Fix weekly linting issues and tests

[kostrykin]

This is a follow-up of #152.

Errors reported here: https://github.com/BMCV/galaxy-image-analysis/actions/runs/16406291782/job/46352869343

⚠️ I'm not bumping the tool versions here, because no new functionality is added, nor are runtime errors fixed.

Fixed linting issues

• .. WARNING (TestsCaseValidation): Test 1: failed to validate test parameters against inputs
  • tools/2d_feature_extraction/2d_feature_extraction.xml
  • tools/2d_simple_filter/filter.xml
  • tools/mahotas_features/mahotas_features.xml
  • tools/landmark_registration/landmark_registration.xml
  • tools/overlay_images/overlay_images.xml
  • tools/unzip/unzip.xml
• .. WARNING: No valid package requirement tags found to infer BioContainer from.
  Blocked by Only issue MESSAGE_WARN_NO_REQUIREMENTS if there are no containers galaxyproject/planemo#1558
  • tools/bioformats2raw/bf2raw.xml
  • tools/rfove/rfove.xml
  • tools/superdsm/superdsm.xml

Fixed testing issues

• tools/mahotas_features/mahotas_features.xml
  • tool_script.sh: line 9: mahotas-features.py: command not found
• tools/unzip/unzip.xml
  • Test 3: Output collection 'unzipped': expected to have 2 elements, but it had 0.
  • Test 4: Output collection 'unzipped': expected to have 4 elements, but it had 0.
    Moved to Fix support for files without extensions in unzip tool #155