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At the moment you can't disable the usage of partitions. But based on recent discussions we will likely soon modify all RMW implementation to switch from using partitions to only topic names. An upcoming DDS spec will allow forward slashes in the topic name and we will start using that (all vendors except OpenSplice already support that). There will be more information about why this is being changed.
It would be great if you could share information about your work. I know at least two groups which are working on / having a Connext micro based RMW impl. It would be really good to merge these efforts rather than duplicate the work.
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