Addresses #5739 and cleans up copy.py

The copy action_plugin is not easy to read. Part of this commit is taking that file, restructuring it, and adding comments. No functionality changed in how it interacts with the world.

The fix for #5739 ends up being the assumption that there is a cleanup 'rm -rf' that happens at the end of the copy loop. This was not the fact before and we made a bunch of tmp directories that we hoped would end up being cleaned up. Now we just use the tmp directory that the runner provides and cleanup inline if it is a single file to be coppied or after the loop if it is a recursive copy.

As a part of this we did end up having to change runner to provide a flag so that we could short the inline tmp directory removal. This flag defaults to True so it will not change the behavior of other modules that are being called.
Dug into the remaining FIXME and replaced with comments to document the expected behavior.
Merge pull request #5885 from risaacson/issue5739_4

Addresses #5739 and cleans up copy.py