Makefile updates for 1.2-DRAFT

[elichad]

• changes tip/note/warning messages to ETT style (only in 1.2-DRAFT for now, but could also do this in 1.1)
• Makefile updates:
  • upgrade panflute to 2.1.3 (<2 doesn't work on my machine)
  • use nav_order for appendix as well as main spec
  • change sed scripts to find/replace the new message boxes for the PDF
  • update sed scripts for internal links as these weren't working properly
• change <div id="provenance"></div> at start of pages to # Title {#page-name} (i.e. a custom heading ID) to support the single-page links better
• Conda env updates: versions not chosen with a lot of care, just newer versions that work with the Makefile where the old ones didn't
  • upgrade panflute to 2.1.3
  • upgrade nodejs to 14.8

With these changes I'm able to run the Makefile on my machine and generate a PDF with working internal links.

One thing still to do is fix the images in the PDF - pandoc doesn't handle the raw HTML in introduction.md well

[stain]

Great, just remove the scripts/pandoc-admonition.py calls now from Makefile