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Steps: 1. Modify files in different folders 2. Open Git Status for one of the folders => All files from 1. are listed in Unstaged section, good 3. Press on Stage All button => Only files under the folder from 2. are staged PUT on /gitapi/index/file/{id}/{path} with no params should result in staging all files in the repo, no matter what the path is.
Staging the files individually and "Unstage All" work fine.
Fixed with http://git.eclipse.org/c/orion/org.eclipse.orion.server.git/commit/?id=dee2d20cfba476841ceedb4c87767011f9850c57.