Can arduino properly deal with files from multiple folders?

I've been developing a rather large project and would like to organize files using folders. However, when I have two folders and want to include files from one another, Arduino will fail to compile. Check the screenshot below for a minimalist example:

I know this is due to some weird behaviors of Arduino compiler in a sense that it will copy all files to another temporary directory before compiling them, but are there any walk around? Thanks!

A relevant question is:

Include header from another directory - Using Arduino / Programming Questions - Arduino Forum

An interesting fix is just put everything else into a folder called src (anything else won't work). I guess this is because by calling it src Arduino will recognize it as a library?

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