Markdown is a great idea, but are there markdown based solutions for 1) figure numbering and caption handling, 2) references, 3) automatically updating an index

Markdown is a great idea, but are there markdown based solutions for 1) figure numbering and caption handling, 2) references, 3) automatically updating an index? Anyone in academia needs to worry about all of these, and solutions in Word are sufficiently worse than LaTeX, which automatically updates all references, heading numbers, regenerates figures that have changed, and tracks your index for longer documents like theses.