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Spring and Hibernate dependencies are not being resolved

I am having this error message for all the imported packages "The import org..... cannot be resolved". and my Spring and Hibernate dependencies are not being resolved. I have tried multiple solutions to fix this error but nothing seams to work, below are the solution I've tried.
Maven => Update Project but same error. Also did => Force Update of Snapshots/Releases
I have also tried to Right-click on the project and choose Properties, and then Maven. Uncheck the box labelled "Resolve dependencies from Workspace projects", hit Apply, and then OK
Deleted my local Maven repo, the .m2 directory and Restarted Eclipse.
https://i.stack.imgur.com/LCUta.png
'''
<modelVersion>4.0.0</modelVersion>
<groupId>com.luv2code.springdemo</groupId>
<artifactId>spring-crm-rest</artifactId>
<version>1.0.0</version>
<packaging>war</packaging>
<properties>
<springframework.version>5.0.6.RELEASE</springframework.version>
<hibernate.version>5.4.1.Final</hibernate.version>
<mysql.connector.version>5.1.45</mysql.connector.version>
<c3po.version>0.9.5.2</c3po.version>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</properties>
<dependencies>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${springframework.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>${springframework.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${springframework.version}</version>
</dependency>
<!-- Add Jackson for JSON converters -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.9.5</version>
</dependency>
<!-- Hibernate -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version>
</dependency>
<!-- MySQL -->
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysql.connector.version}</version>
</dependency>
<!-- C3PO -->
<dependency>
<groupId>com.mchange</groupId>
<artifactId>c3p0</artifactId>
<version>${c3po.version}</version>
</dependency>
<!-- Servlet+JSP+JSTL -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
</dependency>
<dependency>
<groupId>javax.servlet.jsp</groupId>
<artifactId>javax.servlet.jsp-api</artifactId>
<version>2.3.1</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<!-- to compensate for java 9 not including jaxb -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.0</version>
</dependency>
</dependencies>
<build>
<finalName>spring-crm-rest</finalName>
<plugins>
<!-- Builds a Web Application Archive (WAR) file from the project output
and its dependencies. -->
<plugin>
<!-- Add Maven coordinates (GAV) for: maven-war-plugin -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.0</version>
</plugin>
</plugins>
</build>
'''

You need as first step to run from terminal in your project root directory the mvn clean install command. In this way you will "install the package into the local repository, for use as a dependency". After that for sure you need to refresh your workspace and run a mvn update

A major problem is apparent from the picture you provided, but I'm not sure how you got it into this state.
By default, Maven projects will have a source directory at "src/main/java" and "src/test/java". Your source directory appears to be just "src", so it's finding classes in "main/java/com/..." so it wants the packages to start with "src.main.java.com...".
You appear to have overridden the settings in the .classpath file somehow. If you're using Maven in Eclipse, you should let the m2e plugin determine the classpath.
From what I can see, if you remove the "src" source directory and replace it with "src/main/java", it will more likely be able to compile your code.
Update:
To answer your question in the comment (this is too long for a comment):
Neither. I would suggest copying the project to a location outside of your workspace, if it isn't already outside of the workspace. If the project was already located outside of the workspace, now delete the project, but DO NOT delete the contents. If the project was located inside the workspace, as you've now copied it out, you can delete the project. At this point, go to the location where the project lies outside of the workspace, and delete the ".classpath" file from that location. Now, import the project back into Eclipse. If your project is conventional otherwise, this will "reset" it to a sane organization with respect to m2e.

how to fix "java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory" error when run java jar application

we are using eclipse+spring tool suite to build java application, we can start the application in eclipse IDE, but if we export as jar with all dependency jars, and run it on linux machine. we always gets error as following:
Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
at com.ctrip.framework.apollo.demo.api.SimpleApolloConfigDemo.<clinit>(SimpleApolloConfigDemo.java:22)
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
here is our POM.xml below:
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>apollo</artifactId>
<groupId>com.ctrip.framework.apollo</groupId>
<version>1.3.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>apollo-demo</artifactId>
<name>Apollo Demo</name>
<packaging>jar</packaging>
<properties>
<java.version>1.7</java.version>
<github.path>${project.artifactId}</github.path>
</properties>
<dependencies>
<dependency>
<groupId>com.ctrip.framework.apollo</groupId>
<artifactId>apollo-client</artifactId>
<version>${project.version}</version>
</dependency>
<!-- for spring demo -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
</dependency>
<!-- for spring boot demo -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
<exclusions>
<exclusion>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-log4j2</artifactId>
</dependency>
<!-- for refresh scope demo -->
<dependency>
<groupId>org.springframework.cloud</groupId>
<artifactId>spring-cloud-context</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</dependency>
<!-- take over jcl -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.7.25</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.25</version>
</dependency>
</dependencies>
</project>
2.1 we already included slf4j-log4j12 and slf4j-api as depdency.
2.2 the application can run normally in eclipse IDE window.
2.3 if we export executable jar including all dependencies, and ship jar on linux machine, run the jar file will get the above error.
2.4 we also checked generated jar package on windows with winRAR, the slf4j and log4j* jar package were there, see picture below.
we have struggled this for half day, but did not get any progress. Hope each expert can share with us some light or any suggestions. really appreciated!!!

You need to tell maven to compile the dependencys like this, the jars are compiled but you need the src in youre jar and not the jars in there:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.0.0</version>
<configuration>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
and dependencys normaly have a <scope>compile</scope> tag, to tell the compile that they are needed at runtime

I've faced a similar problem few days ago, right I add the jar libraries but the core (scripts/classes) of the jar file are no included due some reason I was able to solve that problem by right click on the jar file go to properties and set the class path for the classes of that jar folder.
if you wanna check that the jar file has no class Def inside it explore the jar file from the explorer and double click on any class you'll see a page showing up and says there's no script for this class and it asks you to set the class path.
Another approach I tried which also worked for me is I've imported the same jar files on netbeans and they worked 100%

Spring MVC weblogic ClassNotFoundException

I'm trying to setup a basic spring-mvc project with weblogic. I get this stacktrace
weblogic.application.ModuleException: java.lang.ClassNotFoundException: org.springframework.web.servlet.DispatcherServlet
at weblogic.application.internal.ExtensibleModuleWrapper.prepare(ExtensibleModuleWrapper.java:114)
at weblogic.application.internal.flow.ModuleListenerInvoker.prepare(ModuleListenerInvoker.java:100)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:192)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:187)
at weblogic.application.utils.StateMachineDriver$ParallelChange.run(StateMachineDriver.java:83)
Truncated. see log file for complete stacktrace
Caused By: java.lang.ClassNotFoundException: org.springframework.web.servlet.DispatcherServlet
at weblogic.utils.classloaders.GenericClassLoader.findLocalClass(GenericClassLoader.java:1025)
at weblogic.utils.classloaders.GenericClassLoader.findClass(GenericClassLoader.java:986)
at weblogic.utils.classloaders.ChangeAwareClassLoader.findClass(ChangeAwareClassLoader.java:83)
at weblogic.utils.classloaders.GenericClassLoader.doFindClass(GenericClassLoader.java:607)
at weblogic.utils.classloaders.GenericClassLoader.loadClass(GenericClassLoader.java:539)
I have no custom code, I used IntelliJ and Spring. Can you help me?

Your jar dependencies are missing. You have to import them manually or in case of using Maven, add thee lines to your pom.xml, that assures all the dependencies.
<properties>
<spring.version>4.3.2.RELEASE</spring.version>
</properties>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${spring.version}</version>
</dependency>
Then you can clean and rebuild your project. It should be ok.

In same cases this is due to a conflict within WebLogic internal libraries and your application, may be you should try to use this :
<prefer-application-packages>
<package-name>org.springframework.*</package-name>
</prefer-application-packages>

Maven Dependency Nightmare

I am very new to programming and am working my way through a tutorial for Hibernate that includes using Maven. Everything seemed to be going well until I try to mvn compile or spin up my HSQLDB server using the recommended command in the tutorial:
mvn exec:java -Dexec.mainClass="org.hsqldb.Server" -Dexec.args="-database.0 file:target/data/tutorial"
At that point I get a build failure which I will include below, along with my pom. It seems to be telling me that poms are missing for the dependencies but I have no idea how to correct that problem. Any help will be greatly appreciated so that I can move forward with my learning experience.
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.hibernate.tutorials</groupId>
<artifactId>hibernate-tutorial</artifactId>
<version>1.0.0-snapshot</version>
<name>First Hibernate Tutorial</name>
<build>
<!-- we dont want the version to be part of the generated war file name -->
<finalName>${project.artifactId}</finalName>
</build>
<dependencies>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.0.7.final</version>
</dependency>
<!-- Because this is a web app, we also have a dependency on the servlet api. -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>3.1.0</version>
</dependency>
<!-- Hibernate uses slf4j for logging, for our purposes here use the simple backend -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>1.7.14</version>
</dependency>
<!-- Hibernate gives you a choice of bytecode providers between cglib and javassist -->
<dependency>
<groupId>javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.18.1-GA</version>
</dependency>
</dependencies>

Using search.maven.com, it appears that the Hibernate dependency name is hibernate-core-5.0.7.Final. That is, a capital F in Final. So try with
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.0.7.Final</version>
</dependency>
instead

log4j.properties being ignored

I have a Java EE 6 Wicket application deployed with maven using IntelliJ IDEA 9.0.3 on glassfish v3.0.1. I use slf4j-log4j12-1.5.6 with slf4j-api-1.5.8 and log4j-1.2.16 for logging.
It was previously working fine when I deployed through netbeans or eclipse, however when I deploy with IntelliJ IDEA my log4j.properties file is ignored and glassfish's logging handles my log messages. I do not think IDEA has anything to do with it, something else must have changed I just can't figure out what.
I have verified that my log4j.properties file is in my WEB-INF/classes directory and the slf4j/log4j jars are in the WEB-INF/lib directory of my war. Is there some sort of configuration I am missing to make this work?
thanks.
edit: Updated with more info, posted pom dependencies.
Here is the relevant section from my pom.xml:
<!-- Guava -->
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>r05</version>
</dependency>
<!-- Test -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.7</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.glassfish.extras</groupId>
<artifactId>glassfish-embedded-all</artifactId>
<version>3.0</version>
<scope>test</scope>
</dependency>
<!-- Java EE 6 -->
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>bean-validator</artifactId>
<version>3.0-JBoss-4.0.0.Beta3</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>6.0</version>
<scope>provided</scope>
</dependency>
<!-- Wicket -->
<dependency>
<groupId>org.apache.wicket</groupId>
<artifactId>wicket</artifactId>
<version>1.4.9</version>
</dependency>
<dependency>
<groupId>org.apache.wicket</groupId>
<artifactId>wicket-auth-roles</artifactId>
<version>1.4.9</version>
</dependency>
<dependency>
<groupId>org.jboss.weld</groupId>
<artifactId>weld-wicket</artifactId>
<version>1.0.1-Final</version>
</dependency>
<!-- Hibernate -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>3.5.1-Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-annotations</artifactId>
<version>3.5.1-Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-commons-annotations</artifactId>
<version>3.2.0.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>3.5.1-Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-c3p0</artifactId>
<version>3.5.1-Final</version>
</dependency>
<!-- Database -->
<dependency>
<groupId>postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>8.4-701.jdbc4</version>
</dependency>
<!-- Logging -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.5.6</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
</dependencies>

Update: I tried to reproduce the issue. I created a simple Wicket project (same version as you):
mvn archetype:create \
-DarchetypeGroupId=org.apache.wicket \
-DarchetypeArtifactId=wicket-archetype-quickstart \
-DarchetypeVersion=1.4.9 \
-DgroupId=com.mycompany \
-DartifactId=my-wicketapp
Which has a simple log4j.properties logging to the standard output.
log4j.appender.Stdout=org.apache.log4j.ConsoleAppender
log4j.appender.Stdout.layout=org.apache.log4j.PatternLayout
log4j.appender.Stdout.layout.conversionPattern=%-5p - %-26.26c{1} - %m\n
log4j.rootLogger=INFO,Stdout
log4j.logger.org.apache.wicket=INFO
log4j.logger.org.apache.wicket.protocol.http.HttpSessionStore=INFO
log4j.logger.org.apache.wicket.version=INFO
log4j.logger.org.apache.wicket.RequestCycle=INFO
Then:
I added all your dependencies (or modified the versions of existing one to match yours)
I just did some cleanup e.g. in the Hibernate dependencies, you don't need to declare them all, leverage the transitive dependencies mechanism
I added relevant repositories and pluginRepositories
I added glassfish's javax.servlet dependency to make the build pass
I added the embedded-glassfish plugin to test the whole thing
I made a few other unrelated changes
I changed the compiler settings to 1.6
I declared slf4j-api in the dependencyManagement element to control nicely the version in transitive dependencies.
The full pom.xml looks like this (so anybody can reproduce):
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.mycompany</groupId>
<artifactId>my-wicketapp</artifactId>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<!-- TODO project name -->
<name>quickstart</name>
<description/>
<!--
TODO <organization> <name>company name</name> <url>company url</url>
</organization>
-->
<licenses>
<license>
<name>The Apache Software License, Version 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<repositories>
<!-- For Hibernate Artifacts -->
<repository>
<id>repository.jboss.org-public</id>
<name>JBoss repository</name>
<url>https://repository.jboss.org/nexus/content/groups/public</url>
</repository>
<!-- repository for Java EE 6 Binaries -->
<repository>
<id>java.net2</id>
<name>Repository hosting the jee6 artifacts</name>
<url>http://download.java.net/maven/2</url>
</repository>
</repositories>
<pluginRepositories>
<!-- GlassFish repository for the embedded-glassfish plugin -->
<pluginRepository>
<id>glassfish</id>
<name>GlassFish Maven 2 Repository</name>
<url>http://download.java.net/maven/glassfish</url>
</pluginRepository>
</pluginRepositories>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>3.5.5-Final</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>r05</version>
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.servlet</artifactId>
<version>3.0.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>bean-validator</artifactId>
<version>3.0-JBoss-4.0.0.Beta3</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>6.0</version>
<scope>provided</scope>
</dependency>
<!-- WICKET DEPENDENCIES -->
<dependency>
<groupId>org.apache.wicket</groupId>
<artifactId>wicket</artifactId>
<version>${wicket.version}</version>
</dependency>
<dependency>
<groupId>org.apache.wicket</groupId>
<artifactId>wicket-auth-roles</artifactId>
<version>${wicket.version}</version>
</dependency>
<dependency>
<groupId>org.jboss.weld</groupId>
<artifactId>weld-wicket</artifactId>
<version>1.0.1-Final</version>
</dependency>
<!--
OPTIONAL <dependency> <groupId>org.apache.wicket</groupId>
<artifactId>wicket-extensions</artifactId>
<version>${wicket.version}</version> </dependency>
-->
<!-- LOGGING DEPENDENCIES - LOG4J -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
<!-- JUNIT DEPENDENCY FOR TESTING -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.7</version>
<scope>test</scope>
</dependency>
<!-- GLASSFISH EMBEDDED FOR TESTING -->
<dependency>
<groupId>org.glassfish.extras</groupId>
<artifactId>glassfish-embedded-all</artifactId>
<version>3.0.1</version>
<scope>test</scope>
</dependency>
<!-- JETTY DEPENDENCIES FOR TESTING -->
<dependency>
<groupId>org.mortbay.jetty</groupId>
<artifactId>jetty</artifactId>
<version>${jetty.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.mortbay.jetty</groupId>
<artifactId>jetty-util</artifactId>
<version>${jetty.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.mortbay.jetty</groupId>
<artifactId>jetty-management</artifactId>
<version>${jetty.version}</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<filtering>false</filtering>
<directory>src/main/resources</directory>
</resource>
<resource>
<filtering>false</filtering>
<directory>src/main/java</directory>
<includes>
<include>**</include>
</includes>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<testResources>
<testResource>
<filtering>false</filtering>
<directory>src/test/java</directory>
<includes>
<include>**</include>
</includes>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</testResource>
</testResources>
<plugins>
<plugin>
<inherited>true</inherited>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
<optimize>true</optimize>
<debug>true</debug>
</configuration>
</plugin>
<plugin>
<groupId>org.mortbay.jetty</groupId>
<artifactId>maven-jetty-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<configuration>
<downloadSources>true</downloadSources>
</configuration>
</plugin>
<plugin>
<groupId>org.glassfish</groupId>
<artifactId>maven-embedded-glassfish-plugin</artifactId>
<version>3.0.1</version>
<configuration>
<serverID>server</serverID>
<name>server</name>
<app>${project.build.directory}/${project.build.finalName}.war</app>
<port>8080</port>
<instanceRoot>${project.build.directory}/gfe-${maven.build.timestamp}</instanceRoot>
<!--contextRoot>${build.finalName}</contextRoot-->
<autoDelete>true</autoDelete>
<!--configFile>${basedir}/domain.xml</configFile-->
</configuration>
</plugin>
</plugins>
</build>
<properties>
<wicket.version>1.4.9</wicket.version>
<jetty.version>6.1.4</jetty.version>
<slf4j.version>1.5.6</slf4j.version>
</properties>
</project>
And when I run the project with the embedded-glassfish plugin:
$ mvn package
...
$ mvn embedded-glassfish:run
...
and access http://localhost:8080/server in a browser, I get my logs in the standard output as expected:
...
INFO: [WicketApplication] Started Wicket version 1.4.9 in development mode
********************************************************************
*** WARNING: Wicket is running in DEVELOPMENT mode. ***
*** ^^^^^^^^^^^ ***
*** Do NOT deploy to your live server(s) without changing this. ***
*** See Application#getConfigurationType() for more information. ***
********************************************************************
I wonder if this is representative or not.
I have checked the war, log4j.properties is indeed in WEB-INF/classes. I don't have a log4j.jar, i have slf4j-log4j12.jar.
slf4j-log4j12.jar is not a replacement for log4j.jar, slf4j-log4j12.jar is a binding for log4J version 1.2, you still need log4j.jar. From the SLF4J documentation:
Binding with a logging framework at deployment time
As mentioned previously, SLF4J
supports various logging frameworks.
The SLF4J distribution ships with
several jar files referred to as
"SLF4J bindings", with each binding
corresponding to a supported
framework.
slf4j-log4j12-1.6.1.jar: Binding for
log4j version 1.2, a widely used
logging framework. You also need to
place log4j.jar on your class path.
I wonder how you got this working under NetBeans and Eclipse.

I had the exact same problem.
Log4j alone works great:
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
But if I try to use Slf4j over it, then my "src/resources/log4j.properties" file is not found anymore, even if Maven add it to a directory that is on the classpath.
So, this doesn't work out of the box:
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.6.4</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>1.6.4</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<version>1.6.4</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.6.4</version>
</dependency>
To make it work, you have to explicitly add the "log4j.properties" to the classpath or tell the server where to find it! A way to achieve this is (this example is on Windows):
-Dlog4j.configuration=file:C:\[pathToYourProject]\trunk\target\classes\log4j.properties
In Eclipse (if this is what you use), you can add the same line to your Run Configuration / VM arguments.

I suggest removing all the slf4j dependencies and change your logging code to use the Log4j API directly (if this is not too much work, don't know the size of your project). Once this works, consider if you really need the flexibility offered by slf4j. If you do, pick up the correct version of slf4j (slf4j-log4j12 might not be the correct one to use for log4j 1.2.16) and integrate it back in.
I encountered slf4j recently, and in the end removed it altogether because I ran into similar configuration problems.

I had the same problems. The solution is simple - all logging dependencies should be before the glassfish on the classpath.
Note that older Maven2 versions have some problems with the classpath consistency. I use 2.2.1 which have this issue fixed (it was fixed in 2.0.9, I think).

Have a look at the log4j manual. The section "Default Initialization Procedure" describes how log4j will try to find the initialization file. Maybe you can try some of this options to get things work.

The two most likely things that spring to mind are:
make sure the log4j.properties file is in WEB-INF/classes of the deployment. I assume you mean it is in your WEB-INF/classes in your codebase, but have you confirmed this is the case in the war that sent to glassfish
make sure your log4j.jar is in your deployed WEB-INF/lib
Since it's working in some deployment scenarios, I suspect your war packaging when running via Maven is the problem. The above points should help you confirm this.

I have the following logging dependencies :
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>0.9.17</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.5.8</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>1.5.8</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.14</version>
<scope>runtime</scope>
</dependency>
under /src/main/resources/ i have a logback.xml defining the various aspects (appenders,..). This gets picked up by maven and copied to WEB-INF/classes
hope that helped

I would support Adriaan Koster's answer. If your pure log4j doesn't work however, try the following. Create simple class like this
import org.apache.log4j.Logger;
public class LogTest {
private static Logger log;
public static void main(String[] args) {
log = Logger.getLogger(LogTest.class);
}
}
...and put breakpoint in org.apache.log4j.helpers.Loader#getResource method. It tries to pull log4j.xml from classloader:
url = classLoader.getResource(resource);
So you can easily look inside the classloader and see what paths it uses (and why it can't find your log4j.xml).

It is also very important that log4j library was compiled after all modules of the libraries used in the project. If you will not set it as last object, the logs from later modules/libraries wouldn't be displayed in a standard way for log4j.properties.

For people using spring boot:
It appears to ignore -Dlog4j.configuration=file:... You can instead use -Dlogging.config=file:/etc/myconfig/log4j.xml. It must be xml format.
You can also edit the file logback-spring.xml in your java source dir eg src/main/resources/. This is the standard place for the default logging config.
A good source of further information: https://www.baeldung.com/spring-boot-logging

What worked for me: Adding log4j2.properties (or log4j2.xml) to my class path root (tomcat/webapps/ROOT/WEB-INF/classes/). Parameter-value logging is now enabled.
Background: I noticed log4j 1, 2 and slf4j jars in my build. We have slf4j imports in many java files. hibernate.properties was being used and hibernate.show_sql=true worked but I could not enable parameter-value logging. My log4j.properties in the classpath root was being ignored - when the mvn packaged war was run in tomcat. But when I ran it from eclipse, log4j.properties worked and I could enable parameter-value logging.
log4j2.properties used:
appender.console.type = Console
appender.console.name = STDOUT
appender.console.layout.type = PatternLayout
appender.console.layout.pattern = [%-5level] %d{yyyy-MM-dd HH:mm:ss.SSS} [%t] %c{1} - %msg%n
rootLogger.level = info
rootLogger.appenderRef.stdout.ref = STDOUT
logger.hibernate.name=org.hibernate.SQL
logger.hibernate.level=debug
logger.hibernate-type.name=org.hibernate.type
logger.hibernate-type.level=trace
Based on: https://www.codejava.net/frameworks/hibernate/how-to-configure-hibernate-logging-with-log4j2
Search for log4j/slf4j: find /usr/local/tomcat/webapps/ROOT -name '*slf4j*' -o -name '*log4j*'