The command and shuffleboard integration tests were removed because
their unit tests counterparts already provide adequate coverage. Java
already removed these.
A lot of these are breaking changes. frc::Timer was replaced with the
contents of frc2::Timer. The others were in-place argument changes or
removing deprecated non-unit overloads.
The old headers were moved into folders because doing so avoids polluting
the system include directories.
Folder names were also normalized to lowercase.
