As advised I removed every version of tomcat on my system.  There were two or 
three others besides the version I was running:
/usr/share/java/tomcat5
/etc/tomcat5
/var/lib/tomcat5
I have always started Tomcat with the sh startup.sh script, in my home 
directory, with CATALINA_HOME set to that Tomcat, and my webapps in that 
versions webapps directory.  When I used Tomcat 5.5 (not these copies) in my 
home directory, there was no problems with the logs, the problems only started 
after moving to Tomcat 6.0.02.  So that wasn't the problem.
Anyhow, I took Chucks advice and moved to the latest version 
apache-tomcat-7.0.5.  Thing works fine out of the box.  Webapp runs, and the 
new catalina.out is 42MBs, better than 50MBs, but still clogged.  Here is a 
sample of some of log entries:

line 43 Jan 8, 2011 6:29:10 AM org.apache.tomcat.util.digester.Digester 
characters
    ... all Digester logs
line 900623 Jan 8, 2011 6:32:41 AM org.apache.tomcat.util.file.Matcher 
tokenizePathAsArray
        FINER: Tokenizing path [ant.jar]
    ... all Matcher logs
line 521583  Jan 8, 2011 6:38:11 AM 
org.apache.jasper.compiler.SmapUtil$SDEInstaller addSDE
        FINE: constant pool count: 378

FINE: 160 read class attr -- 'SourceFile'
Jan 8, 2011 6:38:58 AM org.apache.jasper.compiler.SmapUtil$SDEInstaller 
copyConstantPool

Jan 8, 2011 6:38:58 AM org.apache.jasper.compiler.SmapUtil$SDEInstaller 
copyMembers
FINE: member attr count: 2
...
Jan 8, 2011 6:39:00 AM org.apache.catalina.core.StandardWrapper allocate
FINER:   Returning non-STM instance
...

line 934632 Jan 8, 2011 6:41:03 AM org.apache.catalina.core.ApplicationContext 
log
INFO: IntegratedTestResultAction.perform for -5519451928541341468               
      (<- This is the line where my webapp log starts.)


Here is the properties file settings that the distribution come with:

1catalina.org.apache.juli.FileHandler.level = FINE
1catalina.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
1catalina.org.apache.juli.FileHandler.prefix = catalina.

2localhost.org.apache.juli.FileHandler.level = FINE
2localhost.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
2localhost.org.apache.juli.FileHandler.prefix = localhost.

3manager.org.apache.juli.FileHandler.level = FINE
3manager.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
3manager.org.apache.juli.FileHandler.prefix = manager.

4host-manager.org.apache.juli.FileHandler.level = FINE
4host-manager.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
4host-manager.org.apache.juli.FileHandler.prefix = host-manager.

java.util.logging.ConsoleHandler.level = FINE
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter

org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers = 
2localhost.org.apache.juli.FileHandler

org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level 
= INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].handlers
 = 3manager.org.apache.juli.FileHandler

org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager].level
 = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager].handlers
 = 4host-manager.org.apache.juli.FileHandler

# For example, set the org.apache.catalina.util.LifecycleBase logger to log
# each component that extends LifecycleBase changing state:
#org.apache.catalina.util.LifecycleBase.level = FINE

I changed all THE fine INFO settings to SEVERE, and got the log shown above.  
I'll think about moving to Java update 23 from update 16, but doubt that is the 
problem.  I also added these settings since they seem to be the majority of the 
log entries I don't want to see.:

org.apache.jasper=SEVERE
org.apache.tomcat.util.file.Matcher=SEVERE
org.apache.tomcat.util.digester.Digester=SEVERE

So to me, it really does seem like TOmcat is not using this file, but I don't 
know where to configure anything to make sure.

In the catalina.bat file it says:

if not "%LOGGING_CONFIG%" == "" goto noJuliConfig

set LOGGING_CONFIG=-Dnop

if not exist "%CATALINA_BASE%\conf\logging.properties" goto noJuliConfig

set 
LOGGING_CONFIG=-Djava.util.logging.config.file="%CATALINA_BASE%\conf\logging.properties"

:noJuliConfig

set JAVA_OPTS=%JAVA_OPTS% %LOGGING_CONFIG%

 
if not "%LOGGING_MANAGER%" == "" goto noJuliManager

set 
LOGGING_MANAGER=-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager

:noJuliManager

set JAVA_OPTS=%JAVA_OPTS% %LOGGING_MANAGER%

In the catalina.sh script it says:

# Set juli LogManager config file if it is present and an override has not been 
issued
if [ -z "$LOGGING_CONFIG" ]; then
  if [ -r "$CATALINA_BASE"/conf/logging.properties ]; then
    
LOGGING_CONFIG="-Djava.util.logging.config.file=$CATALINA_BASE/conf/logging.properties"
  else
    # Bugzilla 45585
    LOGGING_CONFIG="-Dnop"
  fi
fi

But as I said above, I use the sh startup.sh command on my system to start 
Tomcat, but there is not mention of logging.properties in that script.
As Konstantin suggested I looked at the catalina.policy file also.  I notice 
the java logging.properties file is also mentioned there, but as I showed in my 
last e-mail, I have changed the settings in that file also.

grant codeBase "file:${catalina.home}/bin/tomcat-juli.jar" {
        permission java.io.FilePermission
         "${java.home}${file.separator}lib${file.separator}logging.properties", 
"read"; 

        permission java.io.FilePermission
         
"${catalina.base}${file.separator}conf${file.separator}logging.properties", 
"read";

Another problem with this logging situation is that my webapp takes more than 
two minutes to load after startup.  What should I try next?

> Date: Fri, 7 Jan 2011 18:01:48 +0300
> Subject: Re: Tomcat 6 logging clog
> From: knst.koli...@gmail.com
> To: users@tomcat.apache.org
> 
> 2011/1/7 Caldarale, Charles R <chuck.caldar...@unisys.com>:
> > From: Tim Space [mailto:qwertypo...@hotmail.com]
> > Subject: Tomcat 6 logging clog
> >
> >> I'm tried modifying both files to no effect:
> >> /apache-tomcat-6.0.20/conf/logging.properties
> >
> > Step 1: move to the current Tomcat version, not one that's nearly two years 
> > old.
> >
> >> /jdk1.6.0_18/jre/lib/logging.properties
> >
> > Not used by Tomcat.  (You should also update your JVM.)
> 
> It is used by Tomcat.
> (Note the rules in catalina.policy that allow reading that file).
> 
> Properties not defined $CATALINA_BASE/conf/logging.properties are
> taken from there.
> 
> Best regards,
> Konstantin Kolinko
> 
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