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/.
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Using ant simplifies the task. Here is an an ant build.xml file I use to deploy to tomcat 6. (note, I wasn't the origial author of this, but I forget where I got it from)
You have added Tomcat server in eclipse, eclipse runs the WAR file within your workspace. Eclipse does not use your %TOMCAT_HOME%. To be able to see your WAR in the webapps folder simply drop it in there. You will then be albe to run the war from localhost.
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.
If I understand correctly, you have configured eclipse to use Tomcat by adding a new Server. In that case eclipse deploys the war file in folder inside your workspace, NOT at $TOMCAT_HOME/webapps. I can't remember the path in eclipse's workspace folder from the top of my head - it should be something that contains tmp, server, ...