Is there a way in the IDE to combine the display of many folders with a similar tree into one tree?

Question

NetBeans

Hello.
There are dozens of folders with a similar structure, they contain: models, controllers, tests, templates, js, css ...
But navigation through such a crowd of folders is disgusting, I wanted to combine them into one tree.
It would also be great that if there are similar files in the folders, then mark the parent for each file, and also select the parent when creating a new file.
Or perhaps there is a way to organize work with such a crowd of folders differently?
IDE by and large does not matter, languages ​​PHP, JS, CSS, LESS, Ubuntu OS.
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Sincerely, icetomcat