Reorganizing files in docs (2/2)

[isaacgsmith]

This is a follow-up to pull request #1371. Rearranges files in the docs folder to match the new structure of the documentation in pull request #1364.

Description

Major changes include:

• Changing the folder docs/running to docs/using.
• Moving the folders docs/models, docs/atomic, and docs/configuration into a new folder docs/using/components.
• Creating a folder docs/physics/old_physics (which includes contents of the "Old Physics" section).

Motivation and Context

Issue #1357 called for a a restructuring of the TARDIS documentation. Both the documentation and the file paths now reflect the structure that issue called for.

How Has This Been Tested?

I built the documentation locally, and saw no new errors. I checked the html pages this PR would affect, and they worked properly.

Screenshots (if appropriate):

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have assigned/requested two reviewers for this pull request.

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Codecov Report

Merging #1379 (9ffee87) into master (5236056) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1379   +/-   ##
=======================================
  Coverage   72.39%   72.39%           
=======================================
  Files          66       66           
  Lines        5097     5097           
=======================================
  Hits         3690     3690           
  Misses       1407     1407           

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[jaladh-singhal]

Excellent work @smithis7 - this reorganization was much required!

And it's good to see that you created old_physics dir and moved related files in it. 👏