Documentation Update and Changes for v2 release

[pavlis]

Changes in this branch are completely limited to the docs directory. The changes are, however, extensive.

1. There are changes to most if not all user manual source pages. Some are just wording changes, but there are also a lot of changes attempting to make the manual clearer.
2. There are a number of new figures.
3. There are significant changes that are not in sync with the current master. I have added text in a number of places related to some new features I have implemented in Database and distributed functions that are being implemented in a second branch (cleanup_database) that I believe we are planning to tag as our 2.0 release when we are done testing the extensive changes there.

Because of item 3 this branch should NOT be merged until the related changes in the cleanup_database branch are merged. Otherwise our online documentation will be out of sync with the code base.

I also have a few more FAQ pages I want to finish writing that have not yet been pushed. I'm starting this pull request now so fellow development team members can comment and edit out any typos and confusing/inaccurate statements. @wangyinz , could you, in particular, run this through sphynx to check for any glaring format errors? I have not been able to get sphynx to run on this laptop that I've been using for working on these documentation pages.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 55.24%. Comparing base (5ec8d99) to head (0e1cb5a).
Report is 38 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #459      +/-   ##
==========================================
+ Coverage   53.59%   55.24%   +1.65%     
==========================================
  Files         144      144              
  Lines       22364    22560     +196     
==========================================
+ Hits        11986    12464     +478     
+ Misses      10378    10096     -282     

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[Aristoeu]

I built the docs locally and found some display issues in the browser. I submitted a commit to fix the format issues.

[pavlis]

I've gone through this as much I can locally. I've gotten rid of all the errors sphynx running in with the dev container detects that i think are correct. There are some residual errors I think are related to doxygen documents that are not being created with the make operation I am running.

It would be really good to get this installed. This update to the documentation is released we should soon do our v2.0 release.

WARNING: this branch should ONLY change files in the docs directory. It was forked from master months ago and there could be merge issues from that.

[pavlis]

I see the test are failing. Case in point that the merge needs to be done with care.