fix(htsget): overlap behavior for enclosed regions

[cmdoret]

Context

modos.genomics.region.Region.overlap() does not report overlaps for completely enclosed regions.
This is illustrated by the failing test added in e0d33dc

________________________ test_overlap_contained_region _________________________

    def test_overlap_contained_region():
        """A region fully contained in another overlaps it, both ways."""
        outer = Region(chrom="chr1", start=10, end=100)
        inner = Region(chrom="chr1", start=40, end=50)
        assert outer.overlaps(inner)
>       assert inner.overlaps(outer)
E       AssertionError: assert False
E        +  where False = overlaps(Region(chrom='chr1', start=10, end=100))
E        +    where overlaps = Region(chrom='chr1', start=40, end=50).overlaps

Changes

• overlap logic now correctly identifies contained intervals as overlaps.

[Copilot]

Pull request overview

Fixes two correctness issues: genomic interval overlap detection for fully enclosed regions (used by htsget filtering), and removal of elements from multivalued link attributes in the MODO archive.

Changes:

• Update Region.overlaps() to use proper half-open interval overlap logic (handles enclosed regions correctly).
• Fix MODO.remove_element() to correctly remove an element from list-valued links without writing None back to Zarr attrs.
• Add/adjust tests to cover contained-region overlap and link-list removal behavior (including preserving other links).

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/test_region.py	Adds regression test for overlaps when one region fully contains another.
tests/test_cli_local.py	Updates CLI test expectation for link-list removal result ([] instead of None).
tests/test_api_local.py	Adds API regression test ensuring removing one link preserves remaining links.
src/modos/genomics/region.py	Fixes overlap logic using half-open interval semantics (a.start < b.end && b.start < a.end).
src/modos/api.py	Fixes list-valued link removal to avoid list.remove() return-value bug.

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[almutlue]

Looks good!