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ps2 of https://go-review.googlesource.com/6802 was incorrectly merged by JGit. Take ps1 (e0175cd060) and cherry pick onto ps2's parent (bcf43e956538e3709428b5b0a07407dbfcd26135) using git-core. This creates a conflict because ps1 and the parent bcf43e9 both add text to the same switch statement at the same position in the file. JGit blindly adds both blocks and does not fail. git-core is taking the slightly safer approach by assuming a conflict is possible if both sides are inserting text at the exact same spot in the file.
I thought that we once introduced that some (3?, 1?) lines above and below a changed line could cause conflicts. I'll debug with the use-case you mentioned.
This is a blocker. We currently evaluate EGit on Luna (JGit 3.7.1.20150426175-r) for a bigger project and found by accident that we suffered this bug. Now how can we be sure whether code after fast-forward merging resembles the developers' code? Please look into it.