These libraries settle on standard Java APIs which, of course, you can also use yourself without these libraries.
First of all, Java class files are just sequences of bytes in a well defined format, as specified in JVMS §4, The class File Format. The primary task of the mentioned libraries is to provide tools for processing byte sequences in this format. The second is about getting the definitions of existing or exporting modified or newly created classes.
There are two different way of dealing with the second task. One is to read compiled classes from persistent storage like file systems or jar files, etc. and writing them back to these storage while the particular code is not running, like build and deployment tools do. This should be trivial, as it just boils down to reading and writing bytes.
The other is to manipulate classes at runtime, which can be done by Java Agents via the Instrumentation API. It offers mechanisms for intercepting classes at loading/definition time before their first use, but also redefinition of classes. The latter can’t change them freely, currently, it has to retain all field and method declarations, so it can be mainly used to change the executable code of the methods.
If you want examples for class file processing without additional 3rd party libraries, there are some answers on Stackoverflow
Of course, these examples are only single-purpose code or sketches. If you expand them to something more general or useful, you will soon end up at basically re-implementing these libraries.
