Calling native APIs in Electron

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In the documentation for Electron it states:

In web pages, calling native GUI related APIs is not allowed

I don't understand what is meant by "native GUI related APIs". If I create a web page in Electron and add jQuery and then manipulate some element on the page, this works. I don't have to call back to the main process to perform UI updates. Does "native GUI related APIs" refer to something much more lower level (such as some API that is not based on Javascript)?

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