Most of the changes are scripted replacement of include paths.
Exceptions:
- #includes in the moved file were cleaned up slightly, and include
guards adjusted.
- Places where it was included as "gromacs/legacyheaders/vec.h" were
handled manually and the include order adjusted.
- Removal of unnecessary #include "vec.h" from update.h revealed some
transitive dependencies that were fixed. Some associated include
order cleanup in these files.
- Removed some duplicate includes.
- Remove dependency from linearalgebra/matrix.c to vec.h (only needed
for a single sqr()) to avoid a cyclic math <-> linearalgebra
dependency.
Part of #1415.
Change-Id: I7ece6eafa22139215510148807c5979f8950a885