Update: Restructure the project to make it easy to switch to or from stand alone...

Update: Restructure the project to make it easy to switch to or from stand alone builds, and other fixes.

Move the sources for the program to be under the program/controller directory.
This makes the structure more one to one with how it is installed.
This then makes a drop in place stand alone build easier.

Update the git ignore file:
- Add the FLL directory so that a drop in place stand alone build is unlikely to be accidentally added to this repository.
- Add the config.c and config.h to prevent accidental inclusion of local configuration source file and header file.

Fix incorrect dependencies, adding missing ones and removing non-existent ones.

Make GCC and CLang upper case in descriptions.