I think the problem may have to do with m2e configuration:
https://www.eclipse.org/m2e/documentation/m2e-execution-not-covered.html
I'm not done reading the above doc, but it looks like that there is some configuration we must do and perhaps some stuff needed in the poms.
Apparently m2e has a "lifecycle-mapping" which maps information from the poms to the workspace project configuration and build. Under Preferences->Maven->Lifecycle Mappings you can set the location for the lifecycle map file, open it or reload it. By default it's in the new workspace under .metadata/.plugins/org.eclipse.m2e.core/lifecycle-mapping-metadata.xml, but apparently there is no such file on a fresh install.
As for the working sets, the relevant bit in the log shows this:
[2016-05-09 11:23:32] Importing project papyrus-rt-php
[2016-05-09 11:23:33] Performing Working Sets (Papyrus-RT JUnit Framework)
[2016-05-09 11:23:33] Performing Working Sets (Papyrus UML-RT Profile + Papyrus UML-RT Profile Tests)
[2016-05-09 11:23:33] Performing Working Sets (Papyrus UML-RT Core + Papyrus UML-RT Core Tests)
[2016-05-09 11:23:33] Performing Working Sets (Papyrus UML-RT Tooling + Papyrus UML-RT Tooling Tests)
[2016-05-09 11:23:33] Performing Working Sets (Papyrus UML-RT Codegen + Papyrus UML-RT Codegen Tests)
[2016-05-09 11:23:33] Performing Working Sets (Papyrus XtUML-RT + Papyrus XtUML-RT Tests)
[2016-05-09 11:23:33] Performing Working Sets (Papyrus UML-RT Releng + Papyrus UML-RT Features)
[2016-05-09 11:23:34] Performing Working Sets (Papyrus-RT Website)
[2016-05-09 11:23:34]
so there doesn't seem to be anything different.