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Most of the time the first step to troubleshoot an OSX application problem is to login to the Guest account and see if a problem persist. The reason for this - I presume - is that the ~/Library folder of the guest account does not contain any, possibly corrupt preference files.

Over the years of using my Mac my ~/Library folder has become cluttered with preference files and folders of applications. Some of these applications are no longer installed.
Is there a way to "start over"? Some way to delete all existing preferences, and then let the applications currently present populate it again when the application is started?
Especially the Application Support and Preferences folder is full of old, irrelevant files.

I know I could do a fresh install, but then if I restore the user from Time Machine obviously the ~/Library is restored as well.

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If you log into the Guest account and everything is running as you suspect, simply create a new user (make sure they are an administrator). Log into the new account and then take ownership of the previous user's Documents, Photo's, Music, etc. folders and move them into the new profile. Depending on how many files you have to move this way it is a quick and easy way to "start over." :D

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Yes the process is simple in concept but takes a long time to finish.

  1. Make a backup of your system and perhaps a perfect image of ~/Library
  2. Delete files as you feel is best
  3. Investigate and solve all the broken programs that stored assets in ~/Library as well as settings.

Step 3 repeats quite often and the best way to work on step 3 is unironically, set up a clean new user and troubleshoot / investigate why your broken account doesn't work as expected.

In reality, most programs work fairly well to patch together the files they need in ~/Library and the breakage generally is Apple Loops for Garage band (older versions especially) and keychain / caches of really seldom used passwords that when needed cause frustration and more lost time than any perceived problem that letting thousands of small, probably unused files lie in ~/Library

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Ummm, while there could be damaged files in your ~/Library folder it is more likely to be a damaged preference file. And rebuilding the ENTIRE ~/Library folder would be difficult and time consuming. Possible but a bit of a PITA...

How I would proceed would be to move the contents of the ~/Library/Preferences folder elsewhere (say, to a temp folder on your desktop. then reboot and see how things are behaving.

Once you have determined that the system itself is OK you can start with your Apps. Just launch them one at a time and see how they are doing.

Note that some Apps store serial numbers inside the preference file and you may have to re-register the software to use it.

Oddly enough this is one of the few troubleshooting steps that remains from the Classic Mac O/S.

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  • First, take a backup of your system.

  • In addition to the ideas described in the answer to What programs exist to find and delete orphan files left after deleting an app?, you can use the paid app CleanMyMac 2 that has a feature to remove unused files from applications you may have trashed in the past without using an uninstaller utility.

    Quote from CleanMyMac 2 - Features:

    Delete old apps
    Instantly uninstall programs on your Mac that you no longer use along with all associated files, or remove all files that remain from previously Trashed apps.

    No more Leftovers
    If you used to uninstall applications by dragging them to Trash, then you have tons of apps leftovers! Find and remove them using CleanMyMac2.

  • After removing the orphaned files, if you still wish to redo all your application configurations like a fresh install, then take another backup of your system and delete files from ~/Library/Application Support and ~/Library/Preferences. In the case of applications that use installers (as opposed to drag and drop into /Applications or ~/Applications), you would have to run the installers again.

Note: I have intentionally omitted /Library and the folders within it that are sometimes populated by some application installers. If that cannot be dealt with a test application, it may be risky to do it by hand.

  • How does CleanyMac deal with apps that put directories or several files in Preferences? I suspect not well so you will always be left woth some – Mark Nov 7 '13 at 9:58
  • There are several "app cleaners or uninstallers" that are available that can delete an app along with the files it has placed on the system. These apps primarily rely on the package receipts (in /Library/Receipts) to know what files have been placed in which locations by an application. – M K Nov 7 '13 at 12:44
  • However apps can have files that are not there – Mark Nov 7 '13 at 12:46
  • Apps that do not follow standard OS X practices would, of course, be impossible to deal with through another app. They may be very difficult to deal with even manually (what if an app creates a file on first launch and never accesses it again?) – M K Nov 7 '13 at 12:50

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