Issue #1283738 by halcyonCorsair, cweagans: Allow other commands to add or alter the directories to be created.

This reverts commit 1120019c.

This reverts commit 65b25496.

this is important for SSL certificates which may be symlink to files
that are unreadable by Aegir (which is fine, as Apache can read them
because it starts as root).

I assume the impact on other uses of ->exists() will be negligible.

See #2046249.

Conflicts:
	provision.file.inc

This reverts commit 7358d11d.

Issue #1647830 by sambonner: Fix Incorrect ownership of directories under sites/example.com/private/files/.

first, the symlink was just not created because a variable wasn't
passed properly.

second, permissions were fixed on the directories only on installs,
which is error-prone: we should fix them all the time.

This allows the front-end to be aware of site-specific packages.
We'll then need to ignore them for platform comparison purposes, but
this should otherwise be safe.

This reverts commit bff83f53.