This has been going on for a while with Inkscape. I see it when I try to open PDFs saved with Inkscape. The whole program just dies.
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Since I need PDFs for my LaTeX documents, I save everything as SVG and PDF constantly, making sure to never accidentally open any PDFs.
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Inkscape. Nightmare. But I still use it because it's pretty much the only thing we have on Linux.
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Have you tried draw.io?
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Can it cope with humongous files?
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I never did anything very complicated there. It's useful for drawing things from scratch, but I'm not sure you can edit a PDF or SVG there.
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So it's more of a suggestion for the future than a solution for your current issues. I feel your pain, I hate Inkscape

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I'm not drawing anything from scratch. I'd use tikz for that. This is shapefiles and other GIS.
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Have you tried IPE (http://ipe.otfried.org )?
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No, should I?

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It depends on what you are doing. But IPE plays very well with LaTeX.
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Probably not then. See this to get an idea: https://github.com/otfried/ipe-wiki/wiki/Showcase …
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Very cute. For some of those I use tikz.
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Can you show a sample of a map? I wonder if you could do it programatically.
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Using something like this: http://www.residentmar.io/geoplot/index.html …
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The whole thing barfs and I lose my work when trying to open another file that nonetheless was created using Inkscape.