Fix some issues reported by 'make depcheck doccheck'

Fix some issues reported by 'make depcheck doccheck'

Fix some minor documentation issues and make swapcoords.h not installed,
since that is internal mdrun functionality.

There is a dependency issue in update.h including a non-installed
random/random.h, but this is planned to go away when the stateful RNG is
replaced in mdrun, so left it there for now.  User code probably doesn't
have much use for including update.h, anyways.

Change-Id: I491697f8528d9dd5da299f366ccccf7eecb46f8a