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Most systems seem to read the contents of /etc/hostname and make a call to /bin/hostname during the system startup from an init.d (or similar) script.

Raspbian Jessie appears to have a different way to do this. I've modified the /etc/hostname file to a new name, and I've renamed /bin/hostname to /bin/bup.hostname so that any init scripts will not be able to find it. But the system boots up and uses the new host name, confirmed by running /bin/bup.hostname.

What is going on here?

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Raspbian Jessie uses systemd which reads the /etc/hostname and sets the hostname directly with a system call. See: https://www.freedesktop.org/software/systemd/man/hostname.html

systemd does not use /bin/hostname to set the hostname.

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