Add encoder measurements via thread. This should help with linear encoder accuracy and SW interrupt accuracy. Coupled with changes from the interrupt enhancement branch, the limit behavior should be much improved.

Added a parameter to allow user to set their own SW limit-reached routine (default behavior is still the same). This should also help prevent over-excursion in the swingup test.
Slightly modified swingup test to use new SW limit-reached routine. This should help prevent the system from over-excursing when the soft limits of the program are reached. Theoretically the program shouldn't be able to hit the HW limits anymore.

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