Improve file copy error handling and post-copy verification in copy_file_repository

[alexskr]

Improve file copy error handling and post-copy verification in copy_file_repository

• Replace shallow raise that discarded original exception type and backtrace with raise using e.class, custom message, and e.backtrace
• Move File.exist? check outside of begin-rescue to avoid catching assertion errors unrelated to mkdir, chmod, or copy
• Raise IOError for missing post-copy file to clarify semantics

follow up to #240

[codecov]

Codecov Report

Attention: Patch coverage is 60.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 80.39%. Comparing base (867f9bc) to head (29171a0).
Report is 44 commits behind head on develop.

Files with missing lines	Patch %	Lines
...tologies_linked_data/models/ontology_submission.rb	60.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #243      +/-   ##
===========================================
+ Coverage    79.89%   80.39%   +0.49%     
===========================================
  Files           75       75              
  Lines         5511     6008     +497     
===========================================
+ Hits          4403     4830     +427     
- Misses        1108     1178      +70     

Flag	Coverage Δ
unittests	80.39% <60.00%> (+0.49%)	⬆️

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