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Amphetamine?
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Amphetamine (Free, Mac) - A Caffeine replacement, but better. Why? It is actively developed (Caffeine was last updated on 2010 -- that is five years ago -- if the Mac App Store is to be believed.); and it has far more useful options, like WiFi triggers (I set it to turn on when I'm connected to our office's WiFi), and battery level triggers (toggle off when battery falls below a certain point). You can set-up a keyboard shortcut to toggle it on/off. You can also choose between 4 menu bar icons, one of them being a coffee cup in tribute to Caffeine (I use the Amphetamine pill icon which looks unassuming.)
Caffeine, the app, for your computer. Don’t pour coffee on it. http://lightheadsw.com/caffeine/
Or this one seems to be getting good reviews and might be better maintained, but I haven’t tried it. https://itunes.apple.com/us/app/amphetamine/id937984704?mt=12
> can't close macbook lids without having video plugged in or it goes to sleep
Have you tried Amphetamine? It's a program that keeps your Mac awake. https://itunes.apple.com/us/app/amphetamine/id937984704?mt=12
Amphetamine is another app that can do that: https://itunes.apple.com/us/app/amphetamine/id937984704?mt=12
Plus unlike Keyboard Maestro, it has triggers for battery power so your Mac can still sleep when disconnected from power.
https://itunes.apple.com/us/app/amphetamine/id937984704?mt=12
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Amphetamine is what I've used on my Macs for a few years now.
not only does it have the option to set schedules for when your Mac will sleep, it also has an option where certain apps will trigger it to activate.
There is also a app in the app store that puts a toggle in the menu bar if you would rather not open up terminal ever time. Does the same thing but slightly more features. Link
>I want to say it is because the system shuts down the USB port after a period of time? Is this a thing?
Yes, it is a thing.
To conserve power, USB devices can be put to sleep basically when unused. If you're running the USB as the boot disk, I'm not 100% sure why it would turn off that USB port as it should be constantly in-use as you're using the machine. It's possible that it's treating the USB just as a HDD since it has the OS on it and not as a standard USB device.
You can look in System Preferences > Energy Saver and make sure "Put hard disks to sleep whenever possible" is unchecked. If that still doesn't do the trick of keeping that USB alive, you might want to check out the Drive Alive feature of Amphetamine.
This comes up a lot, and I think there is a sticky or FAQ somewhere, but I'm not sure where, maybe someone can link it for you.
Anyway, my one essential is BetterTouchTool (https://www.boastr.net/downloads/). Great little program which allows you to map gestures to actions, and only costs about $4 these days. As a bonus, it includes a nicely customizable set of window-snapping rules.
I find Amphetamine (https://itunes.apple.com/us/app/amphetamine/id937984704?mt=12) useful for preventing the computer from sleeping.
You should probably download Chrome to use on websites which use Flash, but I prefer Safari as my day-to-day browser.
As for anything else...honestly, the stock apps are very good, see how far they get you. For anything you might want to do, there almost certainly exists a more powerful/feature-rich program than the macOS stock app, but there is seldom a better one.
The reason I always feel comfortable recommending Macs is that they come built with everything a given individual could be expected to want, and not much crap...its not uncommon for a random person to want to cut video for a work party or something...and iMovie is right there. Pages/Numbers/Keynote have their limitations, but will handle most use cases very attractively and with little fuss. Need to take a screenshot? Grab is built in (with system level keyboard shortcuts). Want a bash shell? Terminal.
Plenty of good third-party software too, of course, but start with the stock apps generally, I think you'll be pleasantly surprised.
Apps can tell OS X not to sleep, AE was telling OS X it was busy and so it couldn't go to sleep. That's what Caffeine does (although I prefer Amphetamine)