Starting and stopping a GlassFish domain from inside the IDE is different then starting the domain from the command-line.
Starting:
1. NetBeans may alter the "default-web.xml"; to enable HTTP monitoring.
2. NetBeans may start the server in Debug mode.
Stopping:
1. NetBeans may alter the "default-web.xml"; to disbale the HTTP Monitor.
If the user stops the server from the command-line, after they have started it with the IDE, the code that removes the HTTP Monitoring changes from default-web.xml will not execute. This is the easiest way to end up with a server.log full of warnings from the NetBeans HTTP monitor.
We are looking for a fix to that issue.
http://www.netbeans.org/issues/show_bug.cgi?id=116547
[Message sent by forum member 'vbkraemer' (vbkraemer)]
http://forums.java.net/jive/thread.jspa?messageID=236798