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As discussed in Bug 496299 Comment 20, the code generator must support the case when profile applications have been externalized into own resources. In general it should be supported for any profile, but a good example is probably the externalization of the RtCppProperties profile, to be able to generate different code depending on which target or deployment configuration that the code is generated for. Which externalized profile application to use for a specific build needs to be specified in some way, e.g. using a command line option to the code-generator or some build configuration file (similar to the transformation configuration files in the legacy tooling, where this concept is referred to as a marking model).
Currently in MVP3 plan (post v1.0).