Changes from branch luki-mbi/pointer_rewrite (PR #80).
==> Builds:
clang debug: OK
clang release: OK
gcc debug: OK
gcc release: OK
pyrosetta: not tested
mpi: not tested
static: not tested
==> Tests with clang 3.5:
Unit tests: All pass
Integration tests: 2 cosmetic changes:
fold_and_dock
ThreadingInputter
==> Tests with gcc 4.8.2:
Unit tests: All pass
Integration tests: 69 changes
Many trajectory changes, mostly to swa*
Some cosmetic changes (as above)