Update how xml_writer derive scaling factors

[daico007]

PR Summary:

Currently in the xml_writer is indirectly inferring the LJ-14 scaling and QQ-14 scaling from the structure.adjusts. However, since now we populate and store the combining rule in structure.defaults (if that structure is typed and parameterized with foyer), it makes more sense refer that directly from there.

PR Checklist

---

• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[codecov]

Codecov Report

Merging #518 (31a4edd) into main (24c61b9) will decrease coverage by 0.88%.
The diff coverage is 100.00%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #518      +/-   ##
==========================================
- Coverage   70.11%   69.23%   -0.89%     
==========================================
  Files          16       16              
  Lines        1673     1677       +4     
==========================================
- Hits         1173     1161      -12     
- Misses        500      516      +16     

[bc118]

LGTM

It changes one of the dihedral parameter ordering in MoSDeF-GOMC's test cases. I am not sure that this is in this PRs changes, but it happens (maybe another PR outside this one after the last conda package version update). Otherwise seems to work fine.