First see related blog Directory Structure for Integrated Flex and Java Web Applications.  This blog shows how easily one can build such project using maven with sample maven.xml, project.xml, project.properties files.  The samples are for maven version 1.0.2 and not version 2.x.             

<to be continued>

NOTE: You will get an error in maven on the call to the mxml compiler if the path name to an mxml file contains spaces.