>Make sure you do not have another copy of the application on your system.

And here is the issue I have with appstore: How do I tell which app will be 
updated?

Standard "safety" procedure is to have a different partition for different 
OS's, right? So I've got one partition with OS X 10.9.5, a second partition 
with a copy of 10.9.5 that is ready to try a 10.10 update, another partition 
that has the 10.7.5 data that I used to migrate from (and I'm looking for a way 
to set up a virtual machine to run 10.7.5 in the future because at least two 
programs that I use won't work in 10.10 without buying an update, and I hate 
10.9.5).

But in general: I've got multiple copies of XCode, which wants an update. I've 
got multiple copies of some programs that I've gotten from the appstore. At no 
time do I ever see a way to specify "which disk to install on", or "where do 
you want to install this program", or "Drag this into appliations" anymore -- 
everything is now "smarter" than me, but assumes only one OS will be installed 
on the computer, and that anything, anywhere, is valid for use no matter if 
it's in a .dmg that wasn't mounted and contains some really OLD stuff that 
should not be used anymore, kept for reference as an old computer image, but 
still shows up on a right click and "open with xxx".

Sigh.

How do I manage app store updates when there is more than one copy of the app 
on the system, and I want to update the one that is associated with this OS, on 
this root partition, and not the one on some other partition or disk image?

---
Entertaining minecraft videos
http://YouTube.com/keybounce

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