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Noticed several times now: after an interactive rebase of multiple commits some files are not present in the package explorer in the end. Mostly affects new files (added in some commit in a series), but I've seen it also for one modified file. If the missing file is a Java source referenced in other classes there are Java compilation errors. A manual refresh resolves the problem. "Refresh on access" is set for the workspace. Probably related to https://git.eclipse.org/r/#/c/150032/ . Either JGit forgets to include some files in the WorkingTreeModifiedEvent, or EGit's processing of that event is flawed. OS X 10.14.4 EGit 5.6.0.201911012245 JGit 5.6.0.201910302341
Might be related to using "Fixup". Top commit moved back in the history, say to be just on top of the first commit, set to "fixup", then run the rebase. (Which applies without conflicts.)
Though a simple "Reword" shows the same problem.
Reproducer using the EGit repo: 1. check out https://git.eclipse.org/r/#/c/151822/ from Gerrit 2. In the history page, choose "Reword" on the commit with message "[repo groups] move to own package" Result: file MessagePopupTextCellEditor (added in a later commit with message "[repo groups] inline renaming of repository groups") is not refreshed; Java compilation errors in the workspace.
This is a bug in JGit. EGit never gets any WorkingTreeModifiedEvent including the file.
New Gerrit change created: https://git.eclipse.org/r/151910
Gerrit change https://git.eclipse.org/r/151910 was merged to [master]. Commit: http://git.eclipse.org/c/jgit/jgit.git/commit/?id=64f2407f19330d182728feeaf3d2c1a4092a2051