Remove public API of indexing module.

[bdice]

Description

This PR removes a large portion of the public API of the indexing module. It appears the only internal use of the indexing APIs may be the SignacProjectCrawler (now a private class) in Project.index(). We may also choose to make Project.index() private, but I think I would wait for a subsequent PR instead of expanding the scope of this PR.

This depends on #574 and #576.

To-do:

• Update and remove outdated tests / make CI pass.
• Update setup.cfg to remove exclusions for pydocstyle and pytest deprecation warnings for the indexing module.

For tasks to be accomplished in subsequent PRs, see issue #588.

Motivation and Context

Part of signac 2.0 API cleanup.

Types of Changes

• Documentation update
• Bug fix
• New feature
• Breaking change¹

¹The change breaks (or has the potential to break) existing functionality.

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.
• My code follows the code style guideline of this project.
• The changes introduced by this pull request are covered by existing or newly introduced tests.

If necessary:

• I have updated the API documentation as part of the package doc-strings.
• I have created a separate pull request to update the framework documentation on signac-docs and linked it here.
• I have updated the changelog and added all related issue and pull request numbers for future reference (if applicable). See example below.

[codecov]

Codecov Report

Merging #580 (47bcef4) into next (6d9568e) will increase coverage by 0.98%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             next     #580      +/-   ##
==========================================
+ Coverage   82.41%   83.40%   +0.98%     
==========================================
  Files          54       54              
  Lines        5845     5597     -248     
  Branches     1097     1033      -64     
==========================================
- Hits         4817     4668     -149     
+ Misses        785      696      -89     
+ Partials      243      233      -10     

Impacted Files	Coverage Δ
signac/__init__.py	100.00% <ø> (ø)
signac/contrib/__init__.py	100.00% <ø> (ø)
signac/__main__.py	75.17% <100.00%> (+0.45%)	⬆️
signac/contrib/indexing.py	83.51% <100.00%> (+13.25%)	⬆️
signac/contrib/project.py	85.91% <100.00%> (ø)
signac/contrib/collection.py	83.82% <0.00%> (-0.20%)	⬇️

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