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I think the problem is that you are using the public_html directory as both an appBase for your host, and a docBase for your context.
Tomcat is geting confuzzled by this.
Because it is an app_base directory, and you have autoDeploy="true", any directory that you put in public_html becomes a seperate web application/web context - hence 'cal' and 'colors' show up as contexts.
Quick Solution: Edit server.xml to specify your app_base to be a different folder from the one you are using for your context. I would suggest something like '/home/appBase' to make sure it is well out of the way. Restart Tomcat.
Better Solution: Don't declare contexts in server.xml. The preferred method is described as part of the Tomcat documentation