Move the inner part of overlap to `write_overlap`

Add `.cmake` files. The idea is to have a build system independent of
the environment. This allows us to have a customized version of
`ConfigureCompilerFlags.cmake` without the `-ffpe-trap=invalid`
option.

Move the inner part of procedure overlap to a separate procedure
`write_overlap`. overlap was too complex with 6 nested constructs. The
downside is that the initialization of `e` is repeated for every
non-successive overlap. If necessary, we can later add an
initialization on first entry (but an initialization at declaration is
not possible). `write_overlap` has some consistency: all the arguments
are `intent(in)`, scalars or small vectors of intrinsic type, and
`write_overlap` only writes to files. All modifications to flow are
done outside of `write_overlap`.