Refactor ip_2d_feature_extraction tool (fix 3-D + add Zarr support)

[kostrykin]

The tool hasn't been updated for a very long time and the code needs some serious rewriting to update to employ giatools.ToolBaseplate in order to also support 3-D images, Zarrs, and so on.

xref FAIR-imaging/galaxy-image-community#27 FAIR-imaging/galaxy-image-community#64

The convexity feature is removed. There already is solidity for quantification of convexity. The previous implementation rather looks like the "compactness" of the object, but not exactly.

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To be done:

• Update to giatools 0.7.2 when it is available
• Add test case for multi-channel Zarr
• Verify new help section in planemo serve

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[kostrykin]

Blocked by BMCV/giatools#45

[Copilot]

Pull request overview

This PR refactors the ip_2d_feature_extraction tool to modernize its implementation by adopting giatools.ToolBaseplate, enabling support for 3-D images and Zarr format. The refactor removes the deprecated convexity feature (replaced by existing solidity) and updates the tool to current best practices.

Key changes:

• Migration to giatools.ToolBaseplate architecture for improved image handling
• Added Zarr format support with proper validation
• Enhanced 3-D image processing capabilities with appropriate feature handling

Reviewed changes

Copilot reviewed 49 out of 78 changed files in this pull request and generated 3 comments.

File	Description
tools/2d_feature_extraction/2d_feature_extraction.xml	Updated tool definition with new parameters, Zarr support, comprehensive test cases, and improved help documentation
tools/2d_feature_extraction/2d_feature_extraction.py	Complete rewrite using giatools.ToolBaseplate, added 3-D surface computation, Dask array handling, and streamlined feature extraction logic
tools/2d_feature_extraction/validators.xml	Added symbolic link to shared validators
tools/2d_feature_extraction/test-data/*	Added extensive test data including Zarr format examples and expected outputs for isolated feature validation

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