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In my Mac Pro, I have two boot volumes — one stable with Mavericks and one for testing Yosemite. When running Mavericks, I want Spotlight to ignore the entire Yosemite volume, and vice versa. But Spotlight privacy preferences seem to be shared between the two systems.

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Spotlight indexing and searching (or the respective privacy setting) is volume based and not system based. So turning off Spotlight on one volume is enforced, whether you boot from one or the other system volume.

So the only possibility I see is the following solution:

Don't mount the respective alternative volume while booted to one. Or mount it read only (Spotlight will not index it then, but will search it).

Example (while booted to Mavericks):

diskutil info /Volumes/NameOfTheYosemiteVolume

Locate the volume UUID, select and copy this number.

Open Terminal and run the following command to edit the "fstab" file (you will be prompted for your password):

sudo nano /etc/fstab

Then add

UUID=UUIDFoundAbove none hfs rw,noauto

or

UUID=UUIDFoundAbove none hfs ro,noauto

or

UUID=UUIDFoundAbove none hfs ro

The first of these will prevent the drive from being mounted, but if you do mount it using Disk Utility or another means, then the drive will be read and writable.
The second of these will prevent the drive from being mounted, but if you do mount it using Disk Utility or another means, then the drive will be read-only.
The third option will make the disk be treated as read-only, but it will still show up automatically in the Finder when you start your system.

When finished with the edit, press ctrlo followed by Enter or y and Enter to save the changes, and then press ctrlx to exit the editor.

To undo these changes, simply run sudo nano /etc/fstab in the Terminal again to edit the fstab file, and delete the lines you added.

Afterwards revert the Spotlight privacy settings to the default settings.

This should prevent the Yosemite volume being mounted after a restart. As a result Spotlight shouldn't index or search the volume, if you have chosen one of the first two options.

Now boot to the Yosemite volume and repeat all for the Mavericks volume.

The drawback of this solution is that you probably have to hit the alt/opt button while booting to select an alternative start-up volume, because the respective PrefPane shows only your current one.

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