Here's the bash script that I use. It's pretty simple really. It creates a scribble.irx file (for holding your scribbles), and just creates a directory, moves in the pdf, scribble and manifest files, and renames the directory. I now create the manifest file using the jabref template earlier in this thread.
I have another version of the script that I need to merge with this one that also includes an image, or rather the path to an image depending on the journal.
Code:
<image>../_cover-images/$3.png</image>
I make that image line the last thing before the tag that closes the </y-metadata>
This way I only need one copy of each image for each journal.
I have this integrated with my file manager so I just create the manifest file using jabref, and save it in the same directory as the PDF file and then call this script on the PDF file.