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[Ninja] Fix build system self-destructing on clean

Jö Fahlke requested to merge fix-ninja-clean into master

List generated files including CMAKE_CURRENT_BINARY_DIR in DUNE_INSTANCE_GENERATED. This means we do not need to set the source file property GENERATED on the generated files, which is only meant for files generated during build time (e.g. with add_custom_command() or during generate time (e.g. with file(GENERATE)).

Closes: #119 (closed)

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