Is the Maven instance that's installed separately (from the maven.org website) different than the one integrated in an Eclipse installation? If so, could I add the correct environmental variables to make the system look at both instances in order to run a project on either instance?
Difference Between Maven Integrated in Eclipse and Maven from maven.org Website
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The Maven2Eclipse plugin is initially configured with an "embedded" Maven distribution, which is used by default. In the "Maven" section of the Eclipse Preferences, and the "Installations" sub-tab, you can see which Maven distributions Eclipse knows about. You can add additional ones, and you can change which one M2E uses for its builds by checking each distribution.