Cleaning Up My Mac

(None of the links in this article are affiliate links (though the Medium links below are member-only articles), and nothing here was created with AI.)

I opened my Medium newsletter the other day and was confronted with three or four links to articles about what software I should have on my Mac. This isn’t unusual. It seems most, perhaps all, Medium writers who focus on Apple produce at least one article annually that tries to convince other Apple users that these are the best products in their category.

I expect if I read enough of these, I’ll eventually see them converge on a small set of apps, much as everything seems to evolve into crabs. Actually, I think this has already happened, as so many of these lists recommend Raycast.

I’m got going to produce one of those articles, at least not this time. (Even if I do, I won’t recommend Recast. I’m an Alfred user.) This story details the process of cleaning up my Mac, tearing it down and putting it together like new.

I hesitated (for about a minute) to write it, since I wrote a four part series on Medium (Part 1, Part 2, Part 3, Part 4) in late 2024 about upgrading my M1 MacBook Air to my current M3 MacBook Air, but this article is shorter and has some different Valuable Lessons.

Ensuring Safety

Unless you’re ten years old and are touching a computer for the first time, the most fundamental step in this process is protecting your data. It doesn’t matter if you’re recreating your current environments or abandoning Windows for Linux or MacOS (a decision I applaud), nothing is more important than your data.

To ensure its safety, make sure you have backups. In fact, make sure your backups have backups. (I’ll have a cautionary tale about this below, because it’s no fun making a statement like this without juicy disaster stories for illustration). I not only run Carbon Copy Cloner (CCC) every few days; I also manually copy important files and directories to external media. I give more detail on this process later in this article. Time Machine, provided by Apple, is also a perfectly good backup option

My Documents folder, Photos, and Music are all backed up in CCC, but they’re also kept on iCloud, Apple’s cloud storage service. iCloud isn’t a backup; it’s a sync service, whose primary purpose is making sure all connected devices have access to the same files. But it’s still an important part of my backup strategy. You can do much the same with Dropbox or OneDrive.

Hardware redundancy is also part of my backup plan. I have a MacBook Air, an iPad Mini, and an iPhone. I never mess around with more than one of these at a time, because if something goes wrong, one or both of the other two can provide access to files and passwords I may need to recover the distressed machine.

Actually, I almost never do this level of maintenance on my phone. The only time it gets wiped and restored is (not always) when a new version of iOS is released, or when I buy a new phone. The phone is really the center of my Apple ecosystem (just as Apple planned it, I’m sure).

Inventory

After ensuring the safety of my data, I look at my software. Like data, software accumulates over time. The old adage that data expands to fill the available space is true, and software is part of the accumulation.

I’m content with many of Apple’s native apps. I use Mail, Reminders and Notes all the time. I like Fantastical for calendaring, but it uses Apple’s Calendar database.

As much as I write, I actually don’t use word processing software very much, but Apple’s Pages is always handy, and I have a standalone license (not MS360) of Microsoft Office that is convenient but not always installed. I do most of my writing in Markdown, a way of adding formatting to plain text, so my writing doesn’t require anything more than a simple text editor. Pre-cleanup, my Mac has more text editors (few of them simple) than I actually need.

So I dust off the Apple Note I made a year and a half ago listing all my software and update the list. I try to prioritize my installs, but really it starts with 1Password, putting Balatro pretty far down the list. I double-check that license data is easily available and I have copies of configuration files so I don’t have to set up again from scratch. This is especially important for things like password managers (and why having backup hardware is important). I keep my licenses in 1Password, which Apple’s Passwords app doesn’t allow. It’s become much easier to get license data from vendors, but I like having local copies as well.

All software is easily available via download these days, but I usually go through and download everything on my list before resetting, then copy it to an external drive. I make copies of browser bookmarks and history. While most browsers have sync services or otherwise make it easy to retrieve bookmarks, I like to be safe (do you detect a theme here?).

Why not do all this from a backup? That’s certainly an option. Apple provides Time Machine and Carbon Copy Cloner will restore your machine back to the state it was in at the last backup. Most often this is good enough, and relatively simple.

But it’s possible you don’t want your system restored to where it was before. Restoring from backup may very well restore the bad along with the good...any problems with your system could well come back with the restore.

Plus, part of the reason for wiping your system is to get a clean start. When you start with just the OS, you have to reinstall your apps manually, and deliberately. You get a chance to look at what you’ve been using and make conscious decisions about what should and should not be on your machine. It may be that, over a period of weeks or months, you reinstall everything you had before, which isn’t especially a bad thing. But a fresh system may help you see your application stack, and maybe even your hardware, in a new light.

How it went

After a couple of hours of planning (which included starting this article), I was ready to wipe the system and reinstall. It took a couple of tries to convince the computer I wanted to actually reinstall MacOS 26 from scratch, but I had the OS reinstalled and configured in about an hour, and installing and configuring software and copying data took another few hours. I started a little after noon and had the system up and running at more-or-less my original specification before five. It might have gone quicker from a backup, but that wouldn’t have resulted in a clean, fresh system. Of the 43 applications I had installed, I reinstalled 30. We’ll see how long I go without the others.

Oops

It wasn’t until the next day I discovered a hole in my backup plans. My system was leaner and meaner, but seemed a little too lean. An important folder in my Documents directory was missing, not one I’m in every day, but the home of critical files. I have no idea how or when it got deleted, just that iCloud, the loyal and thorough sync system, had synced my Documents folder up the the cloud without that folder.

No reason to panic; I maintain multiple backup methods for a reason.

First I went to CCC. Without a doubt some version of the folder was available there. Unfortunately, since my most recent backup was before I’d reinstalled MacOS, I’d need to use Apple’s Migration Assistant to restore any older data. By this point I’d spent hours putting the system back together; I wasn’t eager to start again from scratch. I decided to keep this option in my back pocket.

My next option was my external drives. Besides CCC, I use Beyond Compare (BC), a file/folder comparison utility, to make copies of folders. In this case I use it like a fancier version of the Unix utility rsync. Using BC’s Folder Sync functionality, I can copy new or modified files from one location to another, or even create exact copies of a folder in a different location.

I regularly use Folder Sync to update copies of my local folders to a couple of different external drives. In search of my missing folder, I looked at the first of my two external SSDs. Interestingly (and concerningly!), the folder wasn’t there. This seemed odd, since I tell BC to update the receiving folder; the SSD should have had cumulative copies of everything in my Documents folder; nothing should be erased. (For those wondering, I tend to not worry about earlier versions of files. One of these days I’ll set up a local git repository if I feel I need it.)

Feeling a bit more desperate now, I pulled out my other SSD. I have two partitions on this drive: my CCC backup partition, and a storage partition that should look more or less like the first SSD I checked. And here I found my missing folder. With a sigh of relief, I copied the folder to my local drive, then immediately made a new CCC backup and a new copy to both SSDs.

For any readers thinking maybe my backup process is a bit much, I hope this is a lesson in you can’t have too many backups. Humans make mistakes; sometimes we’re able to work our way out of them.

Lessons Learned

The biggest lesson learned, of course, was to make sure I actually have the data I want. The near loss of that folder tells me I need to be more diligent and systematic about my various backup procedures. Yes, I probably could have recovered it from my CCC backups, but that might have meant losing half a day of work. And maybe the next time I do this I’ll give Migration Assistant a try, just to see how it works.

I also learned more about the quirks of Apple’s iCloud. I’ve been automatically syncing my Documents folder to iCloud for over a year. But when I rebuilt my system, it didn’t automatically restore my iCloud data back to my local drive. Instead, it puts the online Documents folder into the Finder sidebar and makes it act like a local folder. I had to manually initiate the copy from iCloud to my local drive, then tell iCloud to keep all my files downloaded at all times. It was after this, of course, that I discovered my missing folder.

It was the same with Apple Music. I have a large library of music I own, ripped years ago from CDs, as well as music downloaded from Apple Music. This had also been copied to local backups, but these weren’t current. Downloading everything from Apple’s servers was a long process.

If I’m asked to prioritize the order of reinstalling my software, I’d have to say browser first, then password manager. Since I use Safari, the browser is already there, and it pulls history and bookmarks from its own iCloud backup. 1Password has to be reinstalled, but it does the same with its encrypted database. Without a browser, I can’t download anything, and without passwords I can’t log in to anything.

The next priority is to restore data, or at least make sure it’s accessible. In the Apple ecosystem, email, calendar, reminders, notes and contact data are all available through iCloud, so knowing your Apple ID takes care of a lot of fundamental data. If you’re not in the Apple ecosystem, or are not as wedded to its sync system, you’ll need to bring this information back from your own storage or backups.

After that, the reinstallation of software depends on your own priorities, and can take place at a more deliberate pace. The whole point of this exercise is to bring you to a sane and useful environment for work or play, minus months or years of clutter.