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The geometry of the windows is saved in sigil.ini. So if you delete that file you will reset it to the default layout (and remove other settings as well). (Deleting the sigil folder will also delete your clips, searches, user dictionaries, etc. so I wouldn't recommend that).
Since the docking/undocking works fine in Linux (even with 5+ undocked and minimized/maximized), it looks like another problem with Qt5.0.1
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