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I'm in the process of planning an upgrade from OS X El Capitan to macOS High Sierra, and I'm using things like Homebrew, Composer, Elasticsearch, and — by extension — Java.

I'm using MAMP Pro with the files stored in: /Library/WebServer/Documents/.

I need to know if these things will remain intact after the upgrade, or whether I have to install them again afterwards?

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All the software installed in macOS (along with the ones you mentioned) remain intact between OS upgrades.

However, it is advisable to keep an up-to-date backup before performing the upgrade.

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    I used Time Machine about 30 minutes ago. Commented Aug 11, 2018 at 9:53
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    If you are sure you have a working backup, you can go ahead and perform the upgrade.
    – Nimesh Neema
    Commented Aug 11, 2018 at 9:54
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    @WayneSmallman You may also wish to refer to this answer: apple.stackexchange.com/a/332616/279727
    – Nimesh Neema
    Commented Aug 11, 2018 at 9:58
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    I've completed the update without problems. I've also checked with the web applications, which are also working. Commented Aug 11, 2018 at 14:14

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