To set up make a large flat area about 13*13 is appropriate and find the centre spot. Place the turtle one block behind it facing the middle. Dig under it and put an ender chest (for depositing items).
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Then place place an MFR item collector behind the turtle. Cover the floor in conveyor belts and arrange them so everything heads towards the collector. I find it helpful to mount the conveyor belts onto rednet cable so that I can turn them off as I am working on the area. You don't have to use conveyors. Any system you can come up with to return saplings (and force nuggets if using dartcraft trees) will work fine, including water or obsidian pipes, so long as everything is routed back into the turtle.
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(And yes, I see that I have not centred my turtle correctly but this is just a demo
)
When you boot the program up for the first time you will see this screen.
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Arrange the ender chest, saplings and comparison log like I have done. It is vitally important that you remember the comparison log - in fact I think I programmed the turtle to error if it detects one of these three items is not present in the right slot.
You will also be asked to input some data. The first question is for telling the turtle what tree you are farming. If it recognises the tree it will be able to more accurately keep tabs on fuel consumption. Whether or not it recognises the tree it will at least say what it is farming. After going through all the set up the turtle screen will look like this.
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If you set the Loop mode to for loop like I have done you can tell how many iterations you want to have done.
There is bonemeal in that ender chest too btw. It will attempt to take bonemeal out when it needs to and it puts bonemeal into slot 2. If there is no bonemeal in the ender chest it doesn't matter it will just go into slow mode. Should you add bonemeal into the chest at a later date though I believe it will still get it even if it is in slow mode and then it will run fast again. I might be wring about that though.
Here is the little turtle in action.
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