Thanks for your replies guys. It's not an external drive. It's an internal. I'll try that spotlight preferences thing but for now I don't mind ejecting the drive in order for the Mac App Store to not look at the Snow Leopard volume. It won't be there forever. Just temporarily until I'm certain there's nothing left to transfer over. Thanks again!
I have just clean installed M.Lion and left my Lion install on another internal partition, and when I opened the Appstore I had a similar issue to what you described. Some of my apps reported to be already installed as the Appstore could see them on the Lion partition.
The steps I took to fix this were as follows:
1) Turn on Spotlight privacy for the Lion partition as described above.
2) Opened terminal and ran the following commands to delete and reset my Spotlight index:
To reset the spotlight index, you should disable indexing of the root volume first:
sudo mdutil -i off
Then delete the Spotlight index:
sudo rm -R /.Spotlight-v100
Then reset the data cache for your Mac’s hard drive:
sudo mdutil -E /
To force Spotlight to immediately start re-indexing your hard drive (this might take a few hours and is probably best left to run overnight), enter this command:
sudo mdutil -i on /
There are probably other ways to do this without using the Terminal command line, however I wanted to be sure the Spotlight index was gone/reset.
Hope this helps.
Thanks for your detailed reply. I think a lot of people will gain from this. As for me, though, I will just continue to eject the Snow Leopard volume upon startup of the Mountain Lion volume. Just because it's not going to be like this permanently. I'd rather not go tampering with Spotlight and Terminal just for another week or so of having a dual OS setup. But thank you very much for your expertise on the matter!
I had the same problem, having 2 internal SSD's, one with Snow Leopard, and one with Mountain Lion in my MacPro.
The problem is 2-ways: also updating apps on the Snow Leopard drive is a problem. So tinkering with Spotlight is not an option, I want both volumes searchable in Spotlight.
My solution: in Disk Utility, with one click you can unmount/deactive a volume. Then open App Store, install your apps, then mount/activate the volume again in Disk Utility. Two clicks and solved.
I think this is a flaw in the App Store, and have sent a message to Apple:
You can automate this quite easily with a little command line work.
Like you said, you need to prevent the paritions that are not being used from mounting on boot.
I have 4 drives, 2 Mountain Lion installs and a Time Machine for each. So, I didn't want them seeing each other.
Check this post, his solution worked great for me.
The terminal command you can use to edit /etc/fstab is,