Steps to enable jdev debugging with emctl command -
1) emfind MdsCmds.pm
2) Modify subroutine (sub registerMetadata()) in MdsCmds.pm to add - "-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8001" and the final block will look like -

<code>
my $cmd = "$JAVA_HOME/bin/java  -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8001 -cp $CLASSPATH ".
            "-DORACLE_HOME=$ORACLE_HOME ".
            "-DMW_HOME=$mwHome ".
            "-DINSTANCE_HOME=$INSTANCE_HOME ".
            "oracle.sysman.emctl.extensibility.EmctlMetadataService $cmdArg @args";
</code>
3) connect jdev in debug mode and provide the same port as updated in my $cmd.