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I had set up a set of instructions for a demo of the web app functionality, which included cleaning out the work directory of tomcat (in case you create several modules with the same packages, which is likely in the demoing context). Jesse Glick interpreted this as deleting the tomcat directory from the user directory. However, doing so while the IDE is running (even if the server itself isn't) apparently leads to problems (I can't remember right what it was right now; in any case you have to restart the IDE to fix it). Jesse's motivation: However it's not quite like deleting a directory in the IDE *installation* which is of course at your own risk. The tomcat406_base dir is in the *user directory* and is created on demand by the tomcatint module when it wants to run Tomcat - it is essentially a disposable directory. So it feels like it should be safe to "revert" the user directory to its state before you ran Tomcat for the first time, by deleting this subdirectory. I suppose tomcatint is storing some extra piece of information elsewhere which tells it that there is already a tomcat406_base dir in the userdir and that it should not autocreate one - this seems a little weird to me.
I'd guess that the server registry holds some information from the basedir in memory. The current behavior I believe is that basedir is created when you open server registry. This code has changed drastically in Tomcat 5, but the basic behavior may be the same. A counterargument against waiting with the creation until I actually deploy is that some users may want to tweak the Tomcat configuration by hand editing the text file before they start the server, and creation of the basedir on deployment makes it harder. There are some additional issues: the data displayed in the UI of the Tomcat plugin is backed by the actual files, so what data should be displayed in the basedir does not exist? How should user modifications be handled? I can also imagine that creating the plugin UI which may or may not be backed by a file will be quite difficult.
I do not see this as a priority for 3.6
Tomcat 4.0 no longer supported and this based on 3.5. Please reopen if the bug is applicable to supported versions for NetBeans 6.5