In general, I would like to know if JBoss Tools runs somehow a "mvn package" or something to create the package or if it is a completely separate process.
JBoss Tools uses the WTP deployment engine that isn't related to Maven.
If you are getting different applications when using "mvn package" and the JBoss Tools Publish action, please create a jira on https://jira.jboss.org/jira/browse/JBIDE
Thanks for the answer! The thing is that I use Maven's resource filtering. I need the Maven's process-resources lifecycle phase to be executed just before publishing (using a Maven profile I use for development). Currently, what I'm doing is a "mvn package" or "mvn package -Pdevelopment" and then I publish the project.
I don't if this is possible knowing that the process is controlled by WTP ...
m2eclipse would need to do resource filtering, but I am not sure if it does that.
Could you create a jira and attach an example of your project?