SemTop! is a nifty tool that allows to keep important
windows always on top of the desktop and doesn't allow
other windows to overlap it.
The software resides in the tray area as "drawing-pin"
icon and allows to "pin" necessary windows with single
mouse click. Just press mouse button on tray icon and
drag the "pin" cursor to window which you would like
to keep on top or return to previous state.
Alternatively you can just press some hot-key (which
can be specified in the program settings) when the
window are active.

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