I have several rule files, but some of them conflict with each other and I can’t just run them all at once. There is one for tree cover, another for river edges, etc. Currently, I have to go into the rules.txt file and comment out the ones I don’t want to run. It would be nice to have a new (nested?) menu option that allows me to select the rules I wanted to run.
It would also be nice to select an area of the map and the rules only applied to that area.
I understand the use-case, but of course this will take rather more effort to change. Rather than coding a custom solution for this, I’m inclined to say that such a thing is generally easier to solve by making Tiled scriptable, so that you could hook different menu items or shortcuts to automapping based on various rule files.
While I do plan to work on scriptability this year, that change will still be a way off though. It’s currently on the Roadmap for Tiled 1.3, along with support for projects. In the meantime you may want to look into coding a quick custom solution.