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More writing, intro&methods, half drafted Figure 1

Also includes some Makefile changes:

  • I added -u $gid:$uid parameters to docker runs so that it doesn't create root-owned temporary files in my home
  • there was explicit --mount in case of latex build that I simplified to normal -v (please complain if the mount had some sense that I missed, but it seems to build on CI)
  • make refs now flushes and refreshes the zotero references

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