add parseDiff

* fix bug in download error in validate java class path in @JGit/JGit.m,
 error message must be a string, but status is an int
* slowly updated all references from kernel.org -> git-scm.com
* add help comments in JGit.diff that paths are actually path filters, and
 as such must be relative to GITDIR (subfolder path must be specified)
 and must use "/" to delimit folders, not windows "\" no!
* add links to JGit path filter, tree filter and tree parser classes
* add a hyphen between refs in diff filename
* fix bug in JGit.diff, showNameAndStatusOnly should only ouput list to
 terminal, no stream output!
* add diff, difftool and fetch to jgit.m
* update filterOpts to output paths as 2nd output, not have pop input and
 separate refs from paths if 2nd output requested
* update jgit_help.m, add aliases for branch, checkout and status, add
 diff & difftool
* update parseCheckout to use filterOpts with 2nd arg out instead of pop
 arg in set false.
* clean up whitespace, end all functions "end" and newline