The peripheral API can now be found in the "api" folder of the main ComputerCraft download
For peripherals, the download includes the source files for the two interfaces you need to interact with to make peripherals. All you need to do is create a new block with a TileEntity, and have the entity implement IPeripheral.
For turtle upgrades, create a class implementing ITurtleUpgrade, and call TurtleAPI.registerUpgrade() during your mod load() method. Turtle upgrades can either be new tools for your turtle (like the Pickaxe, Sword, etc), or new peripherals that permanently attach to the turtle (like the turtles' Wireless Modem or Crafting Table), and turtles with the upgrades can be created by crafting. In order to correctly store the types of turtle upgrade that each turtle has, each turtle upgrade designed must have a unique "UpgradeID", which is an integer in the range 0-255. When you release your upgrade, please use the following wiki page to choose an unused ID: http://www.computerc...tle_Upgrade_IDs
Both parts of the API include complete, thorough javadoc documentation. To make a mod, add these files to your MCP install, and implement the requisite interfaces. You do not need to and should not distribute the class files for these files with your mod. If all goes well, when you re-obfuscate your mod and install alongside ComputerCraft, your computers should be able to interact with your peripherals using the "peripheral" API, and turtles should be able to be crafted with your upgrades.
Feel free to post any questions about the API you have in this thread, but please read the documenation first, and be aware that this API is designed for users who already know how to produce mods for Minecraft, so we won't help you with basic mod setup.
Happy hacking!