Fix set_files when data_dir is used

[alejoe91]

This PR fixes a bug when running set_files with a data_dir, since downstream steps expect always a list of filenames

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 0.00%. Comparing base (3705cea) to head (1ea427a).
Report is 59 commits behind head on main.

Files with missing lines	Patch %	Lines
kilosort/run_kilosort.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@          Coverage Diff           @@
##            main    #933    +/-   ##
======================================
  Coverage   0.00%   0.00%            
======================================
  Files         33      34     +1     
  Lines       5640    5795   +155     
======================================
- Misses      5640    5795   +155     

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