use files instead of pathlist
add all command help, rev up to bumblebee, simplify JGit help
add MATLABProgressMonitor

* java and jar file to display clone progress for MATLAB on PC, which
 doesn't display \r
* add constant PROGRESSMONITOR =
	 org.eclipse.jgit.lib.MATLABProgressMonitor
* change pathlist to files for add signature
* add branch signature
* clone signature needs uri, which is required input arg
* add pmjar and checks for pmjar in @JGit/ and also in class path
* refactor search for jgitjar and pmjar so that both can be search in
 single pass of classpath
* add some missing semicolons, even on Java commands, suppress output
* MATLABProgressMonitor, add numChar member, and loop over adding
 backspaces, \b, except for endtask, then add newline, also change from
 System.err to System.out
* add clone