Properly setting sampling time for altitude PID with LiDAR. Fixed HW impl tests for lidar_t changes.

2. Switched to level 5 IMU filter
3. logging setpoints
4. Logging for up to 5 minutes
5. Also accounting for time spent during logging when calculating LOOP_TIME
6. Logging during manual mode now, too.

Fixed bug with logging. Was accidentally writing rows by 4 rather than by 1, and would write beyond the limits.
Also properly initializing the initial value of the hw_unix_timer so Valgrind doesn't complain.

This reverts commit 52bea9cd.

char arrays are still statically allocated, but will be truncated if trying to print more to them than space available, rather than just writing to random memory.

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

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

- removed every use of the "subtype" term
- made the "type" term 16 bits
- made sure that every reference to a message type is 16 bits and used correctly
- simplified commands enum names
- implemented setcontrol callback function that switch on the controller and P, I, D, setpoint value to be set and then set them
- partly implemented getcontrol callback function
- NOTE: setpoint is a double. this causes some problems..
- TODO: add setpoints for rate controllers
- TODO: figure out what message ID I should send back when I get a getpid command

- Added a comment saying that we may not need the ID parameter on the MessageType Struct anymore.
- Removed calls of the nature: "MessageTypes[TYPE_ID].ID" and replaced them with "TYPE_ID" because it is the same thing..
- Added function comments in callbacks.c
- Simplified the callbacks.c by having a more generic setval, getval, respval callback function instead of a billion of them for each PID value.

there is now no such thing as a message sub type. There is only a message type.
this simplifies the commands struct greatly.
the commands.c file was aprox 1400 lines and now it is about 150...

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.