Hello there, fairly recently a similar request was discussed here
If you're just seeking a way to open a file from local git repo, you can just paste a file link to it in a note. It would be not a native Joplin note, so it will be opened with external editor.
present
I've given a thought to this problem of connecting files / notes together. Long story short: it takes quite a lot of manual work to setup the two way link between the Joplin database and native file structure. It can be done, but as of now, it's difficult, flaky and not really scalable. Maybe it'll get easier in the future, but as of now, you gotta be very selective with what files you're two-way linking with Joplin.
future
Floating around "Multiple profiles Project" gives me hope as maybe we'll get the ability to package files inside the archive along with the native Joplin notes.
What also could be great for this use case is the following feature
File symlinks to resource folder in markdown export
Example:
ls -R md-exp/
'md-exp/':
e7e06dd06e08d35bda16ace909935f0f.png (symlink)
exported-note.md
md-exp/_resources:
e7e06dd06e08d35bda16ace909935f0f.png (actual resource)
Of course, potentially it can break import but on the upside, it would allow much easier file management after export.
On the closing note, from the perspective of Joplin, I feel there's no intention to be all encompassing emacs-style system, it's a note taking application afterall. It's just we, power users, at times trying to whip Joplin into Confluence. So, we might never get there and it's okay.