Used IWYU to partially clean up some includes

Used IWYU to partially clean up some includes

- Used trunk version
- Works well for C and simple C++ files
  - Does not yet work without manual reverting some changes for more complicated
     files e.g. options.cpp (see issues 105, 111, 135, and 138)
- IWYU doesn't check for conditional compiled code. I ran for
  pme.c and wallcycle.c with -DDEBUG_PME/_WCYCLE

Given that one needs to fix a few issues and have to check for #ifdefs it is
still manual work, but I think quite a bit faster and more complete than doing
it manually.

Change-Id: I7c5569693a4b84f481f0f7afd85f0f01c33295cf