Remove deprecated config APIs.

[vyasr]

Description

This PR deletes config APIs that are deprecated.

Motivation and Context

Resolves #789. The outstanding question is what to do about the Config class and whether it needs to remain public.

Checklist:

• I am familiar with the Contributing Guidelines.
• I agree with the terms of the Contributor Agreement.
• My name is on the list of contributors.
• The changes introduced by this pull request are covered by existing or newly introduced tests.
• The package documentation and framework documentation in signac-docs are up to date with these changes.
• I have updated the changelog and added any related issue and pull request numbers for future reference.

[codecov]

Codecov Report

Merging #847 (88edae6) into master (db2b9fa) will decrease coverage by 0.70%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #847      +/-   ##
==========================================
- Coverage   85.75%   85.04%   -0.71%     
==========================================
  Files          51       51              
  Lines        4683     4675       -8     
  Branches      923      923              
==========================================
- Hits         4016     3976      -40     
- Misses        480      519      +39     
+ Partials      187      180       -7     

Impacted Files	Coverage Δ
signac/common/config.py	89.23% <ø> (+1.55%)	⬆️
signac/common/deprecation/__init__.py	0.00% <0.00%> (-37.78%)	⬇️

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[bdice]

I'll take a stab at the Config object in a separate PR. There are a few awkward bits to refactor there.