Update documentation around use of source classes

[paulromano]

Description

I noticed that our documentation still mentions openmc.Source in quite a few places which needs to be updated to openmc.IndependentSource after #2524. There were also some mentions of CustomSource, which generally we prefer to be called CompiledSource now.

Checklist

• I have performed a self-review of my own code
• I have run clang-format on any C++ source files (if applicable)
• I have followed the style guidelines for Python source files (if applicable)
• I have made corresponding changes to the documentation (if applicable)
• I have added tests that prove my fix is effective or that my feature works (if applicable)

[shimwell]

Changes look good on git and on readthedocs. Thanks for also removing Nuclide, Element
and Macroscopic.

As these are doc changes and not complicated I've enabled the auto merge once the tests pass