fixup! Started porting MicroManager and plugins to commons math 3.

Signed-off-by: Luke Stuyvenberg <stuyvenberg@wisc.edu>
chageme: fixup a commit...

Had to push. This commit must be ammended in the following ways:

All files changed here that were also changed in 090e75b7 should be added
in a commit fixup-ing that one. Any stragglers should fixup whichever
commit they were introduced in.

Signed-off-by: Luke Stuyvenberg <stuyvenberg@wisc.edu>