automake vs. GNU make

>For example, if you have a source file with the same name in two 
> subdirectories (e.g. main.c), do you have to jump through hoops to 
> prevent it from getting confused?

The way I do it is always reference the tree from the build root.

so a/main.c is never looks like b/main.c

and yes I can start a build from the subdirs etc.

non-recursive is the way to go. 

Just require gnu make don't try supporting version 8.79 (rh9) clients just 
make people upgrade....