An Autotools project can be created by importing a project under CVS with new project wizard and using the Managed Make wizard. The ManagedMake wizard allows one to specify a type of Autotools. When this is done, the Build Special Targets will be disabled, even though the project can be built with configuration.
A fix has been applied that resets the builder to be the Autotools special builder and removes the default ManagedMake builder. This allows special targets to work.