By Vik Kumar on May 06, 2013
<WLS server path>/atgpf/common/bin/wlst.sh
connect('<weblogic user name>','<weblogic password>','t3://<server name>:port')
deleteMetadata(application='IncentiveCompensationApp',server='AdminServer', docs='/WEB-INF/oracle/apps/incentiveCompensation/creditSetup/creditRule/ui/flow/ mdssys/cust/Site/SITE/CreditRuleFlow.xml.xml')
Command reference is here which explains the syntax in more details and wild card options to delete more than one MDS document at once.