This seems to work, but it only works if you select an entire folder and run the automator scrpt from there, otherwise if you select individual files it actually searches each file for folders and zips the files within the "package contents" : so workflow looks like this:

in the automator place action "get selected finder items"

followed by "get folder contents"

followed by "run shell script" : keep the shell as /bin/bash and the pass input as "to stdin" the actual script is

xargs -I {} zip {}.zip {}


that's it. save the workflow as a finder selection and select a folder full of files you wish to individually compress, and it works but yes unfortunately it still makes it have that annoying files structure, which i personally can't stand, and also it doesn't seem to like working with other folders within folders and it can't seem to compress .apps very well, lastly i would like to have the option to individually select groups of files from within a folder and zip those.i dunno what's up with that. so maybe someone can take this script and flesh it out? :)