Removes stubs files for v1.0

[IAlibay]

Partly addresses #2443 comment

Changes made in this Pull Request:
Removed:

• core/distances.py
• core/log.py
• core/parallel.py
• core/qcprot.py
• core/transformations.py
• core/units.py
• core/utils.py
• core/KDTree.py
• analysis/x3dna.py

To add:

• test_deprecated.py
• tests in test_transformation.py

PR Checklist

• Tests? (as far as I am aware no new tests are needed here)
• Docs? (added in utils/test_transformation.py)
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #2481 into develop will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #2481   +/-   ##
========================================
  Coverage    90.25%   90.25%           
========================================
  Files          169      169           
  Lines        23219    23219           
  Branches      3009     3009           
========================================
  Hits         20956    20956           
  Misses        1656     1656           
  Partials       607      607

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