java -jar mxquery.jar [queryFile|queryString] flags

where flags can be one or more of the following:
-printVariables: prints all persistent variables used in your engine
-printExpTree: prints the query tree of your XQuery Expressions.
-ignoreResult: result is not displayed (result is displayed by default)

Advanced flags:
-printStore: prints all variables ever declared as persistent in the XQuery/XUpdate expressions, during the same session.

Background: if the mxquery.jar is invoked from a java program (as in the sample JavaGUI, for example) and persistent variables are used, next time a query is run through the mxquery engine the variable values are restored from last run (i.e., they are not re-initialized). This is done using a memory store. This flags allows all variables to be printed.