Revert "disabled tagdex, tempdir removal to fix test interference"

This reverts commit 78e83042231364644670920383e2211a46c0fe10.
ensured root_dir is reset and load_app is passed the instance directory

the first time around, `root_dir` is set to the absolute path of that
instance
ensured original CWD is restored

this should not be necessary, but need to eliminate variables for now
added debugging statements to trace execution path