Note that the JLex documentation only discusses features and syntax that are specific to JLex, as compared to other scanner generators. For a more general explanation of scanner generators as well as some examples of how lexer generators are used, you may find the Flex documentation helpful. Similarly, the CUP documentation only discusses specific features and syntax of CUP, and you may want to peruse the Bison documentation for a more general discussion of LALR parser generators.
Note: The JLex documentation states that "the dot (.) will match any input except for the newline." This is misleading -- a dot matches any character except \n and \r.