mdlib: clean up -Wunused-parameter warnings

Clean up (most) of unused params, nbnxn stuff still need cleanup
Also this commit removes some dead (unused) functions

Change-Id: I9aae68266f66a149565c3e5f6e06810db4de287b
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>