You shouldn’t need the .proto files at all in order to *use* the
messages from other applications; that’s what the generated language
source files are for. Java being what it is, you should just be able to
use the .class files from your .jar without including either the .proto
or .java files at all, just like you would use .class files in any
other .jar-based library you use in your system: arrange for the .jar
to be in your classpath, like you would do with any other library .jar,
and then consume the appropriate classes in your own code, like you
would with any other library.
-- 
Christopher Head