Fix file extension pedanticisms that clang++ hates

Signed-off-by: Garrett Cooper <yanegomi@gmail.com>
Revert "Use the share/ copy of atf-run.hooks now that 0.17 is in"

This copy still has issues...

This reverts commit 35ca4b2c60b6123c67fc0e6f7c1cc51da89bb2b9.