The Eclipse SDK, or Eclipse Classic as it now tends to be called, has been building and releasing for just about 10 years, using the PDE Build system. Our releases are based on map files, which contain the IDs, SCM, and co-ordinates of the plugins we need to build.
When moving from CVS, where you can tag individual files, to git, where you tag a commit (the repo), this can cause headaches.
The common practice of tagging the projects that change for each week's I-builds means that cvs2git generates a master branch that looks like a fir tree :-) The delete commits remove all of the projects that weren't tagged. That makes the commit accurate, but that's not the shape of the git repo we want. A little scripting and we moved the tags from the delete commits back onto the main branch.
The other problem comes from the practice of tagging the release (R3_6) but only branching projects that change (R3_6_maintenance). In order for cvs2git to make the branch correct, the first commit on the R3_6_maintenance branch is delete commit. To make the important maintenance branches look correct, you can fix this one of 2 ways. Either rebase the branch around the delete commit (before you publish it to the public), or pre-condition the CVS repo so that all projects that are tagged R3_6 are branched R3_6_maintenance as well.
The scripts I used to fix Platform UI are in the org.eclipse.migration/scripts directory.