Can't unlink clones that have a mask applied

Summary:

I imported a PDF into Inkscape and got some "Clone of: Group of 2 objects; clipped; masked" type objects. I tried to unlink and ungroup them but it says "No clones to unlink" or "No groups...", so I am unable to make them simple paths. I also can't select their originals because those are in the defs section of the SVG. When I export the SVG into PDF, these objects are not visible.

Steps to reproduce:

  • Open Inkscape
  • Use Ctrl+O or Ctrl+I and select this PDF: http://static.omnipathdb.org/uc.pdf
  • Choose the Poppler based import (see notes below)
  • Select the imported stuff and Ctrl+Shift+G until no more groups
  • Select any arrow in the middle
  • Try Alt+Shift+D or Ctrl+Shift+G or Shift+D and see the messages in the status bar :(
  • Ctrl+Alt+Shift+S and choose PDF for file type
  • Open the PDF in a viewer (I used evince): the arrows are not visible

What happened?

See above.

What should have happened?

I think the clones should've been converted to groups and the groups to paths. If the original is invisible in defs maybe Inkscape could copy it in the appropriate place or make it visible somehow? These objects are clipped and masked. I guess this weird situation arises because the arrows and the arrow heads are originally separate objects, they have a < 1.0 opacity and we want to avoid to have darker parts where they overlap. To achieve this, the arrows were generated by using the transparency group feature of TikZ. If I use the "internal" import feature of Inkscape, the arrows become paths but it restores the situation I wanted to avoid: the overlap of the arrows and their heads doubles the opacity. (Also the internal import fails to find the fonts by name and completely messes up the kerning so the labels need to be manually rewritten, but this is another issue.) I don't have enough insight to judge how difficult to make the arrows and the heads to single paths, but it would be nice to have a built-in method to achieve this, kind of how TikZ has the transparency group feature. Also, I actually didn't really want to unlink or ungroup those objects, my trouble started when they disappeared in the exported PDF. So if this somehow could be fixed, it would be already fantastic.

Version Info:

- Inkscape Version: Inkscape 1.0 (4035a4fb49, 2020-05-01), Pango version: 1.44.7
- Operating System: Arch Linux x86_64 (up to date)
- Cairo version: 1.17.2+25+gaee96d175
- Poppler version: 0.88.0
Edited by Nathan Lee