In Jsmooth , is classpath for the .jar? Don't say it matters and can be left blank for the jar (implicit location), current directory maybe left blank better than a dot, if anything probably .\ (with a backslash for windows - means current directory).
for main class you can probably just say "PercentIdentity" as the classpath and paths get searched so if there is only one there in the .jar it will be chosen.
about implying where the jar is it is probably given a blank notation or in some configuration documents it is given the notation . , dot is usually used for web sever purposes unless it is part of . in windows or ./ in unix meaning "this directory its in".
If you wish to learn a small quantity of C/C++ you can get away with a short one liner using execv() function and an array or execlp() function and a list, However you will need to learn a large quantity of C/C++ to use the **args pointer array to pass command line parameters.