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Maven jandex plugin does not generate index for local custom maven repositories (sometimes)

I have a multi module maven project wie quarkus modules and some custom libraries which are local maven repositories (so they can be used by the other maven projects/modules). However, so that local maven repositories are recognizable und usable by your other local maven projects, you have to manually index them for some reason. I.e. add a config like this for quarkus index to the application.properties of the project including the local maven repo dependency:
quarkus.index-dependency.<index-name>.group-id = <group-id-of-local-maven-repo>
quarkus.index-dependency.<index-name>.artifact-id = <artifact-id-of-local-maven-repo>
The problem is, this causes issues for me becausse if you have 3 layers of project dependencies, say:
Project A (custom local maven repo library)
Project B (custom local maven repo library, includes Project A dependency)
application.properties (indexing Project A library dependency)
Project C (Local maven project for an end product, includes Project B
library dependency - and through it indirectly Project A).
application.properties (indexing Project B library dependency and config for datasources or other app related things)
Then when you generate an uber-jar (fat jar) of Project C for deployment, it for some reason uses application.properties of Project B in the packaged jar, instead of from the project which im building (Project C). Thus, the app is missing key configs and does not work. Maven seems to use an inverse priority here, which i dont know if thats a bug or not. When i asked about this, i was simply told that:
"My dependencies should not have application.properties".
I tried to find a way to prevent manual indexing via application.properties and found the maven jandex plugin - which is supposed to generate an index. The next problem is, this seems to only work in some projects but not in others in the dependency hierarchy, resulting in the same situation as before, and i don't understand why. This is the pom.xml config for the plugin i have included in all 3 projects (the entire pom.xml for all is too long, so let me know if you need more info):
<properties>
...
<jandex.skip>false</jandex.skip>
...
</properties>
...
<build>
...
<plugin>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.5</version>
<inherited>true</inherited>
<executions>
<execution>
<id>make-index</id>
<goals>
<goal>jandex</goal>
</goals>
</execution>
</executions>
<configuration>
<skip>${jandex.skip}</skip>
</configuration>
</plugin>
...
The odd thing is, this works to the extend that i no longer have to index Project B library dependency in Project C application.properties, but Project B library dependency still has to manually index Project A library dependency - thus rendering the entire exercise futile. Project C having an application.properties was never the issue, and is obviously needed. Project B still requires a properties file to point to Project A now, how do i solve this?
I have a parent module POM in the root folder containing all these projects, over which this maven jandex dependency is distributed to all modules, so it looks like this:
Maven parent module (contains all dependencies and versions used by all project sub modules)
Project A (custom local maven library repo), own pom.xml with inheritance from parent module
Project B (custom local maven library repo, includes Project A library), own pom.xml with inheritance from parent module
application.properties - Indexes Project A dependency manually, this is the problematic one which needs to go!
Project C (Local maven project for REST API etc., includes Project B library), own pom.xml with inheritance from parent module
pom.xml (parent module POM, containing maven jandex dependepency among others)
Edit: One of the projects, "entity", where all the database access objects are stored, does not run the jandex plugin during mvn clean install. This is the POM of the project:
<?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">
<modelVersion>4.0.0</modelVersion>
<groupId>com.compamny.project</groupId>
<artifactId>entity</artifactId>
<version>1.0-SNAPSHOT</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-hibernate-orm</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-hibernate-validator</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-resteasy-reactive-jackson</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jdk8</artifactId>
<version>2.13.3</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.smallrye/jandex-maven-plugin -->
<dependency>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.0</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.0</version>
<inherited>true</inherited>
<executions>
<execution>
<id>make-index</id>
<goals>
<goal>jandex</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
When i force the execution of the jandex goal with mvn io.smallrye:jandex-maven-plugin:3.0.0:jandex it creates an META-INF/jandex.jdx file, but it does not produce one when i run mvn clean install. This is not a solution since i need to build the project, run the jandex plugin and install it into my local repositories separately. Also, notice that im using the "io.smallrye" version of the jandex plugin since the "org.jboss" version seems to not work at all.

I figured it out. The jandex plugin was set in the <pluginManagement> section of the POM configuration, which made it not run on mvn clean install. I had to move it to the plugins section so it gets executed. Thanks #Ladicek for making me look closer and keep trying!

How can I remove maven dependency jar in Eclipse

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.

using super pom only for testing

I have a lot of maven projects, which are dependent on each other.
I already have a super pom for the actual projects and this works pretty well.
Now I want to create a super pom for all my integrationtests projects. I did it the same, but every time I run maven test it failed.
[ERROR] Failed to execute goal on project *: Could not resolve
dependencies for project ::jar:0.0.1-SNAPSHOT: The following
artifacts could not be resolved: ::jar:0.0.1-SNAPSHOT,
::jar:0.0.1-SNAPSHOT, ::jar:0.0.1-SNAPSHOT, ::jar:0.0.1-SNAPSHOT: Could not find artifact *:***:jar:0.0.1-SNAPSHOT -> [Help 1]
The problem is that maven looks for jar files but my project consists of war projects. Here is my 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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>***</groupId>
<artifactId>***-parent_IntegrationTests</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>pom</packaging>
<name>***_IntegrationTests</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.0</version>
</plugin>
</plugins>
</pluginManagement>
</build>
<modules>
<module>../***</module>
<module>../***</module>
<module>../***</module>
<module>../***</module>
<module>../***</module>
<module>../***</module>
</modules>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
</dependencies>
Is there a way to tell maven to use the war files instead of jars?
Edit: Sorry if it is not clear enough. I want a single maven project to run all my integrationtest projects. each one is a maven project. Therefor I want to use a pom with modules (all the integrationtest project) in it. But every integrationtest project contains dependencies to my other projects and the problem I want to fix is that maven does not find my compiled projects because it looks for jar files but my projects are war files.

You can reference WARs as dependencies by using <type>war</type> in the dependency.

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: 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.