Any section of the torchlight 'tree' can have a sub-folder called 'merge' where you can add new content to be merged into the existing content without replacing it.
Currently, several mods are incompatible, hence why I released the 'RespecPotion [Plays nice with other mods]' mod. The only time you should completely replace an existing element and not use the merge folder is when you're changing an existing element or removing it. If your mod is simply adding more content you should use the 'merge' folder.
For an example of this behavior, look at: viewtopic.php?f=20&t=5554&p=58658#p56932 and viewtopic.php?f=20&t=5629
That's the redone respecpotion mod and bank mod. Both use the merge folder to add items to general item vendor without blocking or ruining other mods that might edit that vendor.
All the updated pet shop mods would be able to make good use of this too. They've got a good number more pets than my original mod.