http://jakarta.apache.org/tomcat/tomcat-4.1-doc/appdev/index.html

the url above discusses the organization in detail.
It also discusses how to use ant to build and deploy and test
you application.

To answer what I think your question:

I put the classes in:
$CATALINA_HOME/webapps/some_project_name/WEB-INF/classes/package/name/Hello.class 
for example.

One of the things that seems to bite people is the servlet invoker was disabled in 
4.1.12 for 
security reasons. Look in the README file for the changes and it will discuss it.
I think there is also mention in conf/web.xml but not sure.

Use the appdev document above, it will make life easier for you
and then you too can tell  the same to the people on the list who post 
subject: URGENT-TOMCAT is broken and ate my whole program
or similiar :-) have fun!

At 03:51 PM 12/22/2002 -0500, you wrote:
>Hello All!
>
>I just upgraded Tomcat 4.0.6 to 4.1.18, but I can't figure out where I should put my 
>class files.  I tried following directories.
>
>$CATALINA_HOME\common\classes
>$CATALINA_HOME\webapps
>$CATALINA_HOME\webapps\ROOT
>
>However, none of them worked.  In the case of Tomcat 4.0, I can put classes in 
>$CATALINA_HOME\classes directory, but  there is not such a directory in 4.1.  Could 
>you tell me where I need to put class files?
>
>Thanks in advance.
>
>
>
>
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