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OnTopReplica is a Windows application that allows you to clone a window then crop a subregion of it and keep it always on top (useful if you're trying to keep a YouTube Video always showing).
Is there any alternative for Linux installations (specifically Ubuntu or Linux Mint)? I tried looking for some sort of Compiz plugin that could emulate this, but I'm not sure where to start...
Would it be enough to size the window to the portion you want, remove the decorations (title bar etc) and make the resulting window always-on-top? Most window managers can do this.
That requires so much more work on the end-user with less features (for example, OnTopReplica allows you to resize the region you crop to zoom in or out on it easily).
I use ontopreplica all the time on Windows, I have bookmarked this a long time ago, not sure if the functionality is the same or if it follows your mouse.
Maybe try a on browser solution, if its especially for video there is plenty of options.