How can I remove maven dependency jar in Eclipse - java

I'm really new to Maven and just converted my app-engine project to a Maven project.
I've added dependencies in the pom.xml file in order to get rid of the errors.
but now I get in my code
The method getPart(String) is undefined for the type HttpServletRequest
So after doing a bit of research on Stack Overflow it appears I need to have a single and updated package of servlet-api to make that work properly.
Apparently I may have a conflict with an older version that is in my Maven dependencies but I never added it in the pom.xml and now I'm stuck with this jar not knowing why it is imported and how I can delete it.
Here is my pom.xml:
<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>my-project</groupId>
<artifactId>my-project</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>war</packaging>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.1</version>
<configuration>
<webResources>
<resource>
<directory>${basedir}/src/main/webapp/WEB-INF</directory>
<filtering>true</filtering>
<targetPath>WEB-INF</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
<plugin>
<groupId>com.google.cloud.tools</groupId>
<artifactId>appengine-maven-plugin</artifactId>
<version>1.3.1</version>
<configuration>
<deploy.promote>true</deploy.promote>
<deploy.stopPreviousVersion>true</deploy.stopPreviousVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
</dependency>
<dependency>
<groupId>com.mailjet</groupId>
<artifactId>mailjet-client</artifactId>
<version>4.2.1</version>
</dependency>
<dependency>
<groupId>com.google.appengine.tools</groupId>
<artifactId>appengine-gcs-client</artifactId>
<version>0.8</version>
</dependency>
</dependencies>
<properties>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</properties>
</project>
and here are images of what I get in Maven dependencies in my build path.
my guess is that the error comes from having a 2.5 version of the servlet-api.
So any help is greatly appreciated, I saw something about the exclusion
tag but don't even know where to put it as it doesn't look like anything in the pom.xml is asking for this jar.

You'd better open in Eclipse your pom.xml file and switch to the "dependency hierarchy" tab. Look for the undesired library (type in "serlvet" in the filter) and add exclusion on it through the context menu. This will modify your pom.xml file.

Delete project from workspace and don't check Delete project content on disk. Delete the jar from .m2 folder as well. Import the project using eclipse. Open the pom file and click on dependency Hierarchy. Select the the jar you want to delete. Right click and click on Exclude Maven Artifact. Next time you run the proejct it will not download the jar.

Related

Eclipse JDT core Java runtime error - java.lang.NoSuchMethodError

I could not find any helping document regarding this error hence I am posting this question.
I am trying to use locally built Eclipse JDT core jar in my project. I followed the flowing steps.
Created an eclipse workspace as described in Link
Built eclipse.jdt.core using the mvn -P build-individual-bundles package
Added the resulting jar file that is created in the target folder to my project (i.e., project A) as a maven dependency.
After the above steps, I could successfully compile project A and now it gives me the following runtime error.
Exception in thread "pool-2-thread-1" java.lang.NoSuchMethodError: org.eclipse.core.runtime.SubMonitor.split(I)Lorg/eclipse/core/runtime/SubMonitor;
at org.eclipse.jdt.core.dom.ASTParser.createAST(ASTParser.java:820)
at utils.JavaASTUtil.parseSource(JavaASTUtil.java:87)
at change.CFile.<init>(CFile.java:32)
at change.RevisionAnalyzer.buildGitModifiedFiles(RevisionAnalyzer.java:310)
at change.RevisionAnalyzer.analyzeGit(RevisionAnalyzer.java:130)
at change.ChangeAnalyzer.analyzeGit(ChangeAnalyzer.java:243)
at change.ChangeAnalyzer.analyzeGit(ChangeAnalyzer.java:228)
at main.MainChangeAnalyzer$2.run(MainChangeAnalyzer.java:99)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
pom.xml of the project is given below
<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>AtomicASTChangeMining</groupId>
<artifactId>AtomicASTChangeMining</artifactId>
<version>0.0.1-SNAPSHOT</version>
<repositories>
<repository>
<id>local-maven-repo</id>
<url>file:///Users/xx/Documents/Research_Topic_2/</url>
</repository>
</repositories>
<build>
<sourceDirectory>src</sourceDirectory>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.5.1</version>
<configuration>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<!--Below is the locally built jdt core jar -->
<dependency>
<groupId>org.eclipse.jdt</groupId>
<artifactId>org.eclipse.jdt.core</artifactId>
<version>3.23.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.eclipse.core</groupId>
<artifactId>runtime</artifactId>
<version>3.10.0-v20140318-2214</version>
</dependency>
<dependency>
<groupId>org.eclipse.birt.runtime</groupId>
<artifactId>org.eclipse.core.resources</artifactId>
<version>3.10.0.v20150423-0755</version>
</dependency>
<dependency>
<groupId>org.eclipse</groupId>
<artifactId>osgi</artifactId>
<version>3.10.0-v20140606-1445</version>
</dependency>
</dependencies>
</project>
Does anybody have any idea about the runtime error?
Thanks a lot!
org.eclipse.core.runtime.SubMonitor is actually in the org.eclipse.equinox.common plug-in.
According to the Javadoc the split methods were added to SubMonitor in version 3.8 of org.eclipse.equinox.common. This corresponds to Eclipse release 4.6.
Do experiments on org.eclipse.core version. You might need to upgrade the version of org.eclipse.birt.runtime. Select the version that contains the method SubMonitor.split().

Classloader with Maven built jar

I am working on a project which contains a number of subprojects. The structure is something like Project 1, Project 2 and ProjectClassLoader.
Using separate configuration files, I pass in the binary names of the classes from Projects 1 and 2 that need to be loaded each time as arguments to the ProjectClassLoader project.
The ProjectClassLoader gets a handle to the system classloader
ClassLoader loader = ClassLoader.getSystemClassLoader();
which in theory allows it to load any classes which are contained in the classpath.
I'm using Maven to build the projects and handle their associated dependences. Thus each project has it's own individual pom.xml file. The ProjectClassLoader defines a parent pom.xml over Projects 1 and 2 which inherit from this. The parent pom contains dependency entries for both Project 1 and 2.
My understanding was that any dependencies specified in the pom.xml files of these projects would get added to the classpath at runtime. However when trying to load classes using the system classloader, I'm getting class not found execptions.
I have tried using the mvn:exec plugin which I understand includes the dependencies in the classpath when executing jars on the command line but this has not worked.
I'd grately appreciate any help in furthering my understanding of why I can load the classes even though the dependencies are defined in the pom...Thanks in advance
Can you check if your pom matches this configuration a bit?
<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">
...
<properties>
...
<exec.maven.plugin.version>1.2.1</exec.maven.plugin.version>
...
</properties>
<build>
<plugins>
...
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
</plugin>
...
</plugins>
<pluginManagement>
<plugins>
...
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>${exec.maven.plugin.version}</version>
<configuration>
<executable>java</executable>
<arguments>
<argument>-classpath</argument>
<!-- automatically creates the classpath using all project dependencies, also adding the project build directory -->
<classpath />
<argument>com.example.Main</argument><!-- your mainClass -->
</arguments>
</configuration>
</plugin>
...
</plugins>
</pluginManagement>
</build>
<dependencies>
...
<dependency>
<groupId>groupId.for.project1</groupId>
<artifactId>project1</artifactId>
</dependency>
<dependency>
<groupId>groupId.for.project2</groupId>
<artifactId>project2</artifactId>
</dependency>
...
</dependencies>
<dependencyManagement>
<dependencies>
...
<dependency>
<groupId>groupId.for.project1</groupId>
<artifactId>project1</artifactId>
<version>${project1.version}</version>
</dependency>
<dependency>
<groupId>groupId.for.project2</groupId>
<artifactId>project2</artifactId>
<version>${project2.version}</version>
</dependency>
...
</dependencies>
</dependencyManagement>
...
</project>
Where you fill them with the correct artifacts.
You should then be able to start it with:
mvn exec:exec
Can you post your configuration for your pom plz if it doesn't match, that way it's easier to understand what exactly you currently have in your pom.

Maven compilation error for android Project "error: package R does not exist "

I am trying to set up a MAVEN project with Android application.
I have this pom file
<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.myproject</groupId>
<artifactId>userprofile</artifactId>
<packaging>jar</packaging>
<version>1.0-SNAPSHOT</version>
<name>userprofile</name>
<url>http://maven.apache.org</url>
<dependencies>
<dependency>
<groupId>com.google.android</groupId>
<artifactId>android</artifactId>
<version>4.1.1.4</version>
<scope>provided</scope>
</dependency>
</dependencies>
</project>
and during MAVEN compile I get this error (about 100 times, ie as many times as it is used in my methods)
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
src\main\java\com\myproject\userprofile\BaseActivity.java:[52,43] error: package R does not exist
Process finished with exit code 1
Any idea about this error? On the web I either find unanswered questions about similar error output. I have no experience on MAVEN, so I believe I am missing something here.
R class is build by your IDE during compilation. MAVEN cannot find the R class because by default the class can be found under build folder. You need to add something like this
<sourceDirectory>build</sourceDirectory>
<outputDirectory>target</outputDirectory>
telling MAVEN that you have some resource files under build folder and you want to make them available to compile so add them under the target folder which will be under your project.
so now I have
build
|----res
|----src
src
|----main
|----java
|----res
target
After a quick look, I believe you're missing the build element. Maven is building the project with current sources, R and other gen classes have not been generated yet. At least you need something like (after dependencies tag):
<build>
<finalName>${project.artifactId}</finalName>
<sourceDirectory>src</sourceDirectory>
<pluginManagement>
<plugins>
<plugin>
<groupId>com.jayway.maven.plugins.android.generation2</groupId>
<artifactId>android-maven-plugin</artifactId>
<version>3.7.0</version>
<extensions>true</extensions>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>com.jayway.maven.plugins.android.generation2</groupId>
<artifactId>android-maven-plugin</artifactId>
<configuration>
<sdk>
<!-- platform or api level (api level 16 = platform 4.1)-->
<platform>16</platform>
</sdk>
</configuration>
</plugin>
</plugins>
</build>
Also the packaging must be apk:
<packaging>apk</packaging>
I would strongly recommend to start reading the Android Maven documentation along with samples.
This error might happen if you had modify the package name that generate by archetype:generate, for me, I use android-quickstart to generate the module structure :
mvn archetype:generate \
-DarchetypeArtifactId=android-quickstart \
-DarchetypeGroupId=de.akquinet.android.archetypes \
-DarchetypeVersion=1.0.11 \
-DgroupId=com.yy.android.gameLibs \
-DartifactId=sample
akquient recommend me to use "com.yy.android.gameLibs" as package name and I accepted, I compile this module successful and worked. After that, I change the package name as "com.yy.android.sample" also change the Androidmenifest.xml package attribute, therefore the module report that error, I follow back the generate command and choice package name myself to solve this.
Modify packaging to apklib, like this:
<packaging>apklib</packaging>
And add build goal at end of pom.xml like this:
<dependencies>
<!--Android deps -->
<dependency>
<groupId>com.google.android</groupId>
<artifactId>android</artifactId>
<version>4.0.1.2</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>com.jayway.maven.plugins.android.generation2</groupId>
<artifactId>android-maven-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<sdk>
<platform>17</platform>
</sdk>
</configuration>
<extensions>true</extensions>
</plugin>
</plugins>
</build>

Maven is not automatically building default folder path in eclipse

I am using Eclipse Indigo. I installed the maven package on eclipse. I configured the Pom and nearly everything is fine. Just maven is not building the default folder bath
src/main/java
Here is the pom.
<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>TestProject</groupId>
<artifactId>TestProject</artifactId>
<version>0.0.1-SNAPSHOT</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.5.6</version>
</dependency>
<dependency>
<groupId>com.lowagie</groupId>
<artifactId>itext</artifactId>
<version>2.0.7</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.6</version>
<configuration>
<ajdtVersion>1.6</ajdtVersion>
</configuration>
</plugin>
</plugins>
</build>
</project>
I cleaned the project,installed and build it.... also I upgradet the project... the dependencies are all fine... no error at all.. why isn't the folder build ?
Eclipse's integration with maven is (to say at least) appalling. If you want to create a new project: create the pom and the folders, and then run mvn eclipse:eclipse to create the project files for eclipse. The simple solution that I've followed for a couple of years is to use the community edition of Intellij.
Aswering your second question: well... again, the integration is so poor that sometimes you'll need to close and reopen the project for eclipse to read the new changes. Most of the time, a refresh + clean project will force eclipse to read the project configuration.

Maven: javax.servlet specification deployed

I've a web application configured with Maven which uses a library, also configured with Maven and when I package geronimo-servlet_3.0_spec-1.0.jar is included in WEB-INF/lib and I don't understand why.
I check the library with mvn dependency:tree
$ mvn dependency:tree | grep geronimo
[INFO] +- org.apache.geronimo.specs:geronimo-servlet_3.0_spec:jar:1.0:provided
I check my web app:
$ mvn dependency:tree | grep geronimo
$
However when I run mvn:package the file gets included in WEB-INF/lib.
When I run mvn tomcat:run I can see:
INFO: validateJarFile(/home/stivlo/workspace/private/src/main/webapp/WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Why and how to avoid? Thank you.
UPDATE 1: as requested I add the pom.xml
<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>org.obliquid</groupId>
<artifactId>test-webapp</artifactId>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<name>private webapp</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<repositories>
<!-- For Jakarta ORO -->
<repository>
<id>mvnsearch</id>
<name>Maven Search</name>
<url>http://www.mvnsearch.org/maven2/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.8.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.4</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<finalName>private</finalName>
</build>
</project>
UPDATE 2: I followed the advice of Stephen C and modified the build section as follows:
<build>
<finalName>private</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war</artifactId>
<version>2.1</version>
<configuration>
<overlays>
<overlay>
<groupId>org.obliquid</groupId>
<artifactId>test-webapp</artifactId>
<excludes>
<exclude>WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar</exclude>
</excludes>
</overlay>
</overlays>
</configuration>
</plugin>
</plugins>
</build>
However geronimo*.jar still gets included. I guess I've made a mistake in this configuration.
UPDATE 3: Stephen C. says that I should use
the groupId the artifactId of the WAR
file that contains the JAR file(s)
that you are trying to exclude.
I didn't know that WAR files could have a groupId and artifactId, in fact in my pom.xml I don't see any. My project builds a WAR file and has a groupId and an artifactId and those were the ones I tested above without success.
The dependency causing the problem is the following (is a JAR, not a WAR):
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
If I try to use the groupId and artifactId listed in this dependency I've the following error:
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-war-plugin:2.1.1:war
(default-war) on project test-webapp:
overlay [ id
org.obliquid.helpers:obliquid-helpers]
is not a dependency of the project. ->
[Help 1]
If I try to use the groupId and artifactId of the JAR included by org.obliquid.helpers:
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>)
I have the same error.
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-war-plugin:2.1.1:war
(default-war) on project test-webapp:
overlay [ id
org.apache.geronimo.specs:geronimo-servlet_3.0_spec]
is not a dependency of the project. ->
[Help 1]
Reading the War plugin documentation, I found a section about creating skinny WARs. So I tried the following:
<build>
<finalName>private</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.1.1</version>
<configuration>
<packagingExcludes>WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar</packagingExcludes>
</configuration>
</plugin>
</plugins>
</build>
Still without any success, geronimo-servlet_3.0_spec-1.0.jar is still there!
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.1.1:war (default-war) on project test-webapp: overlay [ id org.obliquid.helpers:obliquid-helpers] is not a dependency of the project. -> [Help 1]
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.1.1:war (default-war) on project test-webapp: overlay [ id org.apache.geronimo.specs:geronimo-servlet_3.0_spec] is not a dependency of the project. -> [Help 1]
UPDATE 4: I discovered that the target/private.war file is not a zip of target/private/ directory, but the exclusions are done at packaging time and not by deleting files in target/private/ -- This means, I've to re-test all the things I did before.
Suggestion of gouki: doesn't work, the JAR is still there also in the WAR file.
Suggestion of Stephen C., maybe mis-understood: actually I just noticed that the pom.xml is always invalid whatever groupId/artifactId I put of the three possibilities explained above. So they didn't work for me.
What I found in the documentation (packagingExcludes), works.
Now, if I had to choose one of he answers I would choose Stephen C., because he helped me pointing at the documentation of the WAR plugin (I was reading in the wrong places). However I'd accept an answer that doesn't work, at least in the way I tried (probably wrong). So I'm not going to accept any answer, and add a new answer myself with the final working configuration.
UPDATE 5: I post the relevant part of the pom.xml of obliquid-helpers, that mentions geronimo-servlet_3.0_spec. I've marked it optional and with scope provided, still it gets included by a web-app, unless I mark it as "packagingExclude" in the maven-war-plugin configuration.
<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.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<packaging>jar</packaging>
<name>obliquid-helpers</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<repositories>
[...]
</repositories>
<dependencies>
[...]
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
<version>1.0</version>
<scope>provided</scope>
<optional>true</optional>
</dependency>
</dependencies>
</project>
Clearly, something has a dependency on that JAR file. If it is not showing up in the dependency tree, perhaps it is due to a dependency of your webapp WAR file on another WAR file that has this dependency.
If that is the case, then you could get add an <excludes> to the <overlay> element of the build descriptor for the WAR file plugin; e.g.
...
<build>
<finalName>webapp</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.1</version>
<configuration>
<overlays>
<overlay>
<groupId>xxx</groupId>
<artifactId>yyy</artifactId>
<excludes>
<exclude>WEB-INF/lib/whatever.jar</exclude>
</excludes>
</overlay>
</overlays>
</configuration>
</plugin>
</plugins>
</build>
...
If you are using WAR file overlays, you should always include the clean target in the build. Otherwise you can get old dependencies hanging around in the WAR file. (IIRC, there is a Warning in the Maven output each time you build an overlaid WAR without cleaning!)
In fact, this could be the root cause of your problems. For instance, if previously you had the "geronimo" as an ordinary dependency and you haven't run mvn clean since then, the JAR file could still be hanging around.
Based from your pom.xml, the only dependency that might have dependency on geronimo servlet is
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
Can you try excluding the geronimo in this dependency?
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
<exclusions>
<exclusion>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
</exclusion>
</exclusions>
</dependency>
First I want to thank gouki and Stephen C. for helping me. However their proposed solution didn't work for me. I'm grateful to them, but I can't accept their answer, because it would be misleading since it didn't work for this problem. I've upvoted Stephen C. answer, because he pointed me to the right documentation, which was essential to solve the problem.
Reading the WAR plugin documentation, especially the war:war mojo section, I've found an example on how to create Skinny WARs, which did the trick. So here is below the working configuration, to be added to the build section:
<build>
<finalName>private</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.1.1</version>
<configuration>
<packagingExcludes>WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar</packagingExcludes>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
The archive part is probably not really needed, but I will find out when I deploy the WAR. The part that does the trick is the packagingExcludes tag, that can contain a comma separated list of tokens to exclude from the WAR before packaging.

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