Fix parallel make builds

[rem1776]

Description
fixes for parallel make's with autotools (make -j). Also cleans up any targets pointing to include files since they aren't needed. draft for now since this will need to be updated for the diag_manager updates.

Fixes # (issue)

How Has This Been Tested?
make -j on the amd box.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• New check tests, if applicable, are included
• make distcheck passes