[flang] Separate temporary and user-specified object files

This patch updates the `flang` bash scripts to differentiate between
object files provided by the user and intermediate object files
generated by the script. The latter are an "implementation detail" that
should not be visible to the end user (i.e. deleted before the scripts
exits). The former should be preserved.

Fixes https://github.com/flang-compiler/f18-llvm-project/issues/1348

Differential Revision: https://reviews.llvm.org/D116590