Bluetooth: controller: Cleanup makefiles

Cleanup controller's root makefile and add folder level
makefile to have better control over dependencies.

Also explicitly include folder paths in c files to clearly
depict the dependencies.

Change-id: Iac7b3a86eff11082111049ba48559c74f6c4d3fb
Signed-off-by: Vinayak Chettimada <vinayak.kariappa.chettimada@nordicsemi.no>