Turn generate_neurobagel_example_jsonlds.sh into makefile

[alyssadai]

The script operations may be better handled with a makefile. Mainly because you have to make sure that the script is being run only from the repo root dir (and a bunch of other stuff is also needed). But we're all human, so we might run it from the wrong dir, and then the docker commands are going to create a bunch of root-ownder folders in the repo - which is annoying.

makefile would make this all a lot easier. And it could also do the submodule getting / branching and so on for you. So I suggest we do that. If this is too big a move, let's split this off into its own PR

Also, we should simplify the internal mountpoint from /data/neurobagel/bagel-cli to /data.

Originally posted by @surchs in #410 (comment)