Persist jcr/xml in hierarchy path structure.

https://www.pivotaltracker.com/s/projects/684825/stories/75644184
I've updated it to persist the jcr/xml as suggested: a structure like [basedir]/localhost/8080/rest/123.jcr.xml.
Many identifiers will be of the form "pid:55".
I suspect we only want to replace the ":" if it is associated with a port, not all colons.
However, we should appropriately encode the URI that is being converted to a directory path so that the converted characters are valid on the three filesystems: Mac, Windows, Linux