As has been said earlier, subsetter.jar is not a runnable jar. It is a library for use by other code. To make it work as a command line tool a piece of driver code to parse the command line and then call the library correctly will need to be written.
Also, sfntly doesn't currently have any specific support for the Graphite font tables. The Graphite specific tables are for layout (equivalent to the OpenType advanced layout tables - GSUB, GPOS, GDEF). sfntly won't mangle them but it can't read or edit them except at the most basic byte level. You could subset the font, if you wrote the code for it, but you would only be able to remove the glyphs which are likely in TrueType outline format. You wouldn't be able to subset the Graphite layout tables. Because of that you would also have to make sure to not renumber the glyphs since that would invalidate the Graphite tables.
There's currently no plans for supporting the Graphite tables though I would be happy to have somebody take that work up.
Stuart