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Added in bug 338200, the REST API for staging always calls "git add" twice[1]: first as "git add {path}" and then as "git add -u {path}". The later should be only called when a file need to be removed from the index. [1] org.eclipse.orion.server.git.servlets.GitIndexHandlerV1.handlePut(HttpServletRequest, HttpServletResponse, Path)
Closing as part of a mass clean up of inactive bugs. Please reopen if this problem still occurs or is relevant to you. For more details see: https://dev.eclipse.org/mhonarc/lists/orion-dev/msg03444.html