Build the src contents into a jar which will then contain class files and our manifest.  Jar typically code.jar

Then sign the jar with
 jarsigner -keystore ../cert/key.store -storepass foobar code.jar foo

as per: http://introcs.cs.princeton.edu/85application/jar/sign.html

then you can run it:
java -javaagent:XXX -classpath code.jar foo.bar.Foo