[Ninja] Fix build system self-destructing on clean

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)