reverting adding absolute_path

[JeffWigger]

Acknowledgment

• I acknowledge that this contribution will be available under the Apache 2 license.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Summary

Discussed reversion of the addition of absolute_path. Also as discussed, support for outputs with absolute paths will be readded later (Not in this PR) without the need to explicitly set the absolute_path option.
This reversion broke the test test_shell_cmd_outputspec_8d. I rewrote it such that it does not need an absolute path in the outputs.

Checklist

• All tests passing
• I have added tests to cover my changes
• I have updated documentation (if necessary)
• My code follows the code style of this project
  (we are using black: you can pip install pre-commit,
  run pre-commit install in the pydra directory
  and black will be run automatically with each commit)

[codecov]

Codecov Report

Merging #489 (6ddae3b) into master (07a8074) will decrease coverage by 0.06%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #489      +/-   ##
==========================================
- Coverage   83.00%   82.94%   -0.07%     
==========================================
  Files          20       20              
  Lines        4037     4033       -4     
  Branches     1117     1115       -2     
==========================================
- Hits         3351     3345       -6     
- Misses        491      492       +1     
- Partials      195      196       +1     

Flag	Coverage Δ
unittests	82.86% <100.00%> (-0.07%)	⬇️

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Impacted Files	Coverage Δ
pydra/engine/specs.py	88.13% <ø> (-0.12%)	⬇️
pydra/engine/helpers_file.py	79.49% <100.00%> (-0.64%)	⬇️

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