Have you considered using Perl for this task?

See system, File::Find or File::Glob::bsd_glob.

Also, you will need to learn about how files work in general. It is unwise to try to write to a file of the same name as a file you are trying to read from.

I don't understand how you are using "snapid.xsl" to make changes when you're using an output redirection (>) from the Java script. Do you mean to use a pipe (|); otherwise, methinks the output from the Java command will overwrite the contents of '.\Script\snapid.xsl'.