On tomcat shutdown : it fails to close the application threads (references threads and thread local).
After calling the shutdown command, I have to kill the process manually using :
kill <pid> (but sometimes a simple kill is not enough => I have to use a kill -9)

Stack trace from the catalina.out :

Nov 15, 2010 11:10:37 AM org.apache.coyote.http11.Http11Protocol pause
INFO: Pausing Coyote HTTP/1.1 on http-8007
Nov 15, 2010 11:10:38 AM org.apache.catalina.core.StandardService stop
INFO: Stopping service Catalina
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping subversion
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping ssh-slaves
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping maven-plugin
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping dashboard-view
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping copy-to-slave
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping dependencyanalyzer
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping email-ext
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping emotional-hudson
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping svn-tag
Nov 15, 2010 11:10:38 AM hudson.PluginWrapper stop
INFO: Stopping build-timeout
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/hudson] appears to have started a thread named [hudson initialization thread] but has failed to stop it. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/hudson] appears to have started a thread named [com.google.common.base.internal.Finalizer] but has failed to stop it. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/hudson] appears to have started a thread named [Loading job xxxxxxx] but has failed to stop it. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/hudson] appears to have started a thread named [Loading job xxxxxxx] but has failed to stop it. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@1f: Authentication: org.acegisecurity.providers.UsernamePasswordAuthenticationToken@1f: Username: SYSTEM; Password: [PROTECTED]; Authenticated: false; Details: null; Not granted any authorities]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@1f: Authentication: org.acegisecurity.providers.UsernamePasswordAuthenticationToken@1f: Username: SYSTEM; Password: [PROTECTED]; Authenticated: false; Details: null; Not granted any authorities]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [hudson.model.Run$1@1571dff]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@b61f11ff]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@a06d25]) and a value of type [org.acegisecurity.context.SecurityContextImpl] (value [org.acegisecurity.context.SecurityContextImpl@1f: Authentication: org.acegisecurity.providers.UsernamePasswordAuthenticationToken@1f: Username: SYSTEM; Password: [PROTECTED]; Authenticated: false; Details: null; Not granted any authorities]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [hudson.model.Run$1@1571dff]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@b61f11ff]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Nov 15, 2010 11:10:38 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/hudson] created a ThreadLocal with key of type [null] (value [org.kohsuke.stapler.Stapler$1@5dd915]) and a value of type [java.text.SimpleDateFormat] (value [java.text.SimpleDateFormat@c4dc9900]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.