dependency on diffutils library
updated goal terms patch with comments and PP info
a manager for Isabelle patches

The manager contains references to available patches, as well as checks whether they are applied. If there are unpatched/invalid files, allows patching them.
log/error methods for the plugin
extension point to provide user interaction handler (from pp.isabelle.core)
a patch handler (organises checks and patching)

Patch status is checked only once during PP run. After patching, PP is paused until Isabelle is restarted.
implementation of patch handler that provides user interaction
better message
Isabelle patch to trace fact terms (assumptions, etc)
Merge branch 'isabelle-patch'