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Long ago, back in the OS 7 and earlier days, it was a snap to perform what was formally called a "Clean Install" of the OS. It would utterly remove the OS and place a brand-spanking new one in its place. Applications and data (other than system preferences and such) would be untouched, and you rarely even had to reinstall a single application. Adjust a few system prefs and you were good as new in no time at all.

I believe this feature went away around OS 8, and since then I've never known of a good way to perform a clean install. Migration Assistant is useless and ranting about it is unhelpful here.

I have a mid-2011 iMac, running "low" Sierra from an external SSD (Thunderbolt). I've got vestiges of Mavericks and all kinds of applications I no longer use floating around, and I feel that it's time to clean up. But every time I've done this in every flavor of OS X, it's ended up being an utter nightmare of lost application files (prefs, extensions, etc.), lost system settings, lost chat logs (Messages, Skype, etc.) and so much more. It's as bad to clean my Mac these days as it always had been on Windows!

My approach to date has been to install a fresh OS on a newly created partition of my drive, and go through countless reboots back & forth between the two systems while I copy applications and their preferences and settings over. Still it's inevitable that something will get lost or not be able to transfer over like mail rules, chat histories, or all manner of other stuff. Eventually I can delete the original partition once I'm confident in the migration (though there are often problems doing that, too!)

So is there a "best practice" or reliable way to completely replace my current macOS Sierra installation with a fresh copy, without losing any application data including preferences, mail & chat histories, app settings, etc.? I'm OK with having to reset basic system settings as I expect that, but losing anything related to my user-installed applications, is really quite unacceptable IMO.

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    Well, the standard method is to boot with Cmd/R & just install over [per support.apple.com/HT201314 ].... but if you're having so much trouble, then maybe you have a deeper issue. I haven't had to go through at kind of mess in 25 years of running Macs. – Tetsujin Jan 13 '18 at 20:26
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    Isn't the concept of a clean install and keeping app settings, histories etc... kind of mutually exclusive? – Agbb Jan 13 '18 at 20:27
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    Well, 'clean' plus 'restore old stuff' is no longer 'clean' either. – Tetsujin Jan 13 '18 at 20:28
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    I haven't done a 'clean' in 20 years... but what would I know? – Tetsujin Jan 13 '18 at 20:40
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    Your definition of a "clean install" is wrong! A clean install is reformatting the drive and reinstalling everything from scratch, OS and apps! – user3439894 Jan 13 '18 at 21:46
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The functionality you're looking for that is closest to the Clean Installation option in the old Mac OS 'System' days is the Reinstall macOS option available from Recovery mode.

See my A bit of history info at end on what the old Clean Installation option was and how it differs slightly from the Reinstall macOS option today.

Reinstalling macOS without deleting applications, data, etc

Prior to following this process, you need to ensure:

  • you have a known good backup of all your data (be it via Time Machine or another process) just in case something goes wrong
  • your iMac is able to connect to the internet during the installation process

Assuming you have the above sorted, follow these steps to reinstall macOS without deleting your apps, data, etc.

  1. Shutdown your iMac
  2. Power up your iMac and immediately press and hold the commandR keys
  3. Let go of the keys when it's clear you're booting into Recovery mode
  4. Soon the macOS Utilities window will appear
  5. Make sure your iMac is connected to the internet
  6. Now choose the Reinstall macOS option
  7. Click the Continue button
  8. Follow the prompts (to select your disk, etc)
  9. Click the Install button

Once completed, your iMac will restart as normal. This process does not erase your drive and therefore all your apps and data should still be in place. In other words, this process does nothing but reinstall macOS over the previous version on your drive.


A bit of history

In the old Mac OS System days users were presented with three options when installing system software:

  • normal (“easy”) installation - this automatically installed all the Mac OS system software appropriate for that particular model of Mac
  • “clean” installation - (see more details below)
  • custom installation - this allowed users to select a specific combination of system software files or to install/update specific files

The old clean installation option was actually designed as a troubleshooting option. This allowed users to discover which item(s) in their original System Folder was causing problems. A clean installation created a brand new System Folder and saved everything in the original System Folder to a different location. It also left user data (and user installed apps) alone. Users could then reinstall system extensions, control panels, etc one at a time from the old System Folder to the new System Folder. This procedure allowed users to determine which item in the old System Folder was the source of a problem.

In Apple's own words:

Perform a clean installation if you can’t determine what is damaged in your System Folder (especially if you think any special software, such as control panels, system extensions, or custom utilities, may be causing the problems you’re experiencing). You should also perform a clean installation if you’re still having problems with your computer after you’ve reinstalled system software by performing a normal installation.

Source: Mac OS 7.1 Installation manual

Today a clean installation has a totally different meaning (even to Apple) to what it did back then. Today a clean installation involves erasing the Mac's startup drive and starting afresh with a totally new installation of macOS, meaning users have to rely on a backup and/or installers to transfer any data or software over. Today's Reinstall macOS option accessible via Recovery Mode is the closest option to replicating the old clean installation option.

Where this differs is that the old option actually kept everything in the original System Folder by copying it to another location so users could move system items (e.g. control panels, system extensions, etc) back one by one to try and determine what was causing problems. This was a troubleshooting process of elimination option.

Today's Reinstall macOS option is not designed so much for troubleshooting as it is simply to reinstall macOS over an existing installation without having to install/migrate apps, data etc.

However, if you're installing a new drive or migrating to a new Mac, then users will need to use Time Machine / Migration Assistant instead (or another backup option) in order to migrate apps and data.

  • Thanks, but in my experience this does not at all "cleanly" install the OS. It simply slaps a fresh copy of files onto your existing OS, right on top of whatever problems are already there. I have never seen this fix anything and in fact just adds a bunch of work (since you now do have to reset any system related settings you had customized) while maintaining whatever the problems were before. I appreciate the effort but I disagree that this is a workable solution at all. – Jonathan van Clute Jan 14 '18 at 0:30
  • That's fair enough, but as I said this is the closest to the Clean Installation option. I know you don't want to hear this, but the other option is to use Migration Assistant. Since you're having problems with that, perhaps you need to ask a question about that option? My experience is that Migration Assistant works very well to do what you're wanting to achieve, although it's best to use it as part of the installation process and not after the installation process if you're reinstalling on the same drive or not wanting to risk duplicating user accounts. – Monomeeth Jan 14 '18 at 0:35
  • Yeah in theory migration assistant is great. In practice, I've always found that it doesn't truly migrate everything, and it offers you almost no ability to pick & choose what you want migrated. You can't select specific applications, settings, etc. And I've always found it ends up missing settings files for various things so critical stuff gets lost, that Murphy's Law says I won't realize until later when I actually need them. It seems the real answer here is that there is currently no way to perform the equivalent of the old Clean Install. Bummer. – Jonathan van Clute Jan 14 '18 at 0:37

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