I've updated the plugin and while trying out the new stuff noticed
that the plugin seems to ignore the web directory name.

Here is what I've done: (for the record I am using eclipse galileo
SR2)
1) created a wtp project with a default content directory (WebContent)
2) checked "Use Google Web Toolkit"
3) checked "This Project has a WAR directory", entered the name and
unchecked "Launch and deploy from this directory"
4) saved the configuration and since I am using tomcat 6 as container,
changed the order of the gwt library as it is written here:
http://groups.google.com/group/google-web-toolkit/browse_thread/thread/98add5c7f6317fd5
(BTW it would be great if the FAQ would mention it)
5) created a module, html page, entry class (all using wizards)
6) ran the project in tomcat
7) created a debug configuration (all according to
http://code.google.com/eclipse/docs/faq.html#gwt_in_eclipse_for_java_ee)

Now the funny thing is, the manual said that the plugin would ask for
a destination, but it did not. Furthermore it created a war directory
and as a result the project did not work. I've then ran the gwt
compiler which did ask for the destination and compiled my project.
After that everything worked perfectly.

Even though the gwt compiler added a line lastWarOutDir=<correct path
here> to the com.google.gwt.eclipse.core.prefs file in
project's .settings directory, every time I lunch the project for some
reason the plugin still creates the war directory.

I've created another similar project. This time I've created a debug
configuration with "Run built-in server" checked. The plugin did ask
for the destination but still created the war directory.

BTW would it be possible to allow lastWarOutDir to accept relative
paths (relative to workspace that is)? We usually put the settings to
source control so that only one person would have to go through all
the setup process.

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