Coq now uses .mlg rather than .ml4 (since https://github.com/coq/coq/pull/8763), so we have to ignore its generated dependency files.  The `native_compute_profile_*.data` files are generated by `Set NativeCompute Profiling` (see https://github.com/coq/coq/pull/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.