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If you undeploy / or /manager then you lose the ability to deploy any application at all. The only workaround is to delete the tomcat directory out of the NB userdir. NB should be smart enough to not allow the user to undeploy these web applications (or at least provide a warning to the user with instructions on how to fix it.)
It seems that this is a new feature of the Tomcat Manager application, this was not possible in the older releases. I agree that it should not be allowed to undeploy the /manager context, however I do not see any harm in allowing to undeploy the ROOT context. TM -> 5.5
F. Checking in src/org/netbeans/modules/tomcat5/Bundle.properties; /cvs/tomcatint/tomcat5/src/org/netbeans/modules/tomcat5/Bundle.properties,v <-- Bundle.properties new revision: 1.26.10.3.2.6; previous revision: 1.26.10.3.2.5 done Checking in src/org/netbeans/modules/tomcat5/TomcatManager.java; /cvs/tomcatint/tomcat5/src/org/netbeans/modules/tomcat5/TomcatManager.java,v <-- TomcatManager.java new revision: 1.76.6.2.2.6; previous revision: 1.76.6.2.2.5 done Checking in src/org/netbeans/modules/tomcat5/nodes/actions/UndeployAction.java; /cvs/tomcatint/tomcat5/src/org/netbeans/modules/tomcat5/nodes/actions/UndeployAction.java,v <-- UndeployAction.java new revision: 1.2.140.2; previous revision: 1.2.140.1 done
Sweet. I didn't realize it was already done. Don't you love when that happens? :)