Due to installation being very complicated, the downloaded file is also an installer. After you download ModManager.jar, simply double-click it (or start it from the command line if you can't double-click jars), and it will install itself.
You can use the "Install Mod" button to install any mod that you've downloaded. Once the mod is in the list, it will be loaded whenever you start Minecraft unless you've disabled it with the "Disable" button. You can also delete mods with the "Uninstall Mod" button. It will take several seconds to load all the game files after you press the "Start Minecraft" button.
If the mod doesn't seem to be loading, but is in the list and not disabled, there may be issues with the structure of the mod. The zip file that needs to be installed should be what would normally go into minecraft.jar. If the mod includes resources or different sets of mod files, you should install the resources normally, then create a new zip with just the mod files (usually .class), and install that zip as the mod. If it still doesn't load, please post the name of the mod and a link to it in this thread.
The order of mods in the list is the order they will be loaded in. Most of the time this won't matter, but if one mod needs to be installed before another, make sure it is loaded after (I know this sounds backwards).
If you want to use multiple jars, put the other jars in the "jars" folder in the bin folder. Whatever version of Minecraft you had installed before you installed the Mod Manager in in there as "Default.jar". Feel free to rename it; you'll get an error message when you first start the Mod Manager, but you can go into the Active JAR tab and click on the new name. All of the files in the "jars" folder will appear in the Active JAR tab, so you can put different versions of Minecraft, snapshots, or heavily-modded versions in there. Note that the Mod Manager will freeze for several seconds when you select a new jar in the Active JAR tab.
What version of Minecraft does this work with? All of them. The code is version-independent.
Do I still need a patch for ModLoader? Nope, the new loading system fixes that.
I get an "Installation failed. Please see the forum page." message when I run ModManager.jar. This happens if the file you're running is not named "ModManager.jar", or if the Mod Manager is already installed. Try doing a Force Update of Minecraft.
I get some error when I click the "Start Minecraft" button. This happens when the Mod Manager can't create the game files. This should never happen, but if it does, Force Update Minecraft, then reinstall the Mod Manager.
This is for any version, or specific to 1.0.0? It seems like it would work for any version. Simmilar to what I thought someone would do for a mod loader. Actually utilize the folder that comes with minecraft for mods. LOL
The "Start Minecraft" button doesn't work for me.
I'm on a Mac.
The buttons sometimes don't work the first time you press them. I'm not entirely sure why. If it doesn't work, try waiting a few seconds and trying again. If you've hammered on the button a good 20 times and it doesn't do anything, let me know.
Private Mod Note
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I made pistons. You might be interested in my mod manager.