Make explicit paths optional in the output file

Currently, the XML paths file contains all of the full explicit paths. This is to simplify processing by systems which consume this information. However, it makes the output file much larger. The explicit paths could be made optional if there was a separate app that could either (a) insert the paths into a XML file without them, or (b) calculate the paths for an XML and append them to a text file.

Similarly, while the most straightforward way to do path diffs is using explicit lists of paths, it may be possible to calculate the diffs from the XML files without generating the explicit paths. That would be useful for cases where the XML fingerprint files are being used only for diffs, rather than for some other purpose.