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1) One way to do this is to turn the names into links, you can do this with the -link option. Point it to the JDK api folder and the standard classes will be turned into links into the those folders, and the links don't have the package prefix. e.g. javadoc -link http://java.sun.com/j2se/1.5.0/docs/api/
2) I have no idea, I've never seen those options.
%I%, %G% variables work only in the SCCS source code control system, which is the one Sun uses.
You would have to use the variables that your source code control system provides.
The syntax about @version is found on this page:
The Java Software convention for the argument to the @version tag
is the SCCS string "%I%, %G%", which converts to something like
"1.39, 02/28/97" (mm/dd/yy) when the file is checked out of SCCS.
Here, "Java Software" means the Java division of Sun Microsystems.