I assume your requirement is a quick deployment and rebuild, since eclipse is the ur IDE. Since you found out that exporting a war file to the webapps folder is not the best option. A few other options:
a) Using sysdeo tomcat plugin - sysdeo deploys the project folder
b) Update the script construct for deployment in a parsed format. - Expand the \ build folder as a sub-application
The first option is the easiest. The second option is cleaner.
[OFF TOPIC] consider switching to tomcat 7
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