In an Eclipse project, I had this pesky error message:
The preferences for the xdoclet runtime does not point to a valid installation.
I wasn't using xdoclet in the project. It turns out that this can occur if some tool (like the WST plug-in) had added xdoclet nature to the project and subsequently removed it. I found a reference to this problem in the Eclipse bug tracker. The bug entry suggested adding and removing xdoclet nature to clear up any left over problem markers. I did this, but then I found out that my project actually had xdoclet nature, along with WST and JEM natures. I guess at some point the project must have been opened by the WST plug-in. The funny thing was that the project did not take on the characteristic look of a WST project in the package explorer. I hand-deleted the various natures from the .project file and then all was well.