The ThirdParty/netcdf/vtknetcdf directory contains a reduced distribution of the NetCDF source tree with only the library source code needed by VTK. It is not a submodule; the actual content is part of our source tree and changes can be made and committed directly. We update from upstream using Git's "subtree" merge strategy. A special branch contains commits of upstream netcdf snapshots and nothing else. No Git ref points explicitly to the head of this branch, but it is merged into our history. Update netcdf from upstream as follows. Create a local branch to explicitly reference the upstream snapshot branch head: git branch netcdf-upstream c3ace7de Use a temporary directory to checkout the branch: mkdir netcdf-tmp cd netcdf-tmp git init git pull .. netcdf-upstream rm -rf * Now place the (reduced) netcdf content in this directory. See instructions shown by git log c3ace7de for help extracting the content from the upstream tarball. Then run the following commands to commit the new version. Substitute the appropriate date and version number: git add --all GIT_AUTHOR_NAME='NetCDF Developers \ GIT_AUTHOR_EMAIL='netcdfgroup@unidata.ucar.edu' \ GIT_AUTHOR_DATE='2011-03-29 18:00:00 -0400' \ git commit -m 'netcdf 4.1.2 (reduced)' && git commit --amend Edit the commit message to describe the procedure used to obtain the content. Then push the changes back up to the main local repository: git push .. HEAD:netcdf-upstream cd .. rm -rf netcdf-tmp Create a topic in the main repository on which to perform the update: git checkout -b update-netcdf master Merge the netcdf-upstream branch as a subtree: git merge -s recursive -X subtree=ThirdParty/netcdf/vtknetcdf \ netcdf-upstream If there are conflicts, resolve them and commit. Build and test the tree. Commit any additional changes needed to succeed. Finally, run git rev-parse --short=8 netcdf-upstream to get the commit from which the netcdf-upstream branch must be started on the next update. Edit the "git branch netcdf-upstream" line above to record it, and commit this file.