Issue with syncing repository with theme's modified code by apps

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I am wondering how others do this.

I have a repository with shopify theme code in it. It is not a minificatedversion of the code. The code that's uploaded in the theme in shopify is a minificated version of the code.

When installing new apps, these apps are adding new code into the code in the live theme. So there are many new files that are non-existent in my code. When I deploy my code, this steps over everything in shopify's theme; all the files that the apps have added are erased. 

How do other developers deal with this? It is very time consuming to find all the files each app has added, also since it's a minificated version, it is not the same as the code in the repository, making this task even more complicated.


Any suggestion is appreciated!

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