Where do XML Publisher output files are stored?

You can get the output file from following location:
-> cd $APPLCSF/$APPLOUT
-> ls -ltr *<request_id>*
where <request_id> has to be replaced by the report concurrent program request_id.

For Example, if my concurrent request is 12345 and it generated pdf output then, i have to put following command to find the file.
ls -ltr *12345*PDF

How do I get the XML file from the server?

You can get the output file from following location:
$APPLCSF/$APPLOUT/o<request_id>.out 
where <request_id> has to be replaced by the report concurrent program request_id.