This is the Catalina base directory (CATALINA_BASE) of the Tomcat
server that is bundled with the IDE ("the internal Tomcat
installation"). Tomcat can be configured to use separate directories
for the configuration files (the Catalina base directory) and the
binaries and shared libraries (the Catalina home directory,
CATALINA_HOME). This is how the internal Tomcat server is set up. This
is different from a typical Tomcat installation.  See
http://jakarta.apache.org/tomcat/tomcat-4.0-doc/RUNNING.txt for more
information.

In the Internal Tomcat server installation, the base directory is
owned by the user and resides in a directory called tomcat406_base
under the directory that the IDE associates with the user. The home
directory is shared by all users who use the same installation of
the IDE, and resides in tomcat406 under the IDE root.

This directory contains the configuration files that the IDE uses when 
it starts the internal server. Expert users can modify these files
with a text editor in this directory. Some properties of the files can 
also be modified through the IDE: open the Explorer window, select the 
J2EE server tab and select the node for the internal server. 

If you wish to deploy classes or libraries that are to be shared by
multiple web modules, they need to be placed in the appropriate place
in the Catalina home directory. Appropriate places are 

$IDEROOT/tomcat406/classes 
$IDEROOT/tomcat406/lib/
$IDEROOT/tomcat406/common/classes 
$IDEROOT/tomcat406/common/lib/

Classes or libraries placed under common can be loaded
both by web applications and by the server itself. Those placed in
classes and lib are only available to web applications. 

Tomcat loads web module elements in the classpath for servlet
execution and debugging in following order:

    1.WEB-INF/classes directory of your web module 
    2.WEB-INF/lib/*.jar directory of your web module 
    3.Bootstrap classes of your JVM 
    4.System class loader classes 
    5.$CATALINA_HOME/common/classes  ($CATALINA_HOME = $IDEROOT/tomcat406)
    6.$CATALINA_HOME/common/lib/*.jar 
    7.$CATALINA_HOME/classes 
    8.$CATALINA_HOME/lib/*.jar 

Do not add shared libraries to the tomcat406_base directory, they will
not be loaded. 

If several developers share the same IDE installation, they need to
exercise caution when adding shared libraries to the tomcat406
directory.  Libraries stored in the tomcat406 directory are shared by
all web modules that are deployed on the server, so there is a risk of 
version conflicts.