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The settings you mention all sound fine, but the I believe the Flex War file may be what you referred to as the flex-tomcat files (specifically the one should be called flex.war from the install folder).
You don't need to deploy the flex.war file to JBoss manually, when you create a project, you just select the file in the wizard and it is extracted and used as a template for the new project. In fact, it may cause a port conflict with your project if you do deploy manually it (unless you tweak some of the config files), so it's probably worth removing it from the deploy folder if you did put it there. The other file, flex-admin.war, can stay without causing issue.
The closest to a tutorial that I am aware of is if you search "New Flex Project" in the help system, it talks about what each of the options should be when creating LCDS projects.
A couple of questions/issues:
1. Is Flex builder 3 supposed to set up services-config.xml with the correct server info? Or am I supposed to do it manually for each server targeted?
2. When deploying to a server launched/controlled from the Flex builder IDE, is there some prior setup that needs to be done beforehand? I have tried deploying to JBoss 4.2 and OC4J standalone, using the process indicated in the documentation, but in each case, when Flex 3 builder is attempting to "publish" or "synchronize" the deployed (WAR) file to the server, I get a null pointer exception in the IDE but no log entry in the server. I can see that the WAR file never even gets generated in the appropriate target directory on the server. I have seen reports from others on this problem, but no indication of a resolution.
I did discover that this NPE issue is a WST eclipse plugin (Webtools) bug in version 2.0.2, which apparently occurs because a Flex project has no EAR file. There is apparently a patch for this at the webtools site. Working on trying the patch.
Still looking at the services-config.xml question.
The patch works fine.
And it appears the services-config file is filled in by Flex builder.