Closing, minimise and change size buttons

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In the old MM1 there was only the yellow button functioning. I put the window in the Dock. Clicking on the app icon in the Dock open the window up again on the screen.

In MMHD we have all three buttons. I have so many times clicked on the read one to just close the window, BUT it closes the application without asking if that is what I want.  >

Minimise the window to the Dock and you can only get it up again when clicking on the specific icon in the Dock. Nothing happens when clicking on the applications icon.