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Coq now uses .mlg rather than .ml4 (since coq/coq#8763), so we have to ignore its generated dependency files. The `native_compute_profile_*.data` files are generated by `Set NativeCompute Profiling` (see coq/coq#950). Finally `.coq-native` is a directory that may be generated in any subdirectory, not only at top level, so we should not use absolute paths for it.
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