When you create a project, you may want to share the settings so that the next person can easily check it out as a project. If given project root matches with exactly one folder in source control system, you may commit the project metadata files back into source control (.project and .cproject). If your project is attached to version control but you don't want it to be committed, you have to add those files to the ignore list.
QNX projects share most of their options in common.mks itself, however, some options (such as the current build variants) are user-specific (i.e. not in the project metadata). You can make them shared by enabling Share project properties on the Main tab for the QNX project properties.