Clean up and refactoring ProcessFrameworkReferences

[wli3]

#11824

There are some clean up need to make for above PR. ProcessFrameworkReferences need to have more unit test. And the methods in ProcessFrameworkReferences is too long.

[sfoslund]

#12199 fixes a bug from the original PR and cleans up comments. Leaving this issue open to track refactoring the task as a whole, which is long and convoluted.