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tomcat cannot see the log4j.xml file after changing the default path

I have a war file that I deployed with Tomcat.
I have a Dockerfile and at the end I build a kubernetes pod.
The problem is that if my property files from my app do exist in the path: /usr/local/tomcat/webapps/myapp/WEB-INF/classes/config/ and not in path /usr/local/tomcat/webapps/myapp/WEB-INF/classes/, so the application does not start.
In config I have connection.properties and log4j2.xml.
I set another path by this method:
RUN sed -i -e 's/^shared.loader=$/shared.loader="${catalina.base}/webapps/napgui/WEB-INF/classes/config"/' /usr/local/tomcat/conf/catalina.properties
Everything is fine except log4j2.xml. The values ​​from Kubernetes are overwritten here in the container on log4j but it seems that this path is not good for log4j because in the container logs I receive errors related to the old log4j. From what I understand, he look for the first time in WEB-INF/classes and if can't find any log4j file then it look in WEB-INF/lib and there is the jar with the old log4j, and hence the errors related to the old log4j. Why not consider the one in the new path and what should be done? Thank you

cannot find files while app running on cloud foundry

When running the app locally, it works. However, after I build a jar with maven and push it to cloud foundry, it cannot find the krb5.keytab file through the local absolute file path
The krb5.keytab's path are setting in my application.yml file. e.g
keytab:
key: krb5.keytab
file: C:\Users\Documents\WorkSpace\MyProject\kafkatool\krb5.keytab
How do I need to change the file path of krb5.keytab so when it's running on cloud foundry the app can still find the keytab?

When your Java application runs on CloudFoundry, it's running in a remote Linux container. It does not have access to your local file system and any files you reference need to be within the Linux container's filesystem, thus no c:\ Windows-style paths are going to work.
Your application, when running on CF, lives in the /home/vcap/app directory (there's also a symlink at /app which points to /home/vcap/app that you can use if you want).
In addition, your application will be executed out of the /home/vcap/app directory so the current working directory will be /home/vcap/app.
Thus, if you need to reference files you can either reference them relative to the /home/vcap/app directory or you can prefix the /home/vcap/app to all paths and use a full path to the file.
If you don't like the idea of hard-coding /home/vcap/app into your application, you can fetch this directory dynamically by looking at the HOME environment variable. When your application runs, the HOME env variable points to /home/vcap/app.

Read external .properties file from the install directory (not the current directory)

I am distributing a Spring Boot application as a zipped "bootJar" using the Gradle Application plugin and the "distZip" task. The end-user will get the zip file, unzip it, and run it by just typing "myApp" (a shell script nicely created by the plugin).
I would like the end-user to create a "myapp.properties" file (a name I chose) and put it in the installation directory, or a "config" directory under the installation directory.
Suppose I set up my embedded (in the jar) application.properties file as follows:
spring.config.import = file:./myapp.properties will only read from the current directory
spring.config.import = file:/etc/myapp.properties will read from the specified directory -- but I don't know what this is at build time (the end-user determines it at installation time)
How can I set up my application so that Spring Boot can read properties from an external file whose location is specified later?
NOTE: I know I can play around with the generated scripts to pass in environment variables or Spring Boot properties, but I was hoping to do this completely within Spring Boot so I don't need to modify the nicely generated shell scripts.

spring.config.import = file:./myapp.properties will only read from the
current directory spring.config.import = file:/etc/myapp.properties
will read from the specified directory -- but I don't know what this
is at build time (the end-user determines it at installation time)
Why overcomplicate this.
Place inside the jar all the properties that you want to be statically configured as default values when you build the application.
Embedded application.properties
server.port = 8080
prop1.element = something
Then the client can create another file application.properties and place it in the same directory with the jar and define more properties which are not already defined.
prop2.element = something2
prop3.element = something3
By default Spring Boot will load properties both from the embedded file as well from the file in the current directory where the jar is placed during startup.
In the external application.properties you can also overwrite properties existing in the embedded application.properties. So if the external file in the current directory same as the jar is the following
prop2.element = something2
prop3.element = something3
prop1.element = something4 <--- this value here will overwrite the value 'something' from embedded file
According to spring doc
SpringApplication will load properties from application.properties
files in the following locations and add them to the Spring
Environment:
/config subdirectory of the current directory.
The current directory
classpath /config package
The classpath root The list is ordered by
Precedence (properties defined in locations higher in the list
override those defined in lower locations).
After having more input from the comments, it seems that you face another issue as well. You start the application from command line from another directory so that is counted as the directory where spring will look for the external configuration instead of where the jar is placed.
So for example let's say that the jar is placed inside the target folder that exists in current directory. You start the application using the following command:
java -jar target/demo-0.0.1-SNAPSHOT.jar
But then the external application.properties existing inside target folder is not loaded from spring because you executed the command from another directory. This can be solved if you start the application in the following way
java -jar -Dspring.config.additional-location=./target/ target/demo-0.0.1-SNAPSHOT.jar
This should not be difficult as you already provide the path where the jar exists in the command line.

How to use external configuration files with Spring boot deployed in Tomcat 8.5

My Spring Boot application (2.1.1.RELEASE) is deployed as a WAR in a Tomcat 8.5 server under a Debian 9 system. It uses, among others, the following files to configure the application :
myApplication.properties (main configuration file for Spring)
log4j2.xml
Both are under src/main/resources.
My question is about how to configure Tomcat and Spring Boot in a way that allow me to have a directory /home/oliver/conf which contains both of these files, in order to override the defaults defined under src/main/resources (which are then in WEB-INF/classes in the exploded WAR).
Below are the steps I've taken.
First, and as a requirement for the project I'm working on, I changed the default Tomcat base directory to point to another place by editing /etc/init.d/tomcat8 :
CATALINA_HOME=/usr/share/tomcat8
CATALINA_BASE=/home/oliver
My /home/oliver/conf folder, which holds the Tomcat and Spring configs, looks like this :
- Catalina/
- context.xml
- web.xml
- server.xml
- ...
- myApplication.properties
- log4j2.xml
- otherAppConfFile.properties
- ...
Because Spring looks for application.properties by default, I'm using the #PropertySource annotation to specify another file :
#SpringBootApplication
#PropertySource({classpath: myApplication.properties})
public class MyApp extends SpringBootServletInitializer {...}
I've tried to add -Dspring.config.location=file:/home/oliver/conf/myApplication.properties to JAVA_OPTS defined in /etc/default/tomcat8, and it works (overrides the embedded file correctly), but for instance if I try to add file:/etc/oliver/conf/log4j2.xml to the previous JVM parameter, it doesn't work.
I read a bit about Spring "environment profiles" but don't wish to use them if possible.
When I launch Tomcat and issue a ps aux | grep tomcat command, I see all the JAVA_OPTS parameters defined as expected, and I also see the following :
-classpath :/home/oliver/conf:/usr/share/tomcat8/bin/.... -Dcatalina.base=/home/oliver -Dcatalina.home=/usr/share/tomcat8
I'm a bit confused about the way Tomcat's classpath and Spring's are related, and how I should solve this issue.
If the classpath I see at launch includes the /home/oliver/conf directory, why are the files inside not overriding the embedded property files (myApplication.properties, log4j2.xml ...) ? Is the folder seen and added to Spring's classpath ?
EDIT :
As a side note, there might be a variety of files under /home/oliver/conf which would need to be taken into account, for instance log4j2.xml + myApplication.properties + keystore.jks so I'm not sure I can rely on -Dspring.config.location and -Dlogging.config entirely.

What I understand from your question is that you are trying to do something like this.
-Dspring.config.location=file:/etc/oliver/conf/log4j2.xml
I think the property spring.config.location is to provide the location of a properties file for configuration and not log4j2.xml.
You can set the location of the log file in myApplication.properties by setting the value for logging.config like
logging.config=file:/etc/oliver/conf/log4j2.xml
Or else you can try
-Dlogging.config=file:/etc/oliver/conf/log4j2.xml
UPDATE
This is what I do in my production systems. Create a file setenv.sh and enter below command.
export JAVA_OPTS="$JAVA_OPTS -Djavax.net.ssl.trustStore=/path/to/keystore/keystore.jks -Djavax.net.ssl.trustStorePassword=changeit -Dspring.profiles.active=qa -Dspring.config.location=/path/to/config/ -Dfws_log=/path/to/logfile/location -Xms512m -Xmx1024m -Dsecret.key=somesecretkey"
You can add any number of key value mappings in this file and all of them will be loaded when your tomcat starts.

How to force Tomcat doesn't write data (like logs, temp, ets) to its own root folder?

I'd like to create a desktop standalone application from my Java/Spring web application. I created MSI-installer that copy all required files to C:\Program Files (x86)\App. But tomcat doesn't have permission and can't write to its own folder. How I can configure tomcat so it would write all app-specific data to other folder? I wouldn't like to install my app to C:\App or user dir.
java.io.FileNotFoundException: C:\Program Files (x86)\App\tomcat\logs\catalina.2016-06-18.log (Access denied)

By setting the environment variable CATALINA_BASE to another directory in your tomcat start script you can configure Tomcat to read/put the working data, configuration and stuff from/to another location. If CATALINA_BASE is set, Tomcat will use the folders %CATALINA_BASE%/bin, %CATALINA_BASE%/conf, %CATALINA_BASE%/logs, %CATALINA_BASE%/temp, etc. for the current instance of Tomcat. This is described in more detail in the Advanced Configuration - Multiple Tomcat Instances section of the RUNNING.txt file in Tomcat's root folder.
If you are planning to ship Tomcat with your application and put all Tomcat files to some user choosable folder you should set CATALINA_HOME to this folder. Tomcat will then use this folder as base directory for everything.
However I think, as you mentioned to ship a standalone application based on Spring, you should seriously take a look at Spring Boot. This will allow you to ship a single fat jar containing all of your application's dependencies (including Tomcat). And this application can simply be started by executing the jar file.
If it's just about the log and temp files, you can set the Java system properties java.util.logging.config.file and java.io.tmpdir in the setenv.bat file under %CATALINA_BASE%/bin to make Tomcat use a custom logging configuration and a different temp dir, respectively. That is the file would look something like this:
set CATALINA_OPTS="-Djava.util.logging.config.file=file:///c:/path/to/log/config.properties"
set CATALINA_OPTS="%CATALINA_OPTS% -Djava.io.tmpdir=c:/path/to/temp/dir"

Find and update all occurrences of "$CATALINA_BASE"/logs/catalina.out to custom path in catalina.sh script.