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java logging level eclipse vs production

For some reason for my website, I am seeing different logging and format between my eclipse development ( debugging locally with jetty ) and the production machine ( tomcat ). Why is that?
What I really want is to increase the logging level to FINE in eclipse, while I am debugging it, but then get rid of FINE in production. But if I cannot do that, I would at least like the 2 places to behave similarly.
Some tomcat configuration. Does not really explain what is happening with Eclipse/Jetty, but maybe it will give someone an idea on how to help me.
+ ls --color -lrt /etc/tomcat6/logging.properties /etc/tomcat6/log4j.properties
-rw-r--r--. 1 root tomcat 547 Oct 30 2017 /etc/tomcat6/log4j.properties
-rwxrwx---. 1 tomcat tomcat 3753 Sep 14 20:37 /etc/tomcat6/logging.properties
+ grep level /etc/tomcat6/logging.properties
1catalina.org.apache.juli.FileHandler.level = CONFIG
2localhost.org.apache.juli.FileHandler.level = CONFIG
3manager.org.apache.juli.FileHandler.level = ALL
4admin.org.apache.juli.FileHandler.level = ALL
5host-manager.org.apache.juli.FileHandler.level = ALL
java.util.logging.ConsoleHandler.level = CONFIG
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = ALL
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level = ALL
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/admin].level = ALL
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager].level = ALL
#org.apache.catalina.startup.ContextConfig.level = FINE
#org.apache.catalina.startup.HostConfig.level = FINE
#org.apache.catalina.session.ManagerBase.level = FINE
#org.apache.catalina.core.AprLifecycleListener.level=FINE
+ more /etc/tomcat6/log4j.properties
log4j.rootLogger=debug, R
log4j.appender.R=org.apache.log4j.RollingFileAppender
log4j.appender.R.File=${catalina.home}/logs/tomcat.log
log4j.appender.R.MaxFileSize=10MB
log4j.appender.R.MaxBackupIndex=10
log4j.appender.R.layout=org.apache.log4j.PatternLayout
log4j.appender.R.layout.ConversionPattern=%p %t %c - %m%n
log4j.logger.org.apache.catalina=DEBUG, R
log4j.logger.org.apache.catalina.core.ContainerBase.[Catalina].[localhost]=DEBUG, R
log4j.logger.org.apache.catalina.core=DEBUG, R
log4j.logger.org.apache.catalina.session=DEBUG, R
Edit 2: jetty is being use via the "jetty-maven-plugin" using the goal "jetty:run", if that helps any.
Edit 3: Changing log4j.properties did not remove "FINE" logging ( I changed all debug/DEBUG to INFO ).
Also, for tomcat, here it is running:
tomcat 24403 1 6 17:22 ? 00:00:27 /usr/java/latest/bin/java -Djavax.sql.DataSource.Factory=org.apache.commons.dbcp.BasicDataSourceFactory -classpath :/usr/share/tomcat6/bin/bootstrap.jar:/usr/share/tomcat6/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat6 -Dcatalina.home=/usr/share/tomcat6 -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat6/temp **-Djava.util.logging.config.file=/usr/share/tomcat6/conf/logging.properties** **-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager** org.apache.catalina.startup.Bootstrap start
I already showed part of the logging properties file above, but here is the full thing:
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
handlers = 1catalina.org.apache.juli.FileHandler, 2localhost.org.apache.juli.FileHandler, 3manager.org.apache.juli.FileHandler, 4admin.org.apache.juli.FileHandler, 5host-manager.org.apache.juli.FileHandler
, java.util.logging.ConsoleHandler
.handlers = 1catalina.org.apache.juli.FileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
1catalina.org.apache.juli.FileHandler.level = CONFIG
1catalina.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
1catalina.org.apache.juli.FileHandler.prefix = catalina.
2localhost.org.apache.juli.FileHandler.level = CONFIG
2localhost.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
2localhost.org.apache.juli.FileHandler.prefix = localhost.
3manager.org.apache.juli.FileHandler.level = ALL
3manager.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
3manager.org.apache.juli.FileHandler.prefix = manager.
4admin.org.apache.juli.FileHandler.level = ALL
4admin.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
4admin.org.apache.juli.FileHandler.prefix = admin.
5host-manager.org.apache.juli.FileHandler.level = ALL
5host-manager.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
5host-manager.org.apache.juli.FileHandler.prefix = host-manager.
java.util.logging.ConsoleHandler.level = CONFIG
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
1catalina.java.util.logging.SimpleFormatter.format=[%1$tF %1$tT %tZ] %4$s %2$s %5$s%6$s%n
############################################################
# Facility specific properties.
# Provides extra control for each logger.
############################################################
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = ALL
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers = 2localhost.org.apache.juli.FileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level = ALL
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].handlers = 3manager.org.apache.juli.FileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/admin].level = ALL
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/admin].handlers = 4admin.org.apache.juli.FileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager].level = ALL
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager].handlers = 5host-manager.org.apache.juli.FileHandler
# For example, set the com.xyz.foo logger to only log SEVERE
# messages:
#org.apache.catalina.startup.ContextConfig.level = FINE
#org.apache.catalina.startup.HostConfig.level = FINE
#org.apache.catalina.session.ManagerBase.level = FINE
#org.apache.catalina.core.AprLifecycleListener.level=FINE
5host-manager.org.apache.juli.FileHandler.level = ALL
5host-manager.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
5host-manager.org.apache.juli.FileHandler.prefix = host-manager.
My biggest confusion is still my inability to see finer grained logging in my jetty/eclipse testing, where it would actually be helpful.

Why is catalina.out empty

I have logrotate working perfectly, only thing is that when the log file is saved with the date at the end of the filename like: catalina.out-20180926. But there is nothing being logged to catalina.out.
Everything is owned by root, tomcat is running under root. I've restarted tomcat as a service and it restarts fine creating a new log file of the restart logs, then nothing is logged until I restart the service again.
My logging properties file looks like this;
handlers = 1catalina.org.apache.juli.AsyncFileHandler, 2localhost.org.apache.juli.AsyncFileHandler, 3manager.org.apache.juli.AsyncFileHandler, 4host-manager.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
.handlers = 1catalina.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
1catalina.org.apache.juli.AsyncFileHandler.level = FINE
1catalina.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
1catalina.org.apache.juli.AsyncFileHandler.prefix = catalina.
2localhost.org.apache.juli.AsyncFileHandler.level = FINE
2localhost.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
2localhost.org.apache.juli.AsyncFileHandler.prefix = localhost.
3manager.org.apache.juli.AsyncFileHandler.level = FINE
3manager.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
3manager.org.apache.juli.AsyncFileHandler.prefix = manager.
4host-manager.org.apache.juli.AsyncFileHandler.level = FINE
4host-manager.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
4host-manager.org.apache.juli.AsyncFileHandler.prefix = host-manager.
java.util.logging.ConsoleHandler.level = FINE
java.util.logging.ConsoleHandler.formatter = org.apache.juli.OneLineFormatter
############################################################
# Facility specific properties.
# Provides extra control for each logger.
############################################################
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers = 2localhost.org.apache.juli.AsyncFileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].handlers = 3manager.org.apache.juli.AsyncFileHandler
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.AsyncFileHandler
# 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
# To see debug messages in TldLocationsCache, uncomment the following line:
#org.apache.jasper.compiler.TldLocationsCache.level = FINE
Any ideas?

After moving from SysV init scripts to the Systemd service units, Tomcat standard output and error streams are no longer logged to catalina.out. If you need to see stdout and stderr logs, you can find them in the journal:
journalctl -u tomcat
If you want to follow the Tomcat stdout+stderr log, you can use:
journalctl -f -u tomcat
See the last 100 lines:
journalctl -n100 -u tomcat
For more information, see systemd and journald documentation.

HikariCP(2.4.6) in Tomcat(8.0.32) lib directory doesn't log

While logging works nicely when the hikari(2.4.6) jar is bundled in the application's war, when we move it to Tomcat(8.0.32) /lib directory, hikari stops logging. I have followed a similar issue in hikaricp github (809) where there was some guidance in achieving this, but I cannot get it to work. For our application it is very crucial to monitor the pool:
2017-02-01 12:27:17.274 DEBUG 26240 --- [l-1 housekeeper] com.zaxxer.hikari.pool.HikariPool : HikariPool-1 - Pool stats (total=10, active=0, idle=10, waiting=0)
so we need a way to get this info in catalina.out
My tomcat setup is as following:
/lib directory:
and my logging.properties:
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
handlers = 1catalina.org.apache.juli.AsyncFileHandler, 2localhost.org.apache.juli.AsyncFileHandler, 3manager.org.apache.juli.AsyncFileHandler, 4host-manager.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
.handlers = 1catalina.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
1catalina.org.apache.juli.AsyncFileHandler.level = FINEST
1catalina.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
1catalina.org.apache.juli.AsyncFileHandler.prefix = catalina.
2localhost.org.apache.juli.AsyncFileHandler.level = FINE
2localhost.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
2localhost.org.apache.juli.AsyncFileHandler.prefix = localhost.
3manager.org.apache.juli.AsyncFileHandler.level = FINE
3manager.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
3manager.org.apache.juli.AsyncFileHandler.prefix = manager.
4host-manager.org.apache.juli.AsyncFileHandler.level = FINE
4host-manager.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
4host-manager.org.apache.juli.AsyncFileHandler.prefix = host-manager.
java.util.logging.ConsoleHandler.level = FINE
java.util.logging.ConsoleHandler.formatter = org.apache.juli.OneLineFormatter
############################################################
# Facility specific properties.
# Provides extra control for each logger.
############################################################
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers = 2localhost.org.apache.juli.AsyncFileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].handlers = 3manager.org.apache.juli.AsyncFileHandler
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.AsyncFileHandler
# 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
# To see debug messages in TldLocationsCache, uncomment the following line:
#org.apache.jasper.compiler.TldLocationsCache.level = FINE
com.zaxxer.hikari.level = FINEST
com.zaxxer.hikari.handlers = 1catalina.org.apache.juli.AsyncFileHandler
Please provide me some info on how to get this working.
Thank you very much

Solution:
First of all, tomcat server internal logging must be changed from Apache Commons Logging to log4j. The procedure to do this is described here.
Assuming having read the links above and downloaded the aforementioned jars from the extras bundle (tomcat-juli-adapters.jar, tomcat-juli.jar)
log4j.properties file should be placed to tomcat/lib directory.
Delete or rename logging.properties file from tomcat/conf directory, so tomcat doesn't pick it up during startup.
Copy the following jars to tomcat/lib directory: log4j-1.2.17.jar, tomcat-juli-adapters.jar
Copy and replace the following jar to tomcat/bin directory: tomcat-juli.jar
After the above steps, tomcat should now log using log4j.
To enable HikariCP logging do the following:
Edit log4j.properties file and at the end add the following line:
log4j.logger.com.zaxxer.hikari = DEBUG
Make sure the following jars exist in tomcat/lib directory:
HikariCP-2.4.6.jar
jcl-over-slf4j-1.7.21.jar
slf4j-api-1.7.21.jar
slf4j-log4j12-1.7.21.jar
jul-to-slf4j-1.7.21.jar
My log4j.properties file:
log4j.rootLogger = INFO, CATALINA
# Define all the appenders
log4j.appender.CATALINA = org.apache.log4j.DailyRollingFileAppender
log4j.appender.CATALINA.File = ${catalina.base}/logs/catalina
log4j.appender.CATALINA.Append = true
log4j.appender.CATALINA.Encoding = UTF-8
# Roll-over the log once per day
log4j.appender.CATALINA.DatePattern = '.'yyyy-MM-dd'.log'
log4j.appender.CATALINA.layout = org.apache.log4j.PatternLayout
log4j.appender.CATALINA.layout.ConversionPattern = %d [%t] %-5p %c- %m%n
log4j.appender.LOCALHOST = org.apache.log4j.DailyRollingFileAppender
log4j.appender.LOCALHOST.File = ${catalina.base}/logs/localhost
log4j.appender.LOCALHOST.Append = true
log4j.appender.LOCALHOST.Encoding = UTF-8
log4j.appender.LOCALHOST.DatePattern = '.'yyyy-MM-dd'.log'
log4j.appender.LOCALHOST.layout = org.apache.log4j.PatternLayout
log4j.appender.LOCALHOST.layout.ConversionPattern = %d [%t] %-5p %c- %m%n
log4j.appender.MANAGER = org.apache.log4j.DailyRollingFileAppender
log4j.appender.MANAGER.File = ${catalina.base}/logs/manager
log4j.appender.MANAGER.Append = true
log4j.appender.MANAGER.Encoding = UTF-8
log4j.appender.MANAGER.DatePattern = '.'yyyy-MM-dd'.log'
log4j.appender.MANAGER.layout = org.apache.log4j.PatternLayout
log4j.appender.MANAGER.layout.ConversionPattern = %d [%t] %-5p %c- %m%n
log4j.appender.HOST-MANAGER = org.apache.log4j.DailyRollingFileAppender
log4j.appender.HOST-MANAGER.File = ${catalina.base}/logs/host-manager
log4j.appender.HOST-MANAGER.Append = true
log4j.appender.HOST-MANAGER.Encoding = UTF-8
log4j.appender.HOST-MANAGER.DatePattern = '.'yyyy-MM-dd'.log'
log4j.appender.HOST-MANAGER.layout = org.apache.log4j.PatternLayout
log4j.appender.HOST-MANAGER.layout.ConversionPattern = %d [%t] %-5p %c- %m%n
log4j.appender.CONSOLE = org.apache.log4j.ConsoleAppender
log4j.appender.CONSOLE.Encoding = UTF-8
log4j.appender.CONSOLE.layout = org.apache.log4j.PatternLayout
log4j.appender.CONSOLE.layout.ConversionPattern = %d [%t] %-5p %c- %m%n
# Configure which loggers log to which appenders
log4j.logger.org.apache.catalina.core.ContainerBase.[Catalina].[localhost] = INFO, LOCALHOST
log4j.logger.org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager] =\
INFO, MANAGER
log4j.logger.org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager] =\
INFO, HOST-MANAGER
log4j.logger.com.zaxxer.hikari = DEBUG

Prevent Tomcat logging from going to stderr?

I currently have multiple web applications deployed in Tomcat which is running as a Windows service. I created/modified most of the logging.properties files to (hopefully) create a separate log file for each web application.
My conf\logging.properties looks like:
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
handlers = 1catalina.org.apache.juli.AsyncFileHandler, 2localhost.org.apache.juli.AsyncFileHandler, 3manager.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
.handlers = 1catalina.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
1catalina.org.apache.juli.AsyncFileHandler.level = FINE 1catalina.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs 1catalina.org.apache.juli.AsyncFileHandler.prefix = catalina.
2localhost.org.apache.juli.AsyncFileHandler.level = FINE 2localhost.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs 2localhost.org.apache.juli.AsyncFileHandler.prefix = localhost.
3manager.org.apache.juli.AsyncFileHandler.level = FINE 3manager.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs 3manager.org.apache.juli.AsyncFileHandler.prefix
= manager.
java.util.logging.ConsoleHandler.level = FINE java.util.logging.ConsoleHandler.formatter = org.apache.juli.OneLineFormatter
############################################################
# Facility specific properties.
# Provides extra control for each logger.
############################################################
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = INFO org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers
= 2localhost.org.apache.juli.AsyncFileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level
= INFO org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].handlers
= 3manager.org.apache.juli.AsyncFileHandler
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.AsyncFileHandler
# 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
# To see debug messages in TldLocationsCache, uncomment the following line:
#org.apache.jasper.compiler.TldLocationsCache.level = FINE
# To see debug messages for HTTP/2 handling, uncomment the following line:
#org.apache.coyote.http2.level = FINE
# To see debug messages for WebSocket handling, uncomment the following line:
#org.apache.tomcat.websocket.level = FINE
Each of my web apps has the following logging.properties file int he WEB-INF\classes folder:
handlers = org.apache.juli.FileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
org.apache.juli.FileHandler.level = FINE
org.apache.juli.FileHandler.directory = ${catalina.base}/logs
org.apache.juli.FileHandler.prefix = prefix.
java.util.logging.ConsoleHandler.level = FINE
java.util.logging.ConsoleHandler.formatter = org.apache.juli.OneLineFormatter
I am currently logging everything within my web applications on the INFO level like so:
Logger.getLogger("LOG").log(Level.INFO, "Stuff to log");
Things seem to be relatively close to how I was hoping. Stdout seems to be correctly going to the individual web application logs, but EVERYTHING also seems to be going to the tomcat8-stderr log as well.
I tried commenting out the ConsoleHandler from ALL config.properties, but I was still getting the same behavior. How do I prevent everything from also being logged in the stderr log?
I added this to my Context.xml, but that did not seem to change anything:
<Context swallowOutput="true">

I was able to fix this by setting the Level of my web application loggers to FINE and changing the web application ConsoleHandler level in logging.properties to INFO.

As documented in Official Tomcat site, the private package-renamed implementation of Apache Commons Logging namely JULI does have exceptions. the .handlers directive is defining the ROOT logger which in turn is the only possible output for calls that are coming directly from ClassLoader of common jars such as the StandardEngine ones or the java.sql driver ones. Unless a specific handler is assigned by class name after which a method call like java.util.logging.Logger.getLogger() could get potentially get a grip.
To use the so called "Facility specific properties" tomcat-juli features of per Engine, per Host and per Context log, the logging.properties in effect is the global tomcat logging configuration initially loaded at Engine startup :
The calls to javax.servlet.ServletContext.log(...) to write log
messages are handled by internal Tomcat logging. Such messages are
logged to the category named
org.apache.catalina.core.ContainerBase.[${engine}].[${host}].[${context}]
This logging is performed according to the Tomcat logging
configuration. You cannot overwrite it in a web application.
However,
JULI [...] supports per classloader configuration, in addition to the regular global java.util.logging configuration. This means that logging can be configured at the following layers:
Globally. That is usually done in the ${catalina.base}/conf/logging.properties file. The file is specified by the java.util.logging.config.file System property which is set by the startup scripts. If it is not readable or is not configured, the default is to use the ${java.home}/lib/logging.properties file in the JRE.
In the web application. The file will be WEB-INF/classes/logging.properties
So after making some various tests, I realized that I was not able to reproduce your issue, as I successfully logged from an application exclusively and entirely to the prefix.yyyy-mm-dd.log file defined in the per application WEB-INF/classes/logging.properties.
I say "entirely" taking into consideration that if the web application uses System.out.print(), the printed stuff will only show up in the "prefix."-files if swallowOutput is set to true in the context.xml (whether it be from the application's META-INF/context.xml or from the ${CATALINA_BASE}/conf/context.xml file.
Tweaking the logging levels to avoid the situation you where is not to my opinion an elegant bypass and I hope you have not settled down to that and will share your final resolution unless the problem vanished since !

Logging Oracle Java Stored Procedure using Java Logging API (java.util.logging )

I've developed a new Java(1.4) Stored Procedure in Oracle (10g). I've never done this before, I usually keep Java and the DB separated but this was a requisite. So I developed a Java code that can be deployed in Tomcat as well as a Stored Procedure in Oracle. For this I used the Java Logging API.
I can execute the stored procedure in Oracle, but I can't find the logs. I would like to know what should I do in order to print the logs, it can be to Oracle logs or trc files, or even, if possible, configure it to print the logs to another specific folder.
Does anyone know how to achieve this?

As appointed by PeskyGnat in this answer you have to create a logging.properties file in the folder:
$ORACLE_HOME/javavm/lib
After you configure this file, you can see the logs in:
$ORACLE_BASE/admin/$INSTANCE/udump
In my case, this was Solaris so the first path was:
/export/home/oracle/app/oracle/product/10.2.0/Db_1/javavm/lib
And the second one:
/export/home/oracle/app/oracle/admin/
As extra information, in order to make easy to find the log file you can type in Bash shell the following:
ls -altr
And this is an example of how the logging.properties file:
############################################################
# Default Logging Configuration File
#
# You can use a different file by specifying a filename
# with the java.util.logging.config.file system property.
# For example java -Djava.util.logging.config.file=myfile
############################################################
############################################################
# Global properties
############################################################
# "handlers" specifies a comma separated list of log Handler
# classes. These handlers will be installed during VM startup.
# Note that these classes must be on the system classpath.
# By default we only configure a ConsoleHandler, which will only
# show messages at the INFO and above levels.
handlers= java.util.logging.ConsoleHandler
# To also add the FileHandler, use the following line instead.
#handlers= java.util.logging.FileHandler, java.util.logging.ConsoleHandler
# Default global logging level.
# This specifies which kinds of events are logged across
# all loggers. For any given facility this global level
# can be overriden by a facility specific level
# Note that the ConsoleHandler also has a separate level
# setting to limit messages printed to the console.
.level= INFO
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
# default file output is in user's home directory.
java.util.logging.FileHandler.pattern = %h/java%u.log
java.util.logging.FileHandler.limit = 50000
java.util.logging.FileHandler.count = 1
java.util.logging.FileHandler.formatter = java.util.logging.XMLFormatter
# Limit the message that are printed on the console to INFO and above.
java.util.logging.ConsoleHandler.level = INFO
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
############################################################
# Facility specific properties.
# Provides extra control for each logger.
############################################################
# For example, set the com.xyz.foo logger to only log SEVERE
# messages:
**<your.class.logger>.level = <level> (i.e.: INFO)**