Complex tools such as git or svn understand a whole set of commands, each of which with their own specific syntax:

git commit --amend -m "Bug fix"

For example, here is a the arg object for the commit command:

@Parameters(separators = "=")
public class CommandCommit {

  @Parameter(description = "Record changes to the repository")
  public List<String> files;

  @Parameter(names = "--amend", description = "Amend")
  public Boolean amend = false;

  @Parameter(names = "--author")
  public String author;
}

And here is add:

public class CommandAdd {

  @Parameter(description = "Add file contents to the index")
  public List<String> patterns;

  @Parameter(names = "-i")
  public Boolean interactive = false;
}

Then you register these commands with your JCommander object. After the parsing phase, you call getParsedCommand() on your JCommander object, and based on the command that is returned, you know which arg object to inspect (you can still use a main arg object if you want to support options before the first command appears on the command line):

// Options available before commands
CommandMain cm = new CommandMain();
JCommander jc = new JCommander(cm);

// Command: add
CommandAdd add = new CommandAdd();
jc.addCommand("add", add);

// Command: commit
CommandCommit commit = new CommandCommit();
jc.addCommand("commit", commit);

jc.parse("-v", "commit", "--amend", "--author=cbeust", "A.java", "B.java");

Assert.assertTrue(cm.verbose);
Assert.assertEquals(jc.getParsedCommand(), "commit");
Assert.assertTrue(commit.amend);
Assert.assertEquals(commit.author, "cbeust");
Assert.assertEquals(commit.files, Arrays.asList("A.java", "B.java"));

Support for complex commands is one of the new features available in JCommander 1.5.

From http://beust.com/weblog/2010/08/08/complex-line-command-syntaxes-with-jcommander