1) You should not modify the configuration files in place while the application 
server is running. Instead, copy the one you want to modify to a temporary 
location, edit it there, and then copy back to deploy. Note that the filesin 
server/xxx/conf are read only on startup. Not sure that you mean by "file 
system access", the app server needs access rights to all the configuration 
files.

2) To deploy your own destinations, create a *-service.xml file, such as 
mydests-service.xml, and place the queue and topic descriptions in there. Copy 
the file to the deploy directory to deploy them, and delete it from there to 
undeploy them.

3) I am not sure I understand what you are asking, but I think you want to 
deploy an exploded directory. You can then easily add/update/remove filesi n 
your application. See 
http://wiki.jboss.org/wiki/Wiki.jsp?page=ExplodedDeployment.

4) You can creat a JAR and deploy it programmatically, but I do not have an 
example.

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