I keep my ledger files in git, mostly so that I can recover if I accidentally touch the wrong part of a file when making a change. I don't do anything fancy with revision control. I just check in a change whenever I've done something nontrivial like reconcile with a monthly statement.
I keep my data files in one directory and scripts that process them in another. I've got an R script that pulls data out of ledger and plots my progress towards goals (save for college, pay off mortgage, save for retirement). Matthew
