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Looks like there are cases when MavenBuilder does not refresh MavenProjectFacade instance after corresponding pom.xml has been modified and saved. Not always reproducible but from code review it appears that if ProjectRegistryManager.refresh could not read MavenProject for whatever reason, MavenBuilder never attempts to re-read it. A workaround is to force update from project right-click menu.
Fixed. http://git.eclipse.org/c/m2e/m2e-core.git/commit/?id=8e465f10e2e4739b7a6fe8ebd1ed117ef8435073 https://github.com/sonatype/m2e-core-tests/commit/1f6a186b6919f280a8699d078707a814e0bb47e6 Also opened separate bug 343568 and corresponding root-cause http://jira.codehaus.org/browse/MNG-5073, which explain why project facade is null quite often.
Moved to https://github.com/eclipse-m2e/m2e-core/issues/