When an Autotools project gets refactored, the project is moved to a different location. This causes problems because the top-level config.status will have directory information that isn't moved. Either all the config.status files need to be changed or else a full reconfiguration should occur on the next build.
A fix has been made to add the project name into the configuration settings file. If the project name doesn't match the current project name, a full reconfigure is performed. Older projects will not be reconfigured the first time after this fix is applied as no reconfiguration is performed if the project information is missing, however, the configure settings file will be rewritten in the new format.