Hai Thorbjørn, thanks for replying. You got me thinking about this, here are my thoughts.
As a fellow coder, I like to keep things simple and stick to the definitions. In this case, the definition is “in a designated automapping rules map file, layers for automapping should start with input_ / output_”
In that case, validating the layers in such a map file results in candidates for automapping rule layers. If the name of a tile layer adheres to the definition (in this case the naming convention), then it is a candidate.
This should not give an error if a layer does not comply to the definition. Or else the definition should be “all layers in a designated automapping files MUST start with input_/output_”.
So, a warning at best indeed (but with an opt-out checkbox). If a layer does not comply to the definition, then it simply isn’t an automapping rule 
You’ve kept the whole concept already simple by using what you have; the .tmx files. Now, if I may, here is another suggestion to keep the tiled user in the loop:
- star/mark any input_/output_ layer that is valid for automapping rules to distinguish them
- star/mark any destination layer as ‘enabled for automapping’
And perhaps a text somewhere saying that automapping is in order at the current open map.
Or, how about some logging (window) ?
The current automapping setup is kind of error-prone, the user needs to be sure to have stuff correct. (as a programmer, I am very okay with that. But not every one is a programmer, eh). So perhaps the rules.txt file could be made visible in the gui, its just lines of string separated by EOL (simple and effective, me like)
Those are my 2 cents, or perhaps 3.
cheers!
(in the meantime I’m gonna try out the commented layer name trick, thanx)