better handle symlinks in Directories

[mr-c]

Fixes #1461

[codecov]

Codecov Report

Merging #1462 (12f7831) into main (0e89055) will decrease coverage by 0.04%.
The diff coverage is 66.66%.

@@            Coverage Diff             @@
##             main    #1462      +/-   ##
==========================================
- Coverage   65.76%   65.71%   -0.05%     
==========================================
  Files          89       89              
  Lines       15628    15638      +10     
  Branches     3933     3937       +4     
==========================================
  Hits        10277    10277              
- Misses       4260     4269       +9     
- Partials     1091     1092       +1     

Impacted Files	Coverage Δ
cwltool/process.py	83.90% <66.66%> (-0.35%)	⬇️
job.py	61.41% <0.00%> (-0.81%)	⬇️
process.py	68.88% <0.00%> (-0.23%)	⬇️

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