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When installing as root (with umask 0022, so shouldn't be an issue here), apache-tomcat-6.0.13 gets installed with too strict access restrictions: files within apache-tomcat-6.0.13/conf are not readable by regular users. As a result, when a regular user attempts to execute a web application project within Tomcat, the Tomcat startup will fail with error message: /home/jlaiho/NetBeansProjects/WebApplication1/nbproject/build-impl.xml:548: Deployment error: Starting of Tomcat failed, Tomcat base dir doesn't exist. See the server log for details. ... however, the directory structure does exist - but the configuration files do not - which is revealed by looking at the server log. The relevant log snippets are attached.
Created attachment 50309 [details] WebApplication1 output when trying to run
Created attachment 50310 [details] Tomcat output when trying to start
... and as a clarification, the problem went away when I removed the .netbeans directory from my non-root user, and provided global read access to the files in the NetBeans-installed apache-tomcat-6.0.13/conf directory. After that, when running a web application project, the personal tomcat directory was created just fine with all the configuration files in place. I assume just removing and recreating the server would have been sufficient, but in this case I didn't have anything valuable in the .netbeans directory, so I decided to do it this way.
*** This issue has been marked as a duplicate of 115367 ***