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fix: make _merge_toml_fragment and _remove_toml_entries use atomic writes - #3972

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Quratulain-bilal:fix/toml-merge-atomic-write
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fix: make _merge_toml_fragment and _remove_toml_entries use atomic writes#3972
Quratulain-bilal wants to merge 3 commits into
github:mainfrom
Quratulain-bilal:fix/toml-merge-atomic-write

fix: preserve original file mode instead of hardcoding 0644

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