[flang] Build intrinsic .mod files in include/flang

The build was putting .mod files for intrinsic modules in
tools/flang/include/flang but the install puts them in include/flang,
as does the out-of-tree build. This confused things for the driver.
This change makes the build consistent with the install and simplifies
the flang script accordingly.

Also, clean up the cmake commands for building the .mod files.

Differential Revision: https://reviews.llvm.org/D98522