fix(xenium_patch): restore --min-transcripts-per-cell in stitch script

[an-altosian]

What & why

XENIUM_PATCH_STITCH fails with:

xenium_patch_stitch_transcripts.py: error: unrecognized arguments: --min-transcripts-per-cell 50

Reproduced with --mode coordinate --method baysor (routes through
BAYSOR_RUN_TRANSCRIPTS_PARQUET → XENIUM_PATCH_STITCH).

Root cause: when stitch_transcripts.py was split into
xenium_patch_stitch_transcripts.py + xenium_patch_stitch_postprocess.py, the
--min-transcripts-per-cell argument and its small-cell filter were dropped from
the transcripts script — but conf/modules.config still injects the flag
(baysor_tiling_min_transcripts_per_cell, default 50). ext.args is opaque
string concatenation, so the mismatch only surfaces at runtime as an argparse
error.

This is not a container issue: pipeline bin/ scripts are staged by Nextflow
and run with the container's interpreter; sopa imports and runs fine in the
sopa_procps-ng_pyarrow image. An argparse "unrecognized arguments" message can
only come from the script's own argument definitions.

Changes

• Restore the --min-transcripts-per-cell argument and the post-stitch
  small-cell filter (reassign sub-threshold cells' transcripts to noise, drop
  their polygons) in bin/xenium_patch_stitch_transcripts.py. The newer
  _ensure_polygon refactor in that script is preserved.
• Repoint tests/test_xenium_patch/test_stitch_transcripts.py from the deleted
  modules/.../resources/usr/bin/ path to bin/ — it had been broken since the
  PR refactor(modules): convert all 19 module-level bin scripts to Nextflow templates nf-core/spatialaxe#154 refactor (masked by the module's stub block in CI).
• Add TestMinTranscriptsFilter: filter behaviour, a no-op control, and a
  subprocess CLI test that reproduces the exact failing invocation.
• Remove the orphan bin/stitch_transcripts.py (superseded, unused).

Testing

Ran inside the module's own container
community.wave.seqera.io/library/sopa_procps-ng_pyarrow:c9ce8cd2ede79d72:

15 passed in 3.89s

including the CLI test invoking the script with --min-transcripts-per-cell 50
(asserts no "unrecognized arguments", exit 0).