The scratchpad UI was intended to provide a very simple mini-ide-like environment for beginner students before they move onto using real IDEs. I can see this isn't what you're after.
The Jobe server is a standard Linux server and you can put data files anywhere you like, giving students the path to them. But ... it should be firewalled to prevent access from anywhere other than the Moodle server, so you won't be able to FTP files onto it yourself. You'll have to get a sysadmin to upload files to it.
If you want to have specific files preloaded into the workspace, it sounds like you need a zero-penalty question. I attach a zip file of a question prototype we call python3_sandbox and a question that uses it. If you import both those questions (they're in Moodle XML format) and preview the example question you should see something like the following, which is a "handy python workspace" we make available to our students. You can preload any additional files you like into this question.
If you want to have specific files preloaded into the workspace, it sounds like you need a zero-penalty question. I attach a zip file of a question prototype we call python3_sandbox and a question that uses it. If you import both those questions (they're in Moodle XML format) and preview the example question you should see something like the following, which is a "handy python workspace" we make available to our students. You can preload any additional files you like into this question.
And when Check is clicked the student would see:
Is that more what you're after? Note, though, that this approach does not give students the ability to use the input() function in an interactive manner - any standard input has to be put into a separate file in advance and uploaded.