This is similar to an issue from a couple versions/years ago (https://sourceforge.net/tracker/?func=detail&aid=1633701&group_id=91119&atid=596024). If I'm working on an .ly file with more than one dot in its file name and I launch the internal PDF viewer, the module opens in jEdit like it's supposed to, but it behaves as though there's no file open--just a blank module with toolbars at the top and bottom.
This issue only applies to LilyPondTool v2.12.932; everything works fine in v2.12.869.
I'm running the development version of jEdit at the moment, but this was a problem in the stable version as well.
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