I have implemented a custom maven mojo to perform some operation on all modules mentioned in the input POM. The mojo works as expected when called from command line like:

mvn plugin_group_id:artifact_id:version:mojo_goal_name

but it doesn't work the same when i make it part of a phase and call the phase like:

mvn phase_having_mojo_as_goal

In this case it does not utilize the reactor and ignores modules.

The plugin POM is:

<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.aaa.bbb.ccc</groupId>
<artifactId>test-maven-plugin</artifactId>
<packaging>maven-plugin</packaging>
<version>1.0.0-SNAPSHOT</version>
<name>release-maven-plugin</name>
<description>Test Plugin</description>
<dependencies>
    <!-- https://mvnrepository.com/artifact/org.eclipse.jgit/org.eclipse.jgit -->
    <dependency>
        <groupId>org.eclipse.jgit</groupId>
        <artifactId>org.eclipse.jgit</artifactId>
        <version>5.7.0.202003110725-r</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/org.apache.maven.shared/maven-invoker -->
    <dependency>
        <groupId>org.apache.maven.shared</groupId>
        <artifactId>maven-invoker</artifactId>
        <version>2.1.1</version>
    </dependency>

    <dependency>
        <groupId>junit</groupId>
        <artifactId>junit</artifactId>
        <version>3.8.1</version>
        <scope>test</scope>
    </dependency>
    <!-- https://mvnrepository.com/artifact/org.apache.maven/maven-artifact -->
    <dependency>
        <groupId>org.apache.maven</groupId>
        <artifactId>maven-artifact</artifactId>
        <version>3.6.3</version>
    </dependency>
    <dependency>
        <groupId>org.eclipse.sisu</groupId>
        <artifactId>org.eclipse.sisu.plexus</artifactId>
        <version>0.3.3</version>
    </dependency>
    <dependency>
        <groupId>org.apache.maven.plugin-testing</groupId>
        <artifactId>maven-plugin-testing-harness</artifactId>
        <version>3.3.0</version>
        <scope>test</scope>
        <exclusions>
            <exclusion>
                <groupId>org.codehaus.plexus</groupId>
                <artifactId>plexus-container-default</artifactId>
            </exclusion>
        </exclusions>
    </dependency>
    <dependency>
        <groupId>org.apache.maven.plugin-tools</groupId>
        <artifactId>maven-plugin-annotations</artifactId>
        <version>3.4</version>
        <scope>provided</scope>
    </dependency>
    <dependency>
        <groupId>org.apache.maven</groupId>
        <artifactId>maven-project</artifactId>
        <version>2.2.1</version>
        <exclusions>
            <exclusion>
                <groupId>org.codehaus.plexus</groupId>
                <artifactId>plexus-container-default</artifactId>
            </exclusion>
        </exclusions>
    </dependency>
    <dependency>
        <groupId>org.twdata.maven</groupId>
        <artifactId>mojo-executor</artifactId>
        <version>2.3.0</version>
    </dependency>

    <dependency>
        <groupId>dom4j</groupId>
        <artifactId>dom4j</artifactId>
        <version>1.6.1</version>
    </dependency>

    <dependency>
        <groupId>org.apache.maven</groupId>
        <artifactId>maven-model</artifactId>
        <version>3.2.5</version>
    </dependency>
    <dependency>
        <groupId>commons-io</groupId>
        <artifactId>commons-io</artifactId>
        <version>2.6</version>
    </dependency>
    <dependency>
        <groupId>jaxen</groupId>
        <artifactId>jaxen</artifactId>
        <version>1.1.1</version>
    </dependency>
    <dependency>
        <groupId>org.apache.maven</groupId>
        <artifactId>maven-compat</artifactId>
        <version>3.2.5</version>
    </dependency>
    <dependency>
        <groupId>org.apache.maven</groupId>
        <artifactId>maven-core</artifactId>
        <version>3.2.5</version>
    </dependency>
    <dependency>
        <groupId>org.apache.maven</groupId>
        <artifactId>maven-aether-provider</artifactId>
        <version>3.2.5</version>
        <scope>test</scope>
    </dependency>
    <dependency>
        <groupId>org.apache.maven</groupId>
        <artifactId>maven-plugin-api</artifactId>
        <version>3.2.5</version>
    </dependency>
    <dependency>
        <groupId>org.codehaus.plexus</groupId>
        <artifactId>plexus-utils</artifactId>
        <version>3.0.15</version>
    </dependency>
</dependencies>
<properties>
    <maven.compiler.source>1.8</maven.compiler.source>
    <maven.compiler.target>1.8</maven.compiler.target>
</properties>

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When you run a goal or phase on an aggregator, it is run on every module.

For standalone goals, this means that the goal is just run on each of the modules.

For a phase, this means that the phase is run on each of the modules. Whether the phase contains the plugin definition is a totally different story.

Your run of the phase happens on every module, but only the aggregator has the definition of the plugin for the phase, the other modules don't have that definition.

You will see that it works if you put the plugin definition in each of the modules or in their parent POM.