The Java language and development platform hasn't changed since you took CSE 131. However, you probably want to know about The Terminal class, which is provided with some of the Java lab code. It can be used for input and output both to the screen and to files. (On UNIX, you can just use Java's standard I/O and capture the output with the script command instead.)
For general Java library questions, a good place to start is with the Sun API documentation. In particular, you may find java.util documentation helpful if you decide to use ArrayList. The java.io documentation is also helpful for its description of the FilterOutputStream class, which is the type of the System.out object sometimes used for println.