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Configure maven plugin version without changing pom.xml manually

Problem Description
I'm working with a collection of old projects from defects4j. My problem now is that since I want to combine those projects with a newer maven plugin, a regression test tool, there are some issue with the maven surefire plugin version.
In the pom.xml that come along with the projects, there are no specifications of surefire version:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<executions>
<execution>
<id>plain</id>
<configuration>
<includes>
<include>**/*Test.java</include>
</includes>
<runOrder>random</runOrder>
</configuration>
</execution>
</executions>
</plugin>
However, the regression tool (made into a maven plugin), require surefire version of 2.14 and above. So I get error like this:
[ERROR] Failed to execute goal edu.illinois:starts-maven-plugin:1.4-SNAPSHOT:select (default-cli) on project commons-lang: Unsupported Surefire version: 2.12.4. Use version 2.13 and above
Efforts Done
I checked several stackoverflow posts, and they talked about the effective pom. When I run mvn help:effective-pom, I can see that the version of surefire used is
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.12.4</version>
Question
Since the project collection in defects4j does not specify surefire version in their pom.xml, is there a way to specify the surefire version used to 2.14 or above from command line? I want to prevent from manually editing the pom every time.
Update
by running mvn dependency:resolve-plugins, i get
Plugin Resolved: maven-surefire-plugin-2.12.4.jar
So it seems to me that somehow maven use 2.12.4 as a default. The reason maybe that I used this version previously. How do I fix this?
Without modifying the pom manually?
Any advice will be welcomed!
Update:
Problem solved by editing maven's super pom.

Maven takes the newest version from the repository if there was no version fixed in your POM, parent POM or the super POM (from which every Maven project inherits).
It is best practise to fix a version "manually" in the POM. The best place for this is a parent POM from which the projects inherit (this means, only one place to change).
You cannot just supply a version from command line. Unless you do some tricks like putting <version>${surefire.version}</version> into the plugin definition and set this property from command line.

I'm 4+ years removed from working with poms so don't remember everything, but consider a couple of things.
First, since the pom you show isn't specifying the version of surefire to use I don't think that the 2.12.4 version can be coming from that directly. Try getting a dependency tree to see where things are coming from. Try How can you display the Maven dependency tree for the *plugins* in your project? for that and a few other suggestions.
Second, I think I recall that in your own pom you should be able to specify the version of plugin to associate with a dependency that doesn't specify one. You'll have to research that option yourself.
I think your best bet is the dependency tree to find what's using what and where things are coming from. If you get the tree and still can't figure out what to do try adding the tree output to your question. (You can edit out parts that are proprietary, or clearly unrelated.)

Why is Maven including multiple versions of the same dependency?

I have a Maven java web app (.WAR) project that includes several libraries, including the Wicket libraries (but I don't think the problem is wicket itself, but rather with maven).
Here's the problem: even tho I only include Wicket 6.20.0, the resulting .WAR contains two copies of the Wicket libraries: 6.20.0 and 6.18.0, as you can see in this screenshot:
Thinking of some conflicting imports I printed the dependency tree using the:
mvn dependency:tree
commnad... but there is no mention of Wicket 6.18.0 in the dependency tree! I also double-checked using Eclipse's "dependency hierarchy" view and I can confirm there's no trace of that import.
I even did a search for string "6.18.0" across the entire workspace with Eclipse, but it's nowhere to be found!
How can I find out what is causing the inclusion of that duplicate version of the library?

Maven doesn't work in this way.
The resolution of more than one dependency with the same artifactId and groupId but with a different version will result to a single dependency (the version used is no determinist).
The presence of two artifacts with the same artifactId and groupId but with two distinct versions in a same lib folder of the WAR is probably related to one of these :
you don't execute mvn clean package but only mvn package.
your use a bugged version of the Maven war plugin. Try to update it to check that.
you have a Maven plugin that copies Wicket jars 6.18.0 in the WEB-INF/lib folder of the target folder during the build of the component.
the maven WAR project you are building has as dependency an artifact of type WAR. In this case, the dependencies of the WAR dependency are so overlaid in the WAR project that you are building.
An interesting Maven issue about duplicated JAR because of WAR dependencies :
JARs with different versions can be in WEB-INF/lib with war as dependencies
Your answer and your comment indicate that actually you have a WAR dependency in your build.
Unfortunately, there is not really a good and long term effective solution to bypass this limitation.
As said in my comment, using the packagingExcludes property of the maven war plugin is a valid workaround for the actual issue :
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.4</version>
<configuration>
<!-- ... -->
<packagingExcludes>WEB-INF/lib/wicket-*-6.18.0.jar</packagingExcludes>
</configuration>
</plugin>
But beware, using that will do your build less robust through the time.
The day where you update the version of the WAR dependency and that in its new version, it pulls again a different version of wicket, you have still a risk to have duplicate jars with two distinct versions in your built WAR.
Using the overlay feature by specifying the overlay element of the maven-war-plugin is generally better as it focuses on the overlay applied for the war dependency. It fixes the problem early.
As a result, you could define to exclude any wicket JARs from the WAR dependency :
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<version>2.4</version>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<overlays>
<overlay>
<groupId>com.whatever.youlike</groupId>
<artifactId>myArtifact</artifactId>
<excludes>
<exclude>WEB-INF/lib/wicket-*.jar</exclude>
</excludes>
</overlay>
</overlays>
</configuration>
</plugin>
This way is better but this is still a workaround.
The day where the dependency WAR is updated and that it pulls new dependencies (other than Wicket) that are declared in your actual build but with different versions, you may finish with the same kind of issue.
I think that declaring a dependency on a WAR artifact should be done only as we don't have choice.
As poms and projects refactoring are possible, introducing a common JAR dependency which the two WARs depend on and that contains only common sources and resources for the two WARs makes really things simpler.

Well, I figured it out while poking around.
I had a dependency of type "war" in the project:
<dependency>
<groupId>com.whatever.youlike</groupId>
<artifactId>myArtifact</artifactId>
<version>1.0.7-SNAPSHOT</version>
<type>war</type>
</dependency>
Apparently (I wasn't aware of this, my fault here) these type of dependencies will include themselves in the classpath by copying all libs to the main WAR /libs folder, but these will NOT show app in the dependency tree / dependency hierarchy.
I solved by configuring an explicit exclusion in the WAR plugin:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.4</version>
<configuration>
<!-- ... -->
<packagingExcludes>WEB-INF/lib/wicket-*-6.18.0.jar</packagingExcludes>
</configuration>
</plugin>

Use clean install and the double dependency will probably be gone.

Because other libs can use same libs but different version or you tried different version and didn't make mvn clean

The command mvn dependency:tree is telling you the correct information - what you are looking at here is an eclipse / build issue.
Clear out all the target and build areas in your project. If need be, check it out from source control to a new folder.
Alternatively you can build your project in IntelliJ IDEA, and see if you get the correct dependencies (most likely you will).

Maven Plugin for project semantic versioning

I'm looking for a maven plugin that will help me manage version names and codes of every build that is made on our CI environment. Something that will be able to attach a prefix to the main version code or even update it (not changing the pom.xml). For example:
project version: 2.0.1
git/svn revision: 2342334
jar output: name-2.0.1-2342334.jar
maven repo: ../path/to/local/maven/repo/<package path>/2.0.1-2342334/
The main requirements to this plugin are:
Must be in Maven Repository (which means that NO additional setting required to add this plugin in my pom.xml and run maven)
Must not edit the pom, each time it's applied
A configuration file, would be great, so I could manage the versioning process
Must be able to edit the output file metadata (so the version will be applied as if it was written in the pom.xml file in the first place)
So far I found only maven-buildmetadata-pluging but unfortunately it's not in Maven Repo, so I'm stuck. Any help would be great.

Hosting your own maven repository is very easy, using either Nexus or Artifactory. You can also use the Artifactory cloud version (I'm not affiliated with them...) so it may solve your problem. BTW - a simple server with Apache does the trick as well, but with more work..,
Regarding the plugins: If you deploy snapshot applications then each gets its own version based on timestamp.
For releases another option is to run an svn info and put the result (or part of it) into the generated artifact. The information can then be accessed by the code.

If you change the version of your artifact the pom has to reflect the change, cause otherwise it's not reproducible.
If you change something in your build process (like added versions, whatever) it has to be reflected in the pom file. Otherwise you can not reproduce the build process with the same result.
You have written not to change the pom file but maintaining a separate file. So the questions is: Why not using the pom file itself, cause it's intended exactly for that purpose.
Furthermore all informations which you mentioned by the maven-buildmetadata-plugin can be achived by using existing maven plugins (like build-helper-maven-plugin, buildnumber-maven-plugin).
The SCM information can be used by using the buildnumber-maven-plugin which provides information like SCM revision number (SVN or GIT hash).
An on the other hand if you don't like to change your pom file manually you can use either the versions-maven-plugin or the maven-release-plugin which automatically can change informations in your pom file and handle all these things automatically.
To maintain metadata in your producted artifacts you can configure all plugins (like ear, war, jar) etc. more or less like this where the buildNumber is comming from buildnumber-maven-plugin:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>${maven-jar-plugin.version}</version>
<configuration>
<archive>
<addMavenDescriptor>true</addMavenDescriptor>
<index>true</index>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
<manifestEntries>
<artifactId>${project.artifactId}</artifactId>
<groupId>${project.groupId}</groupId>
<version>${project.version}</version>
<buildNumber>${buildNumber}</buildNumber>
</manifestEntries>
</archive>
</configuration>
</plugin>
And of course if you really like to use Maven you should have to use an repository manager as already mentioned like Artifactory or Nexus which make life easier.

I just would like to add (although the question is 5 years old and already has an accepted answer) that the Buildmetadata Maven Plugin was not available on the Maven Repo at first, but it is now (since late 2013). People who would like to give it a try find the artifact at the following locations :
com.redhat.rcm.maven.plugin:buildmetadata-maven-plugin
de.smartics.maven.plugin:buildmetadata-maven-plugin
Please note that the name has changed from maven-buildmetadata-plugin to buildmetadata-maven-plugin due to naming conventions.
I'm one of the "original" authors of this plugin at smartics. If you would like to use it, you probably would like to use the fork provided by Red Hat. To my knowledge the two versions do not differ very much and they have not been synced since there is just so much other stuff to do and the plugin seems to be feature stable. ;-)
The source code for both versions is also available on GitHub:
release-engineering/buildmetadata-maven-plugin
smartics/buildmetadata-maven-plugin

As already stated, you have to change the version in the pom. One way of doing that, in combination with the release plugin is:
mvn \
se.bjurr.gitchangelog:git-changelog-maven-plugin:VERSION_HERE:semantic-version \
release:prepare release:perform
Using Git Changelog Maven Plugin

How does Maven understand release:prepare command?

I'm trying to create a plugin which would download and install jars from Maven central as system tools. So I want my line to be like
mvn install-plugin:install org.chaschev:cap4j:1.0
similar to Ruby's
gem install capistrano
This plugin would gather all the needed information about the shortcuts to create from the JAR. I.e. this jar would contain a class implementing an installation interface.
How does Maven understand that in order to execute a command like release:prepare it requires to download the release plugin and to run it? Any better/other way to do this?

Do you mean how the relation between plugin/goal in the comamnd line and plugin implementation is defined? Then the answer is plugin.xml. See plugin.xml for release plugin, e.g. maven-release-plugin-2.0.jar:
<goalPrefix>release</goalPrefix>
...
<mojos>
<mojo>
<goal>help</goal>
...
<mojo>
<goal>prepare</goal>
...
Or do you mean, how Maven discovers which plugins are available? Then the answer is:
There are two default groups where plugins are searched, org.apache.maven.plugins and org.codehaus.mojo
For your own plugin you may want to use name ${prefix}-maven-plugin, e.g. cap4j-maven-plugin
You can keep your name cap4j, but then put the plugin description to your POM, under <plugins>
If you want your build to work at other machines, they should point <pluginRepositories> in POM or in settings.xml to your plugin repository

It is not good to use default Maven groups for your own project.
Instead, define your own group for your plugin, like this:
<pluginGroups>
<pluginGroup>org.chaschev</pluginGroup>
</pluginGroups>
And rename your plugin from cap4j to cap4j-maven-plugin. Then Maven will discover your plugin without further cahnges in POM.
Alternative, without <pluginGroups>, just put following to your POM:
<plugins>
<plugin>
<groupId>org.chaschev</groupId>
<artifactId>cap4j</artifactId>
<version>...</version>
<configuration>
...
</configuration>
</plugin>
...
</plugins>

m2e still gives an error saying "Plugin execution not covered by lifecycle configuration" even with explicit bindings in custom plugin

I'm building a plugin to do some code generation.
I've followed the steps here for how to create a plugin:
http://maven.apache.org/guides/plugin/guide-java-plugin-development.html
Plugin Source:
/**
* #goal helloworld
* #phase generate-sources
*/
public class SampleMojo extends AbstractMojo
{
#Override
public void execute() throws MojoExecutionException, MojoFailureException
{
getLog().info("Hello, world.");
}
}
Usage:
<plugins>
<plugin>
<groupId>com.sample</groupId>
<artifactId>sample-maven-plugin</artifactId>
<version>0.0.1</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>helloworld</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
The plugin works fine on its own, but in Eclipse, I keep getting the "not covered by lifecycle" error.
I read through "How to solve “Plugin execution not covered by lifecycle configuration” for Spring Data Maven Builds" and I assumed that if I created my own plugin and set the #phase and #goal annotations it would get rid of that error. I really don't want to put in the "lifecycleMappingMetadata" node in the pom.
Anyone have any advice on this? Is there something special that I need to write for m2e to get that error to go away?

K. Claszen's answer is correct, but I'd like to fill out some extra details.
A. Why is m2e like this?
The point of this behaviour is to prevent m2e from consuming too many resources with incremental (& potentially never-ending) changes.
B. m2e version 1.1 is not a 'release' yet
Currently m2e 1.1 is still a 'milestone'.
Users would need to install/upgrade-to it with this update site:
http://download.eclipse.org/technology/m2e/milestones/1.1
(I also had to uninstall an 'm2e SCM connector' in order to upgrade it)
Right now, this is potentially more hassle for your users than inserting the 'Quick Fix' snippet in their pom.xml files. But, in the long-term it's good to use it.
C. Overview of making your maven plugin m2e-1.1-compatible
As described by K. Claszen, most of the info is here: M2E compatible maven plugins.
Some key points:
Execution information is defined in a file - src/main/resources/META-INF/m2e/lifecycle-mapping-metadata.xml - see M2E compatible maven plugins for format.
If you have enabled 'incremental execution', your Mojo will need to communicate properly with the Maven API:
Specify a dependency to org.codehaus.plexus/plexus-build-api/0.0.1 (current at time of writing)
Use org.codehaus.plexus.build.incremental.BuildContext, to:
Check whether relevant resources have changed
Notify Maven about relevant write operations executed by the plugin, so that it knows to compile sources, etc.
D. Alternatives
If 1.1 isn't a realistic option for your users, you could:
Create an 'M2E Extension Eclipse plugin' (!!), aka an 'M2E Connector', and contribute it to the marketplace. Good luck with that.
Inform your plugin users to select the M2E 'Quick Fix', and then manually change the <ignore /> line to <execute />. There are other SO questions/answers which cover this.

I think the M2E compatible maven plugins site will give you the information you need. Notice that this works first since m2e version 1.1.