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Hi,
No problem. You can still use the GNU Make for remote builds and MSBuild for local ones, but it will require manually moving the settings around if you want to keep them synchronized. If something does not work with this setup, let us know and we will help you fix it, but it will be somewhat less intuitive and less straight-forward than using the same build system for all configurations, sorry.
Just FYI: for MSBuild projects you can still use VisualGDB Project Properties to edit common settings like Include Directories. We specifically designed a page with the same look&feel as the regular Makefile properties that edits the underlying MSBuild properties to make it easier for users who are got used to the Make-based projects.
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