This is a tutorial for an automated animal farm, this design was tested with Pigs, Cows, and Chickens
Open the Spoiler for the video tutorial!
The Base Building
The farm design itself is a 7x7x7. The bottom two layers are for redstone. So find an area, clear out the 7x7, then surround the inner 5x5 area with a block of some sort (such as glass) 4 high leaving one block on the bottom layer empty on three sides. Then put a roof on it, leaving the center one blank. After that, place slabs on the lower half of the bottom layer of the wall blocks. This will create a 2.5 block high inner area.
Note: the image above does not have the hole in the center of the roof, but it should be there.
You will need to make the following machines as well as have the following redstone components:
1 Mob Counter
1 Vacuum Hopper
1 Redstone Comparator
2 Redstone Torch
2 Tesseracts (or additional Energy Conduits and Fluiducts!)
6 Energy Conduits
In one of the open bottom slots, preferably across from another hole, place the Mob Counter so it is counting inside of the farm. Opposite the Counter, place the Grinder. And in the final slot, place the Breeder. In the roof ceiling, place the Vacuum Hopper.
At this point it should look similar to the following image
Note: In the image above, across is the Breeder, to the left is the Harvester and the right machine is the Mob Counter. And the Vacuum hopper in the top.
Now break out the blocks from the breeder and harvester to the same corner. If possible, save these blocks. Place one of the two Tesseracts in this corner and run the Energy Conduit from the Tesseract to the Breeder and to the Harvester. Place the second Tesseract on top of the Vacuum Hopper and make the Vacuum Hopper output Experience to the Tesseract on the upper portion. This will be the experience output.
Note: Redstone Energy Conduits are used in the image above, but any conduits can be used. The point of this is to get power to the Breeder and Harvester.
Under this build, clear out a 1 block high area, 2 if you are unable to morph into a bat. Under the Mob Counter, place 1 redstone dust. Then place the comparator so it is facing toward the Harvester. To the right of the Comparator, place one redstone dust and one redstone torch. Make sure to not toggle the Comparator into subtraction mode (the first redstone torch on the comparator would be on in this case) In front of the comparator, toward the Harvester, place the final three dust. This should lead into a block. The block on the opposite side, under the Harvester, will be placed a redstone torch.
Note: The above image had the base building removed to better show off the redstone placed. It can be difficult to see if the building was left there.
Now, you're almost done. We need to block off the cable from being accessed by the animals (and causing a miscount on the Mob Counter, or escaping from the pen) so using the Saw and the blocks you (hopefully) saved from clearing out, cut them down into Panels or Covers and cover the cables up from the inside. Once the energy conduits are covered up, you can then safely place in two of the desired animal (Pig, Cow, Chicken) into the pen then fill up the breeder. This will run for quite some time.
Here is a list of additional changes you do to make this more automated or more efficient.
Auto-fill Breeder from below from your storage system.
Place a chest on the back side of the harvester to catch items
Then suck those items into your storage
Be creative! You can use this farm setup to create two additional pens for the cows, chickens or pigs (depending which one you started with).
You can indeed find sacred saplings in dungeon chests, these are as rare as them coming from any source though.
@Phoenix - Lumber Axe wouldn't work on it from the base base, as its taller than the max blocks necessary. A harvester from TE won't have an issue with it though, and itd be lag free (ish.....ykno, besides the growth)
It demonstrates that the MFR harvester can handle pretty much anything you throw at it with its algorithms (it was primarily a test of that originally, but was left in because it's awesome). People no longer have a leg to stand on when arguing that the harvester can't handle a modded tree like the Red|power stained trees or things like the Redwood trees (which have both caused issues in previous versions), it focuses the attention back where it belongs.
Last I looked these could only come from dungeon chests - has that changed?