Revert "better handle symlinks in Directories (#1462)"

[mr-c]

This reverts commit 23acadf.

The test is flaky

[codecov]

Codecov Report

Merging #1483 (ab2716e) into main (0358a41) will decrease coverage by 0.00%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1483      +/-   ##
==========================================
- Coverage   65.74%   65.73%   -0.01%     
==========================================
  Files          89       89              
  Lines       15638    15628      -10     
  Branches     3937     3933       -4     
==========================================
- Hits        10281    10273       -8     
+ Misses       4265     4264       -1     
+ Partials     1092     1091       -1     

Impacted Files	Coverage Δ
cwltool/process.py	84.24% <100.00%> (+0.34%)	⬆️
job.py	61.41% <0.00%> (-0.81%)	⬇️
process.py	69.11% <0.00%> (+0.22%)	⬆️

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