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Other variant of a repository patch based on MUD needed

Given:
A) A multiuser repository (*.rpd) for developement. This MUD includes thematically structured sub-projects with up to 10 developers. Some subprojects have been released for publication, others are still under development.
B) The production repository is the result of merged subprojects. It only contains a subset of sub-projects form the multiuser repository: the sub-projects released for publication. The (full) merge process of sub-projects works as it should. Currently we have about 23 sub-projects published.
All versions of published sub-projects (*.rpds) are archived on the filesystem for further procession (see C).
C) Sometimes changes have to be made in the published subprojects. From results in deviations compared to the previous version of the sub-project a patch is generated. This patch is applied to the PRODUCTION repository.
Problem:
The latter procedure causes the problems. THE PATCH FILE DESCRIBES THE CHANGE CORRECTLY, BUT IT ISN'T APPLIED PROPERLY.
Furthermore: The documentation (
A full merge of the latest version of our currently 23 sub-projects - instead of a patch - is no solution, when only a tiny little change in only one sub-project is neccessary. The greater the number of sub-projects, the greater the effort involved in this process.
Required solution:
A patch path for the production repository is required that differs from the one described in the documentation.