Fix dir.clonetree.

[scossu]

Fixes #461.

I noticed a few issues with dir.clonetree:

1. The base path for the destination is incorrect.
2. The function does not iterate through sub-folders to be cloned.
3. As a consequence of 2, files are also not processed and copied correctly.

This PR attempt to fix these issues.

NOTE the updated description of path2. I wasn't able to verify if this was the intended behavior, since I could not get the cloning to work in the right path and the description did not specify details.

[scossu]

Hi there. I have been using my branch with this fix for a few months with different scenarios now, but the automated tests in this PR won't pass. I can't trace back the /srv/app/.luarocks/lib/luarocks/rocks-5.4/pocket_archive/scm-1/templates/assets error message. Can someone take a look and help merge this into the mainline? Thanks.