Hello Pavan, it's hard to tell exactly but in Eclipse (Eclipse JEE at least) if you declare a tomcat instance in the "server" window, and import your maven modules with m2e, you should be able to deploy to Tomcat without problems. No more needs for command-line clean/install/deploy (as long as your project does not do very dirty stuffs). Check the "m2e-wtp" keyword on Google as it's the plugin doing the bridge between Maven in Eclipse and the server deployment stuffs...
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