Communicate between browser extension and desktop app

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I'm trying to create a chromium program that is both web-based and also has access to the OS. Kinda like a browser extension but also does things that regular applications do, like altering system settings.

I'm stuck on trying to figure out how the program, written in Java, will connect to the JS part of it to control the system or vice versa. What's the best approach to this?

P.S. Fairly new programmer, so responses with external resources will be greatly appreciated.

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