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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 & 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 & 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:

  1. Delete the files com.apple.dock.plist from /Users/”user name”/Library/Preferences. Remember to replace “user name” with your OS >X account name.
  2. 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.

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@bneely Thanks, your assistance is capital! –  BobH Dec 13 '12 at 22:40

2 Answers 2

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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 & Privacy Control Panel, and setting "Allow applications downloaded from:" to Anywhere. The default setting is "Mac App Store and identified developers"

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The answer sounds reasonable, but is there anywhere documentation of what migration assistant does in response to different options selected? e.g. migration from another system vs. external drive (which I chose)? Migrate users vs. settings or both? Documentation of how one might transfer user account, passwords, network settings, etc. without 'corrupted preferences?' Seems like migration assistant users would probably never want links back to the source disk, system, or whatever. –  BobH Dec 14 '12 at 3:30
    
Okay, more searching thru wikipedia & apple.com discussions suggests to me that probably there exists no documentation for what specific items migration assistant moves. I was guessing 'settings' included network settings which are great not to have to redo. Plus several of my apps seemed to have retained their license keys when I reinstalled them--that was quite helpful to. Not sure if that might have been transferred due to selecting 'users' or 'settings'. I saw several folks complaining about lack of documentation. –  BobH Dec 14 '12 at 4:06
    
Users copies all user-related things...such as documents, iPhoto libraries, iTunes libraries, anything and everything that is in the /Users/ hierarchy. This includes all password, preferences, everything. Settings copies anything and everything that is in the global settings files that are not specific to a single user, and are system-wide. Whether you are copying from an old system on another Mac or an external hard drive makes absolutely no difference, if the external hard drive had an existing "blessed" system on it. –  alisamii Dec 14 '12 at 5:04
    
If the external hard drive DIDN'T have an existing blessed system on it, then it was what could be called a data-only drive, in which case migration assistant would copy "absolutely nothing" from that drive. Migration assistant is not a copy utility. It is a utility to migrate the applications and settings and User-specific data from an older machine to a newer machine. It isn't a system clone. –  alisamii Dec 14 '12 at 5:06
    
This is very helpful alisamii. I never found explanation from Apple, but I guess it's like many things: once you understand it, it's intuitively obvious. Anyway I accept your answer & thank you. I'm still trying to figure whether settings were copied to reference an attached drive or if Mtn Lion just hunts & finds an app if it isn't installed locally. I'll understand this eventually I'm sure. –  BobH Dec 14 '12 at 15:13

When you migrated your system from the external drive, the system you moved retained all its hooks and references to programs and files on the external drive.

In other words, the migrated system on your internal drive still thinks it resides on the external drive. When the external drive is missing, the system cannot find everything it expects to use. When you plug the external back in, the system can now find the "missing" parts.

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