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macOS comes with bash (which is a GNU tool), macOS also comes with tools like ls and chmod (which are BSD tools, even though I don't know from which BSD flavor they come from).

Now does the GNU and BSD tools that comes with macOS gets modified by Apple (for example: does Apple remove some features from them or add some features to them), or does Apple leave them unmodified?

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Yes Apple modifies at most open tools that come with MacOS in order to support Apple specific features.

You can see this in the man pages

https://ss64.com/osx/

or if you diff the source

https://opensource.apple.com/

As a specific example compare these 3 links for ls.c;

https://github.com/freebsd/freebsd/blob/master/bin/ls/ls.c

https://opensource.apple.com/source/file_cmds/file_cmds-272/ls/ls.c.auto.html

https://github.com/coreutils/coreutils/blob/master/src/ls.c

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