UpdateAPI tool order of operations update

[glemieux]

Description:

This PR updates the order of operations to correct an issue with the variable additions need to come after updates. The issue is that ncfile is needs to be called prior to the selectvalues call in the add variable routine.

This also adds undefined as a usecase (as a temporary fix).

Collaborators:

Expectation of Answer Changes:

Checklist:

• My change requires a change to the documentation.
• I have updated the in-code documentation .AND. (the technical note .OR. the wiki) accordingly.
• I have read the CONTRIBUTING document.
• FATES PASS/FAIL regression tests were run
• If answers were expected to change, evaluation was performed and provided

Test Results:

CTSM (or) E3SM (specify which) test hash-tag:

CTSM (or) E3SM (specify which) baseline hash-tag:

FATES baseline hash-tag:

Test Output: