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In bug 475932 eclipse.pde repository was "moved" to eclipse.pde.ui. But, we temporarily left eclipse.pde as a submodule of the aggregator since I had read on the internet that having a submodule in one branch, but not in another can present problems if people have to "switch branches". And even though "mars" was basicially done at that point, I was afraid some people might still be working on "mars.2+" at the same time as they were working on Neon (i.e. a few poeple might have to switch back and forth.) I think as we begin "Oxygen" (4.7) that there will be no meaningfuil maintence needed in "eclipse.pde" in Neon (4.6.1) so less risk of people getting confused or "losing work". And, if someone had to switch and work on Mars, they should probbly have that in a separate workspace/clone anyway! Hence, I think after we tag all the projects for "4.6", then would be a good time to remove "eclipse.pde" as submodule from both "master" and "R4_6_maintenance".
I ran across a good reference today, so once this work is done, should send a reminder to people to remove it from their local repositories, explain how, and point them to https://git-scm.com/book/en/v2/Git-Tools-Submodules#Issues-with-Submodules if they ever have to "switch to mars" (and back).
I have now removed eclipse.pde as a submodule of eclipse.platform.releng.aggregator. From what I have read and my own experience this is what people should expect: 1: if you "git pull" the aggregator, it should just disappear. 2. If for some reason you are in a state you can not do a "git pull" and it somehow "gets in the way" (e.g. can not do a commit, because your local clone still has it as a submodule, but origin does not, then I think you can simple do, from aggregator directory, git submodule init, and then just a normal files system "remove" eclipse.pde (perhaps will need to do git-rm to remove from index and your local version of ".gitmodules"). 3. Once we create the R4_6_maintenance branch, there should be no issues switching back and forth between 'master' and R4_6_maintenance ... it won't be in either. 4. If someone wants to so work in R4_5_maintenance (where is is still a valid and needed submodule, then it will be hard to "switch" between that branch and master or R4_6_maintenance. It will appear as a submodule in one place, and an untracked directory in the others. I recommend to do R4_5_maintenance in a completely separate working tree, if possible. If not, please read https://git-scm.com/book/en/v2/Git-Tools-Submodules#Issues-with-Submodules on things you may have to do when you switch back and forth. HTH
Fixed as described.