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