[flang] Fix -intrinsic-module-directory in flang script

The flang wrapper script that was created as bin/flang in an in-tree
build did not have a correct -intrinsic-module-directory option.
It was correct for out-of-tree builds and for both kinds of installs.

The fix is to pick the correct directory based on what exists.

The script is no longer configured by cmake (just copied) so that
mechanism can be deleted from the cmake file.

Differential Revision: https://reviews.llvm.org/D93496