Allowing throttle to be down during autonomous.

Refactored velocity configuration in control algorithm. Made default PID constants the good ones. Corrected the velocity sign. There might be sign errors with the velocity PID constants.

PID nodes have a second parameter, called alpha that is (1 - N*T_s), where N is equivalent to Simulink N.
If alpha == 0, no filtering (default).
Also fixed issue where sampling time for autonomous was 0 for the first iteration.

Increased max pitch/roll angle and maximum output from rate controllers. removed comment from log file being dumped.

Allowed values to be set before Gear switch. Re-enabled x/y controllers and made throttle manual for autonomous mode.

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Shuffled around #include dependencies to allow the control algorithm diagram to be generated without copying code out of control_algorithm.c

Revert "Revert "Merge branch 'master' of git.ece.iastate.edu:danc/MicroCART_17-18 into batch-setpid""

This reverts commit 16eb40ff.

Yes, this is a revert-revert. Brendan broke all the things.

This reverts commit c9fdacfd

- added some comments in commands.c/h about usage of the file
- added a MAX_CONTROLLER_ID and MAX_CONTROL_VAL_ID to the enums in commands.h
- implemented cb_set_control in callbacks.c to work with the new parameter struct
- changes the parameter_struct to now contain an array of pid_controllers instead of a bunch of random PID_t members
- the new parameter_struct array can now be accessed by controller ID as defined in commands.h

Integrated changes from comm_dev (interrupt-driven UART) and updated code to work well with the new style. Compiles, but have not tested running yet.

Autonomous mode is throttle-only. Fixed bug in stringBuilder that would fail to resize byte data. Packets that don't have a matching checksum are thrown away now.