Merge main and address PR #267 review feedback

- Resolve merge conflicts (keep orchestration layer, discard old inline logic)
- Fix docstring paths in generate_bids_tools.py (#1)
- Remove redundant extension=Extension.NII_GZ in longitudinal export (#5)
- Clarify verbose docstring in RunnerConfig (#6)

Author: nx10

scripts/generate_bids_tools.py

@@ -5,8 +5,8 @@
 """Generate BIDS schema constants, utilities, and tests for the rbc package.
 
 Reads the BIDS schema via bidsschematools and generates:
-  - src/rbc/core/bids/_schema.py   (constants + build/parse functions)
-  - tests/unit/test_bids.py (unit tests)
+  - src/rbc/bids/_schema.py   (constants + build/parse functions)
+  - tests/unit/bids/test_bids.py (unit tests)
 
 Run with:
     uv run scripts/generate_bids_tools.py

src/rbc/bids/longitudinal.py

@@ -4,7 +4,7 @@
 
 from typing import TYPE_CHECKING
 
-from rbc.bids import Extension, Suffix
+from rbc.bids import Suffix
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -157,7 +157,6 @@ def export_longitudinal_func(fex: Bids, outputs: FunctionalLongOutputs) -> None:
         outputs.forward_xfm,
         suffix="xfm",
         desc="composite",
-        extension=Extension.NII_GZ,
         extra={"from": "bold", "to": "longitudinal", "mode": "image"},
     )
     if outputs.bold_mask:

src/rbc/orchestration/__init__.py

@@ -46,7 +46,7 @@ class RunnerConfig:
 
     Attributes:
         runner: Execution backend (local, docker, podman, singularity).
-        verbose: Verbosity level.
+        verbose: Enable verbose output (progress bars, info logging).
         tmp_dir: Temporary directory for intermediate files.
     """