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I plan to install Fedora Linux on a machine with an SSD and an HDD. /boot, and the root will have their own partitions on the SSD.

If I want /usr to be on same partition as /, will that occur by default if I set the root mountpoint on an SSD partition and don't specify anything with /usr?

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Yes. All directories are mounted under / and will be on the same volume. The only exception is when you create and format a partition and use a mount point. Then the filesystem on that partition will be used instead.

/usr is no exception to this rule.

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Yes if you do not provide physical partitions for a directory (mountpoint) during installation then they go on whatever media (hard drive) is specified for the root partition (/).

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