Looking further I discovered that when installing as Eclipse plugin, this warning is given:
SwitchYard 0.6 and earlier require a version of m2e-wtp which is incompatible with the version used by JBT 4.0. This means SY <= 0.6 and earlier can only be installed with JBT 3.3 and SY > 0.6 can only be installed with JBT 4.0.
I am, however, unable to find SwitchYard > 0.6 for JBDS
Solved this by adding http://download.jboss.org/jbosstools/updates/integration/juno/soa-tooling/switchyard/ to my update site and installing SY from there.
(I'm not deleting this question as it may help somebody else)
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Indigo is the 'official' Eclipse platform for SwitchYard 0.6 tooling. That said, I used the 0.6 tooling with Juno for quite some time without issues. SwitchYard 0.7 tooling, due out in the next week, will have support for Juno and JBDS 6.0.
That's not the impression I got from https://docs.jboss.org/author/display/SWITCHYARD/Getting+Started#GettingStarted-InstallingEclipseTooling. I updated https://docs.jboss.org/author/display/SWITCHYARD/Installing+Eclipse+Tooling accordingly (hope that's OK)?
I guess the source of confusion there is that the documentation referenced the "latest" version of JBDS, which changed behind the link to JBDS downloads in our docs. :-) It used to be JBDS 5, but now's it 6. I think the note you added is helpful for the time being. Once 0.7 is out we can remove all the Indigo stuff and just reference JBDS 6 and Juno.