I was testing a few apps with options and I noticed that there is a lot of code not being cleaned up from apps during uninstall and I believe the leftover code was interfering with the functionality of new apps.
Is there a policy enforced by Shopify to clean up remaining code upon app uninstall?
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This is an accepted solution.
There is no policy that I'm aware of, but App developers are encouraged to use the script tag to load their stuffs and these get removed when the App is uninstalled.
The Apps team checks this more rigorously these days but older Apps may not use it, or choose not to use it because it makes it appear that the App is performing badly through slow loading (scripts are loaded after the page has finished rendering so if there are a lot of heavy images, or missing font files, for example it takes a long time to load).
Best bet (albeit tedious) is to take a backup of the theme before installing new Apps. That way if you uninstall you can just use the original untainted version of the theme.