Change kit for EAP to place modules under 'modules' directory rather than 'modules/system/layers/base'

MODE-1849 changed the kit to place the modules under 'modules/system/layers/base', which was a new capability added to AS7.2/EAP6.1. (See MODE-1849 for details.)

However, placing modules directly under 'modules' is supposed to still work as before. I think we should continue to use that until the discussion about how the different directory structure and layering will work.