I have used Jboss and deployment happens by dropping war to deploy folder. But when I set my war project to Tomcat server eclipse claims that it is deploying war, but I cannot see my war in webapps folder. And what url is to my war? In jboss I can add app url to jboss-web.xml, so when I set app path to jboss-web.xml I can find my app from http://localhost:8080/my_app_path_in_jboss_web.xml/.
I deploy WARs to the webapps dir all the time without issue, probably ~25 times a day. You shouldn't have any problems with that. If you want more control by all means deploy the directory yourself, but this will most likely require a restart.
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