Modifying a file inside a jar

You can use Vim:

vim my.jar

Vim is able to edit compressed text files, given you have unzip in your environment.

You can use the u option for jar

From the Java Tutorials:

jar uf jar-file input-file(s)

"Any files already in the archive having the same pathname as a file being added will be overwritten."

See Updating a JAR File.

Much better than making the whole jar all over again. Invoking this from within your program sounds possible too. Try Running Command Line in Java