I'm trying to upgrade a perfectly running embedded Tomcat 5.5 to Tomcat 6.0. I understand that all I need to do is replace Tomcat 5.5 jars with 6.0. That's what I did.

So I replaced the following jars:

catalina-5.0.28.jar catalina-5.5.9.jar catalina-optional-5.5.9.jar 
commons-el.jar commons-modeler-1.1.0.jar jasper-compiler-jdt.jar 
jasper-compiler.jar jasper-runtime.jar jmx-5.0.28.jar jsp-api-2.0.jar 
naming-factory.jar naming-resources.jar servlet-api-2.4.jar 
servlets-default.jar tomcat-coyote.jar tomcat-http.jar tomcat-util.jar

with:

annotations-api.jar  catalina.jar    jasper.jar         tomcat-dbcp.jar
catalina-ant.jar     el-api.jar      jsp-api.jar        tomcat-i18n-es.jar
catalina-ha.jar      jasper-el.jar   servlet-api.jar    tomcat-i18n-fr.jar
catalina-tribes.jar  jasper-jdt.jar  tomcat-coyote.jar  tomcat-i18n-ja.jar
tomcat-juli.jar

As soon as I start the server, I get the following message in the logs at INFO level:

INFO: Starting Servlet Engine: Apache Tomcat/6.0.29
Dec 31, 2010 6:04:18 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/usr/local/blah/blue/./WEB-INF/lib/servlet-api.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class

Based on the this explanation, I need to remove a jar file which has a conflicting Servlet.class. I swear to God, there is no other conflicting jar file, I grepped system wide for Servlet.class, it matched only servlet-api.jar.

I also downloaded javaee.jar and replaced it by servlet-api.jar, to same avail.

Having tried lot of these stuff, I did not have much to look upto, so set the tomcat logging level to ALL. In the log I could see that it is trying to check for Servlet.class in each and every jar it is loading until it finds servlet-api.jar and throws "jar not loaded" message as soon as it finds servlet-api.jar. See below:

FINE:  Checking for javax/servlet/Servlet.class
Jan 2, 2011 7:39:33 AM org.apache.catalina.loader.WebappLoader setRepositories
FINE: Deploy JAR /WEB-INF/lib/servlet-api.jar to /usr/local/blah/blue/./WEB-INF/lib/servlet-api.jar
Jan 2, 2011 7:39:33 AM org.apache.catalina.loader.WebappClassLoader addJar
FINE: addJar(/WEB-INF/lib/servlet-api.jar)
Jan 2, 2011 7:39:33 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
FINE:  Checking for javax/servlet/Servlet.class
Jan 2, 2011 7:39:33 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/usr/local/blah/blue/./WEB-INF/lib/servlet-api.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Jan 2, 2011 7:39:33 AM org.apache.catalina.loader.WebappLoader setRepositories

Please note however, that Tomcat starts successfully! And as soon as I hit the URL on the browser, I get blank page(this may be in my case only, I guess 'cuz of my web.xml, sorta different from most. Other people on the internet have got Error 404 instead.) with following log statements(at finest level)

Jan 2, 2011 9:40:01 AM org.apache.catalina.connector.CoyoteAdapter parseSessionCookiesId
FINE:  Requested cookie session id is 0FBA716E3F9B0147C3AF7ABAE3B1C27B
Jan 2, 2011 9:40:01 AM org.apache.catalina.authenticator.AuthenticatorBase invoke
FINE: Security checking request GET /login.jsp
Jan 2, 2011 9:40:01 AM org.apache.catalina.realm.RealmBase findSecurityConstraints
FINE:   Checking constraint 'SecurityConstraint[protected]' against GET /login.jsp --> false
Jan 2, 2011 9:40:01 AM org.apache.catalina.realm.RealmBase findSecurityConstraints
FINE:   Checking constraint 'SecurityConstraint[protected]' against GET /login.jsp --> false
Jan 2, 2011 9:40:01 AM org.apache.catalina.realm.RealmBase findSecurityConstraints
FINE:   Checking constraint 'SecurityConstraint[protected]' against GET /login.jsp --> false
Jan 2, 2011 9:40:01 AM org.apache.catalina.realm.RealmBase findSecurityConstraints
FINE:   Checking constraint 'SecurityConstraint[protected]' against GET /login.jsp --> false
Jan 2, 2011 9:40:01 AM org.apache.catalina.realm.RealmBase findSecurityConstraints
FINE:   No applicable constraint located
Jan 2, 2011 9:40:01 AM org.apache.catalina.authenticator.AuthenticatorBase invoke
FINE:  Not subject to any constraint
Jan 2, 2011 9:40:01 AM org.apache.catalina.core.StandardWrapper allocate
FINEST:   Returning non-STM instance

I'm not sure if the above log message is important, but I'm for all-out disclosure here.

One interesting thing though, I manually created a dummy jsp file containing only "helloooo" just outside WEB-INF folder(no security constraints for this file). This file was accessible and could be displayed. But, all my jsp's and classes are inside WEB-INF(ofcourse).

Sick and tired of this issue, please help me solve it. I've already spent 20-24 hours on this unsuccessfully.

Any pointers directions hints leads?