I do not know if you still have this question on the radar.
In our environment with a large number of projects and many header- cpp- and other types of files, we use these filters.
Filters for headers, resources, and sources are predefined. At this level, we add filters for protobuf and xml when necessary.
Under headers- and source filters, we use subfilters to reflect the various namespaces used in the project (even projects are very large, in part).
You are correct that storing all files in one directory eliminates the need to use include directories or access paths in #include statements.
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