Set EXTRACT_ALL to no for doxygen document builds and resolve all WARN_IF_UNDOCUMENTED and WARN_NO_PARAMDOC warnings

[skliper]

Is your feature request related to a problem? Please describe.
The EXTRACT_ALL flag set to YES defeats the WARN_IF_UNDOCUMENTED and WARN_NO_PARAMDOC enabled errors

Describe the solution you'd like
Set EXTRACT_ALL to NO and explicitly document all elements for at minimum the usersguide documentation.

Describe alternatives you've considered
None

Additional context
None

Requester Info
Jacob Hageman - NASA/GSFC

EDIT - separated original issue, warning file name now in #1589

[skliper]

Note the warning file updates will require updating CI that checks those files.

[astrogeco]

Note the warning file updates will require updating CI that checks those files.

Which update?

[skliper]

Note the warning file updates will require updating CI that checks those files.

Which update?

If the warning file name is updated to be unique per document build (suggestion in 2. above).

Note really a requirement, so feel free to reject if you want.