Some waypoint files for CS 1.5 won't work in CS 1.6. The de_aztec waypoint file had to be updated in this version. I also noticed that some of the waypoints in this version are slighty off due to updates on some maps. They're not totally unusable but could use some minor adjustments/edits.

As for the "untidy" comment, how tidy do you want it? Seriously, are you just looking for a more complete bot.cfg/joebot.cfg file to know all the options? The existing .cfg files are just examples of a few settings but I wouldn't consider them messy.