More muddle improvements

To wit:

• visdep (in the sandbox) now uses 'xdot' to display, not 'xdot.py'. This means that on apt-get based systems, sudo apt-get install xdot should suffice to install the dependencies needed for visdep to work.
• The output of CPIO file generation is tidied up and made easier to understand (although still terribly verbose), and the irritating (at least to me) warnings have been fixed (this was a bug in applying instructions, in fact).
• muddle status will now detect if a git checkout is behind the remote repository, without needing a git fetch, and also reports the checkouts that need attention at the end of its output. See muddle help status.
• A long-standing bug has been fixed in cleaning deployments - this makes packages depending on deployments (which Richard introduced a while ago) work that bit better.