Reorganize adapter file structure and simplify CMake files

[ChristopherHogan]

This work is in preparation for adding the VFD to the hermes/adapter folder, and in anticipation of having a base adapter layer that all adapters can share.

• Replaced all instances of include_directories with the preferred target_include_directories in CMake files.
• Removed empty directories.
• Added a missing install command for the mpiio adapter tests.
• Simplified CMake files by putting more commands in foreach loops.

[coveralls]

Coverage decreased (-0.3%) to 81.05% when pulling 3bc2a8c on chogan/adapter_reorg into 600c9a0 on master.