You would profile the JBoss Server in the following way:

1) download TPTP and find org.eclipse.tptp.platform.ac plugin for your OS
For instance,
org.eclipse.tptp.platform.ac.win_ia32_4.4.1.v200806171132 - TPTP 4.5.0 Windows 
32 bit
org.eclipse.tptp.platform.ac.linux_ia32_4.4.1.v200806171132 - TPTP 4.5.0 Linux 
32 bit

2) add <PLUGIN_DIR>\agent_controller\bin to the PATH variable on windows or 
<PLUGIN_DIR>/agent_controller/lib to LD_LIBRARY_PATH on Linux

3) call SetConfig.bat on Windows or SetConfig.sh on Linux.
These scripts are placed in the bin directory.
If you have some issue with jaxp, it is probably caused by your JDK. 
What JDK are you using? What error are you getting?

4) Start Eclipse

5) Open the Launch configuration of the JBoss server and add 
-XrunpiAgent:server=enabled to the VM arguments tab

6) Start JBoss Server 

7) Open the Profiling and Logging perspective and call the Profile 
Configurations action

8) Create a new "Attach to agent" configuration, select some data collector in 
the Agents tab

9) call Profile

In the meantime, I solved JBIDE-2093. Hoping that the profile action will be 
available in some next JBoss Tools version. 

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