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See IndexDiffSubmoduleTest.testSubmoduleReplacedByFile() and comments in Gerrit at [1]: canonical git reports a clean workspace if a submodule directory is replaced by a file and "git status --ignore-submodules=all" is invoked. JGit reports a modification. [1] https://git.eclipse.org/r/#/c/128057/1/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java@162
New Gerrit change created: https://git.eclipse.org/r/128953
As mentioned in the linked ticket 545162, the current fix on Gerrit does *not* appear to resolve a very similar bug occurring when a submodule is deleted and replaced by a file that has a root folder named like the now-deleted submodule.