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Since you have an rpm, then I guess the binary is probably /usr/bin/sigil (/opt/sigil/sigil.sh is only relevant if you installed sigil using the .run package that can be downloaded from Sigil's web site). You can check by using 'rpm -ql sigil'.
FWIW, that vanishing-file-when-dragged affects all the versions of Sigil that I used (that includes the latest one, 0.5.3).
The .opf file is inside the epub, you can see it when you open the file in Sigil in the Book Browser panel, it's the file before last at the very bottom.
As for dependencies, I don't think Sigil has newer deps (and even if it does, running it from terminal will tell you which libraries you need to install).
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