[ELF][test] Change references of %T to %t.dir

Test files in the same directory share the same %T.  %T is easy to
misuse and cause race conditions (when running concurrently) so it has
been deprecated since D48842 (see docs/CommandGuide/lit.rst).

While here, add `rm -rf %t.dir` so that tests cannot depend on old files lying around.

Reviewed By: jhenderson, ruiu

Differential Revision: https://reviews.llvm.org/D69572