Note: The library is currently being refactored - there will be many breaking changes to the API! MCModify is Java library designed for easily modifying extisting Minecraft files. There are already other libraries like this for Java, Python, C#, C, C++, etc., but if you like the library interface, feel free to use it.
The repository is a NetBeans project and the code is written in Java 7. It is not yet packaged in a typical library format (e.g. .jar) however it is still readily usable.
There is also a version of the library in early development for C++11, available from the cpp branch.