fuzzy_match, todo_tool, approval, file_tools, gateway session/config/
delivery, and hermes_cli config/models. Total: 147 unit tests passing,
9 integration tests gated behind pytest marker.

pyproject.toml

@@ -66,3 +66,10 @@ py-modules = ["run_agent", "model_tools", "toolsets", "batch_runner", "trajector
 
 [tool.setuptools.packages.find]
 include = ["tools", "hermes_cli", "gateway", "cron"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+markers = [
+    "integration: marks tests requiring external services (API keys, Modal, etc.)",
+]
+addopts = "-m 'not integration'"