Dialog I cannot get rid of

Question

The steps here were simple, but unexpected:

1. download a file
2. in finder, rename the file using Keyboard:
   1. Press Enter to start rename
   2. Start typing a new name (but not pressing Enter again)
3. Try to open the file by pressing Command-O

Now this dialog appears and won't go away (it only reacts on moving with the mouse, but clicking on it fails, just as pressing Spacebar, Enter or Esc).

Both Finder and Spotlight now refuse to open any other file.

I tried:

killall -KILL Dock
killall -KILL Finder
killall -KILL NotificationCenter
killall -KILL SystemUIServer

Help (:

Note the file is not damaged, just renamed.

Answer 1

Search for OS X identify process by window I found What process owns a certain window (Mac OS X) which told me this after moving the Window:

RetinaMBPro1TB:bin jeroenp$ ./show-recently-moved-windows.py 
Move target window

List of windows that moved:
{(
        {
        kCGWindowAlpha = 1;
        kCGWindowBounds =         {
            Height = 1094;
            Width = 1130;
            X = 43;
            Y = 45;
        };
        kCGWindowIsOnscreen = 1;
        kCGWindowLayer = 0;
        kCGWindowMemoryUsage = 5246548;
        kCGWindowName = "bin \U2014 Python \U2014 160\U00d776";
        kCGWindowNumber = 23921;
        kCGWindowOwnerName = Terminal;
        kCGWindowOwnerPID = 357;
        kCGWindowSharingState = 1;
        kCGWindowStoreType = 2;
    },
        {
        kCGWindowAlpha = 1;
        kCGWindowBounds =         {
            Height = 153;
            Width = 420;
            X = 1359;
            Y = 182;
        };
        kCGWindowIsOnscreen = 1;
        kCGWindowLayer = 8;
        kCGWindowMemoryUsage = 390292;
        kCGWindowName = "";
        kCGWindowNumber = 23246;
        kCGWindowOwnerName = CoreServicesUIAgent;
        kCGWindowOwnerPID = 87976;
        kCGWindowSharingState = 1;
        kCGWindowStoreType = 2;
    }
)}

Since CoreServicesUIAgent is the owner, I performed this:

killall -KILL CoreServicesUIAgent

That worked. Now I can open the PDF again.

Answer 2

The icon in the dialog box is the clue. It's something to do with Gatekeeper. This article from Apple https://support.apple.com/en-au/HT202491 might help.