Good - you can still use Navigate | File... Navigate | File... for folders - you just need to use "/" or "\" at the end to indicate that you want to see folders (works in PhpStorm v8).
Another solution (for frequently used folders) is to mark it as a favorite. Then you can use the standard Alt + F1, 1 ( Navigate | Select In... | Project View ) to find it in the Project View panel.
For very often used folders - you can just mark it (but not the usual bookmark - the mnemonic bookmark instead - it will associate a letter or number with it).
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