The iwyu tool doesn't handle `config.h` files well, and these includes were
incorrectly removed, which breaks things on some platforms. Add them back to
most `src/*.c` files with `/* IWYU pragma: keep */` to make iwyu ignore them.
We skip `src/hashtable.c` because it is a standalone tool that is platform
independent.

Also add `/* IWYU pragma: keep */` to includes in `src/fileutil.c` that are
needed on some platforms but not others. This means we can remove the special
exemptions to skip this file for the `iwyu` and `iwyu-fix` targets in
`CMakeLists.txt`.