I have strange problem connecting with PhpStorm IDE. I use version 2016.3.2 Build #PS-163.10504.2
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I love using Ctrl + Shift + N for searching files which I need to override. I have 2 project (one new, one old) and in old file searching works fine and in new search only for twig files and nothing else.
Is there any configuration I need to change?
Check filter -- the blue Funnel icon on the right top corner of that popup -- you may have selected to list files of certain types only.
Otherwise -- try universal File | Invalidate Caches...
and restart IDE -- it usually helps in such "suddenly stop working" situations.