Why do apps which are not installed run from an external bootable drive? After a disk crash in my MacBook Pro running Lion, I replaced the drive, installed Mountain Lion, and am rebuilding my system. I used Migration Assistant to transfer from an external bootable clone drive (with the old Lion system)  'users' and possibly 'settings', but not 'applications' or 'other files.' I wanted a clean, new system, but Migration Assistant sure is helpful for not having to re-enter user id info, passwords, network settings &amp; passwords, etc! Half my apps are reinstalled so far.

In the Dock, apps which used to be, but are not yet installed show as a question mark: [OOPS, can't post the pic:"as a spam prevention mechanism, new users aren't allowed to post images"] I guess this means the Migration Assistant transferred info like "apps which are in the dock." An earlier question:
Is there a complete and detailed description of what Migration Assistant copies over?
failed to enumerate precisely what Migration Assistant transfers. I could not find any SystemMigration.log file on my new system.

Now the weird part: When I have the external bootable Lion disk attached, all the missing apps show up in my dock and are executable! Is this is normal? not supposed to happen? It was particularly disconcerting and confusing--I am a pretty novice OS X user!--when the new system had Pathfinder 6 installed and running--and from the backup drive Pathfinder 5 showed up in the dock and got started somehow. Suddenly the drive and other icons on the desktop were showing up twice, with the duplicates often overlapping each other. Plus Pathfinder started asking me to purchase &amp; register! It took me a while to figure out this was from a separate instance which wanted its own license key!

Similarly odd: I have not yet been able to install the great little muCommander app (security violation in Mountain Lion?), yet with the backup drive attached, there it was in the dock and fully runnable.

I have routinely had drives with backup, bootable partitions attached and mounted (when running Lion); e.g. a 1T drive with 400G bootable backup and 600G data. I never have seen this behavior. Is this normal or dangerous? Might I have gotten inconsistent settings onto the 'clean' new system via Migration Assistant? Any other possible causes?

Edit: I later (Feb 2013) discovered a partial solution for this problem provided in a July 2012 post by Martin Bay 
http://martinbay.net/reset-dock-os-x/      which I quote below:


  I’ve just installed Mountain Lion and wondered how the new dock would look like from a fresh installation – so had to figure out how to do that – no problem!
  
  To completely reset the dock back to the original settings do the following:
  
  
  Delete the files com.apple.dock.plist from /Users/”user name”/Library/Preferences. Remember to replace “user name” with your OS >X account name.
  Enter ‘killall Dock’ command in the terminal and press enter
  
  rm /Users/"user name"/Library/Preferences/com.apple.dock.plist
  
  killall Dock
  


This nicely cleaned up (removed the question marks in) my dock.

Finally (March 2013) answered the remainder of my question. Apparently Migration Asst. copies "Login items" = startup programs from the backup disk/system and places them in System Prefs/Users/Login Items, with the link back to the applications directory on the backup drive. So if my external drive was detached these items were 'Unknown' and if attached, they started upon login, from the backup drive. Solution: delete old items from Login Items. Ya live and learn.
Migration Assistant copies everything, including corrupted preferences.

If you want to have a truly clean system, what you need to do is do a secure reformatting of the hard drive that you will be installing the new system on, make sure that you only install applications directly using the installer from the original installation source (and if available, you should get it from the Mac App Store).

On Mountain Lion, the OS will recognise apps installed on an external drive in a previous system as installed on the System. You need to uninstall or delete those apps and then they will not be seen as installed.

As regards the apps you cannot launch due to the GateKeeper security in Mac OS X 10.8 Mountain Lion, that is part of the enhanced security. If you try and launch those apps from within PathFinder, you will not be able to. The first launch must happen in the Finder, and if you get an error telling you that the app cannot be launched due to security settings in GateKeeper, then you launch the app by right-clicking on the app and selecting "Open" from the contextual menu. Then you will get a new dialog box that asks you if you are certain you would like to open the app as it is not signed/recognised.

You can disable that feature by changing the settings in the Security &amp; Privacy Control Panel, and setting "Allow applications downloaded from:" to Anywhere. The default setting is "Mac App Store and identified developers"