fix: PDM removes override URL and some groups from deps in pdm.lock upon adding a new dependency.

[frostming]

Fixes #3446

Signed-off-by: Frost Ming me@frostming.com

Pull Request Checklist

• A news fragment is added in news/ describing what is new.
• Test cases added for changed code.

Describe what you have changed in this PR.

[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 85.57%. Comparing base (3938046) to head (2ac78da).
Report is 76 commits behind head on main.

Files with missing lines	Patch %	Lines
src/pdm/cli/actions.py	33.33%	2 Missing ⚠️
src/pdm/resolver/providers.py	50.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3454      +/-   ##
==========================================
- Coverage   85.57%   85.57%   -0.01%     
==========================================
  Files         112      112              
  Lines       11552    11557       +5     
  Branches     2535     2538       +3     
==========================================
+ Hits         9886     9890       +4     
  Misses       1136     1136              
- Partials      530      531       +1     

Flag	Coverage Δ
unittests	85.37% <75.00%> (-0.01%)	⬇️

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