Eugene,
Actually it is not quite normal. Maven need to know about your plugin repositories and if those repositories are not declared neither in pom.xml nor in settings.xml it won't be find it when you run your build from the command line. However when you run build from the IDE we also use maven and the same settings, so build should work the same way. The only difference is that if you put location of your repository in settings.xml that is located in <m2 home>/conf dir, you need to specify that location in Maven preferences in Eclipse (though those settings only work if you are using external maven location, because we don't have <m2 home> when embedded Maven is used.
the <pluginRepository> section pointing to where freehep-nar can be downloaded is in the project's pom.xml (not in settings.xml. I dont even have a settings.xml file in ~/.m2), shouldnt it be picked up and used by m2eclipse ? (I have copied pom.xml at the end of this post)
We need to make it more explicit, but Maven build is not using indexes registered in the "Maven Indexes" view. Those only used for the artifact search and in few other places in the IDE.
I didnt know that, but now that you say it, it does make sense ...
lease check your maven settings first and make sure that command line and IDE are using the same settings.xml. Usually it is better to put repositories into <user home>/.m2/settings.xml or right into pom.xml
Here is pom.xml for this project (I have no settings.xml):
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";>
 <modelVersion>4.0.0</modelVersion>
 <groupId>myGroupId</groupId>
 <artifactId>myArtifact</artifactId>
 <name>MyName</name>
 <version>0.0.1-SNAPSHOT</version>
 <description/>
 <pluginRepositories>
       <pluginRepository>
           <id>freehep-maven</id>
           <name>Maven FreeHEP</name>
           <url>http://java.freehep.org/maven2</url>
       </pluginRepository>
 </pluginRepositories>
 <build>
     <sourceDirectory>${basedir}/src</sourceDirectory>
     <plugins>
       <plugin>
           <groupId>org.freehep</groupId>
           <artifactId>freehep-nar-plugin</artifactId>
           <version>2.0-alpha-10</version>
           <extensions>true</extensions>
       </plugin>
       <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-compiler-plugin</artifactId>
           <configuration>
               <source>1.6</source>
               <target>1.6</target>
           </configuration>
</plugin> </plugins>
 </build>
 <dependencies>
   <dependency>
     <groupId>junit</groupId>
     <artifactId>junit</artifactId>
     <version>4.4</version>
   </dependency>
   ... (more dependecies here)
 </dependencies>
</project>

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