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I think you should try to use the warp mechanic as much as possible considering how easy it is to use the Thaumcraft api.
I just found out there is both permanent and temporary warp.
I got my idea for extended automation here. And I keep looking here for ideas.
Many of them are bright, I'm just not bright enough to make a mod of them.
Drop them in a folder in the enviroment somewhere, and if you are using IDEA you just rightclick on them and add them as a library.
Not sure about eclipse though
Sadly, MFR's api does not support adding pickable fruits without changing the block itself :(
Edit: Mekanisms API is great! So I added recipes for turning all raw Harvestcraft vegetables into biofuel. Now onto fruits...