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    I tweeted about this last week after getting frustrated with the same problem. For some reason the passphrase is stored in a SQLite database that is separate from the main login/system keychains, and to remove it you have to purge it from ssh-agent and then delete the row from the db:

    ssh-add -D -K
    for f in ~/Library/Keychains/*/keychain-2.db; do sqlite3 $f "delete from genp where agrp = 'com.apple.ssh.passphrases';"; done
    

    Aside from the problem of storing passphrases by default with no option to prevent it, they also removed the GUI askpass-style dialog that would come up out-of-band asking for the key passphrase.

    I would update my openssh-mac tree to work around these bugs but Apple hasn’t posted any of the 10.12 open source code yet.

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      Why the heck would they pull it out of the Keychain?

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      Add this to a growing list of reasons why I am switching to FreeBSD soon.

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        In my opinion, people should stop using proprietary software… Things like these wouldn’t happen in the open source world. I don’t get why people who want their computer to do what they ask them to do use Win/Mac!

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          Because it’s too much work getting a machine that is not a Mac running macOS to do all the things you need them to for, say, work?

          I would love to run something open. Maybe Arch Linux or FreeBSD. But I can’t as my main OS. I need a way to properly work with Photoshop and InDesign files in the event that a client only can deliver a design to me in those formats. I need a machine that at least can go 7 hours without being charged. I need a machine that can print, read a PDF, something, something, something, something reliably.

          There is just so many things that I rely on for making money, and 7 years of Linux variants and main OS and 10+ years as Linux and BSD server experience has not given me any proof that a Linux or BSD machine can fulfill those needs. Not good enough.

          Sure, Gimp can read Photoshop files, but can it do it correctly? Can I edit and save them correctly so they can be opened correctly in Photoshop again? I wouldn’t bet on it.

          I would love to not be in the mercy of Apple, but there is just not any way around it as I see it. Maybe if I only did server-related work, but I don’t. I also do web, Mac and iOS stuff.

          Oh, and running something open on my desktop/laptop, and then have a iPhone or an Android phone in my pocket? The irony shouldn’t escape anyone.

          We need a billionaire who wants to fix this, and don’t want to make any money doing it, so we can get a desktop OS and a pocket-device+OS that is free and at the same level of functionality, UI and UX as what we get from Apple and Microsoft before a lot of people like me can go that route. Unfortunately.

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            At various stages I ran Linux, FreeBSD or OpenBSD as my primary desktop OS for many years (intermingled with IRIX and Solaris), including 7 years of Linux on laptops (2000-2007). I was happy running a Windows in a VM for those applications I needed for my dayjob, but the straw that broke the camel’s back was iffy suspend/resume.

            I’ve been using Mac laptops since the end of 2007 and I can count the number of failed resumes per year on one hand. Yes, it’s a proprietary OS from a company that seems to be moving away from supporting power user features, but for my use case, it’s the best option out there, for now. I need to get stuff done and a desktop I need to tinker with endlessly doesn’t let me do that.

            a billionaire who wants to fix this

            For a long time I thought Ubuntu had a real chance, not of “dethroning” Apple or Microsoft, but of providing a credible alternative. But lately it seems as if they’ve lost focus a little and done too much their own way (cf. Mir and some of the mobile options, which I think take focus away from their original goal). But that’s just my 2c.

            Going off on a real tangent now, but innovating in the desktop UI space is hard. Apple’s UI is still an iterative improvement on NeXTSTEP and Microsoft’s is the same, but based on Windows 95. Not sure where I’m going here, but it’s disappointing that we don’t seem to have progressed much in 20+ years.