The numbered jar files in your versions/* folders work exactly like the old bin/minecraft.jar file used to. Now there are just multiple copies of minecraft.jar all renamed to keep them separate.
If you're using a 3rd-party launcher, you can copy the 1.5.1.jar file in your versions/ folders to wherever your launcher keeps its version of Minecraft. Rename the copy of 1.5.1.jar to minecraft.jar and proceed from there. If this is your situation, this is where my instructions end because I don't know your launcher's setup.
However, you can also use the new Minecraft launcher directly, leveraging its new multi-version features. This is what I'm doing now, since I find it more robust than messing with other launchers. Here's a step-by-step guide to get you to the point where the mod's install instructions will make sense again:
Make a copy of your versions/1.5.1 folder and put it beside the 1.5.1 folder. Rename the new folder, the jar file, and the JSON file all to aether2 + .jar and .json extensions as appropriate (OS X may not show you the extension of the files, in which case don't worry, they'll be unchanged and stay correct). You should now have a versions/aether2/ folder containing aether2.jar and aether2.json.
(The name "aether2" is not important – it could be anything, so long as you use the exact same name in every place where aether2 appears in these instructions. Stick with aether2 until you grok the process.)
Then open the JSON file with a text editor (not Notepad, since it mangles config files; use Wordpad, or get Notepad++). Change the line inside that reads
"id": "1.5.1",
to say aether2 (or whatever you named the files and folder)
"id": "aether2",
and save the JSON file.
Now you will have a nice fresh new Minecraft jar version that you can start modding. This is why the new Minecraft launcher is awesome – it supports multiple versions, including multiple modded versions.
(Yes, you have to use the 1.5.1 version as a starting base. Aether II isn't updated to 1.6.2 yet.)
Now that you've got that, you need a new folder to keep your world saves and mods separate from the vanilla Minecraft files. Create a folder anywhere (I like to keep it in my .minecraft folder though) named whatever you like, but for convenience I suggest (you guessed it) aether2. This folder name doesn't have to match the names under versions/, but it's convenient for it to match.
Finally, you need to create a new launcher profile that will use the new version and new folder. Start the Minecraft launcher and create a new profile, then click Edit Profile. Change Profile Name to something nice like "Aether II". Click the checkbox beside Game Directory and change the end of the path to point at your new world folder, so something like
/Users/YourOSXUserName/Library/Application Support/minecraft/aether2
(or the equivalent on the other operating systems). Now, and this is the all-important part, pick aether2 from the Use version dropdown list. Double-check that your Minecraft login is correct (especially if you share this computer with other Minecraft players), then click Save Profile.
You should now have a nice new login profile that runs a copy of Minecraft that's entirely separate from the vanilla Minecraft release!
You are now ready to install the mod, but first, check that everything is working and log in with the new profile. Create a world, quit, and look in your new .minecraft/aether2/saves/ folder to make sure your worlds with this profile are saving to this folder instead of the main .minecraft/saves/ folder.
Now mod away! When the mod instructions tell you to do something to bin/minecraft.jar, just do that to versions/aether2/aether2.jar instead and it will work the same. When an instruction tells you to put a file in your .minecraft/mods/ or coremods/ folders, put them in .minecraft/aether2/mods and minecraft/aether2/coremods/ folders instead.
And watch for that tricky dot in .minecraft. All modding instructions (including most of my own here) will tell you about your .minecraft folder, but on OSX it's missing the dot. This is normal and not a problem, unless you let it confuse you. This is just an odd difference that Minecraft has on Mac OS X that you have to get used to.
This depends on many factors, including your position as a player and the type of terrain around you.
Mobs will despawn when they are out of a 128 block radius of the player.
This means that for the spawner to be active if the player is anywhere within 128 blocks at the spawner's level, it has to be at least 128 blocks above the ground. This works for pretty much any generic mob farm, and it works in a populated server. Having blocks in an area above level y128 can decrease efficiency of mob spawning, since it has to account for more chunks, though, so here are some other options:
If you want to make a less tall, but still efficient design you can locate the player above the farm so that the despawn radius includes the spawner but excludes the rest of the world. Note that this design is better suited for AFKing, since you will have to make many trips up and down for this to work. This can be used for witch farms, as well as hostile mob farms.
You can also "sanitize" a 128 radius area, by lighting up every cave and surface you can find. This is obviously quite tedious, but it can allow for a ground-level farm that is active no matter where the player is. This works for witch farms as well, and is probably your best efficiency if you are playing on a server.
Best Answer
I believe I found the answer to this!
I had to go into the config files:
I then changed all instances of "canSpawn=true" to "canSpawn=false."
This may work, I will edit my comment if it does.