You need to extract them like they are. Folders included.
so its
Updater.jar
lib\JDirectoryDialog.jar
lib\sqlitejdbc-v036-nested.jar
config\updater.s3db
The Application expects those files in that sub folders, if they are not present its not able to find them.
They are the only files you _need_ to make it work. If you cannot figure out how to extract the others just ignore them. It'll make hashing your files a bit slower, but it will work.
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