Comments, refactoring, and cleanup

[kevinhikaruevans]

• [ ] Not sure if I should have a types.h or have these separated out differently
• [x] Need to decide on the cleanest way to handle +IPD commands
• [x] Add Doxygen comments to new functions
• [x] Move stuff to projects
• [ ] Measure the time for the ISR and the run_queue (or use the Tcf profiling)
• [ ] Update socket status during connect/disconnect
• [ ] Add ability to change the linkId for a request OR add way to automatically choose a free socket