Handle empty GFF and alignment files gracefully

[Copilot]

FlexiDot crashes with ValueError: number sections must be larger than 0 when processing empty GFF files. The error occurs in matplotlib's legend creation when ncol evaluates to 0 from an empty colors list.

Changes

• GFF parsing: Skip legend generation when no features are parsed. Added guard in legend_figure() to return early if colors list is empty.
• Alignment parsing: Added warnings for empty BLAST6/PAF files (already returned empty lists correctly, now user-visible).
• Logging: Warning messages indicate when plots are generated without annotations/overlays.

Example

# Previously crashed
feat_dict = read_gffs('empty.gff3')  
# ValueError: number sections must be larger than 0

# Now logs warning and returns empty dict
feat_dict = read_gffs('empty.gff3')
# WARNING: No annotation records found in GFF file(s). Plot will be generated without annotations.
# Returns: {}

Useful for automated pipelines where some annotation/alignment files may be empty or filtered out.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Error if --gff is empty</issue_title>
<issue_description>Throws error if no annotation records in GFF3 input.

Add checks for empty gff or alignment files and handle gracefully.
Log warning if no annotations of alignments are imported.
If sequences are available, generate empty plot with no annotations or alignments.

  ax[1].legend(
Traceback (most recent call last):
  File "/Users/adamtaranto/.condaenvs/flexidot/bin/flexidot", line 8, in <module>
    sys.exit(main())
             ~~~~^^
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/flexidot/app.py", line 284, in main
    list_of_png_names = polydotplot(
        seq_list,
    ...<27 lines>...
        line_width=line_width,
    )
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/flexidot/plotting.py", line 1070, in polydotplot
    feat_dict = read_gffs(
        gff_files,
    ...<3 lines>...
        filetype=filetype,
    )
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/flexidot/utils/file_handling.py", line 350, in read_gffs
    legend_figure(
    ~~~~~~~~~~~~~^
        colors=colors,
        ^^^^^^^^^^^^^^
    ...<6 lines>...
        filetype=filetype,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/flexidot/utils/file_handling.py", line 761, in legend_figure
    ax[1].legend(
    ~~~~~~~~~~~~^
        ncol=((len(colors) - 1) // max_legend_length_row) + 1, framealpha=1
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )  # vertical legend
    ^
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 337, in legend
    self.legend_ = mlegend.Legend(self, handles, labels, **kwargs)
                   ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/matplotlib/legend.py", line 550, in __init__
    self._init_legend_box(handles, labels, markerfirst)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/matplotlib/legend.py", line 907, in _init_legend_box
    len, np.array_split(handles_and_labels, self._ncols)):
         ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/adamtaranto/.condaenvs/flexidot/lib/python3.13/site-packages/numpy/lib/_shape_base_impl.py", line 782, in array_split
    raise ValueError('number sections must be larger than 0.') from None
ValueError: number sections must be larger than 0.
```</issue_description>

## Comments on the Issue (you are @copilot in this section)

<comments>
</comments>

• Fixes Error if --gff is empty #27

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