how are android security permissions checked at run-time?

This question has been asked before at How does Android enforce permissions?. While the discussions there are good, the question is still not fully answered.

In the development environment, exceptions are thrown when the app tries to do something that requires permissions not declared in AndroidManifest.xml. So how does the run-time system implement the run-time checking?

I guess it's most likely done in the core framework, which may or may not need support from native code. But I don't know what source code files in AOSP are relevant to this.

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