By “files are there” are you referring to the workspace files you created?
If not, then you probably need to add fixtures in your hooks for the custom workspace you created.
Then export those fixtures with the bench export fixtures command.
Push it to git and then you’ll be able to install the app with the workspace.
This can be done for any doctype records you want to be auto populated on install of the app. (It won’t bring the stores public/private files though.)
thanks for your tip. I am referring to the workspace files being created. It is definitely there…
However, on re-installing the app with bench update, the workspace is not updated.
I had an old app (which I deleted from my git server) still on the server.
That app had a fixture for the workspace. After removing that app also from the server, it works as expected…