CmdSupport
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After installing, .bat files are often invisible in the Project tree

After folding/unfolding that part of the tree files become visible (and "openable"):

I'm having the same issue, PhpStorm v8.0.3
Sometimes I have the same issue on my mac without plugin installed. I tend to believe it has nothing todo with my plugin...
I'm having the same issue, Windows 7, PyCharm 4.5.4