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The files and directories you mention are generated by the build system (rosbuild) in packages which have not been migrated to catkin yet. For packages under version control I add those to my svn:ignore.

As for the make eclipse-project error: see rospkg/issues/39 and ros/issues/20. In summary: older versions of the eclipse-project target generated some files in the package root -- CATKIN_IGNORE to be precise -- which caused rospack to subsequently ignore those directories. The updates to catkin and ros/mk (see answer by Dirk Thomas on 'rosmake does not find my package') should fix this.

In the meantime just removing the generated CATKIN_IGNORE file should at least allow you to build the package again.

The files and directories you mention are generated by the build system (rosbuild) in packages which have not been migrated to catkin yet. For packages under version control I add those to my svn:ignore. (or similar).

As for the make eclipse-project error: see rospkg/issues/39 and ros/issues/20. In summary: older versions of the eclipse-project target generated some files in the package root -- CATKIN_IGNORE to be precise -- which caused rospack to subsequently ignore those directories. The updates to catkin and ros/mk (see answer by Dirk Thomas on 'rosmake does not find my package') should fix this.

In the meantime just removing the generated CATKIN_IGNORE file should at least allow you to build the package again.