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I come from the Windows and Linux world. Is there an alternative window manager for OS X such that I can move the "stoplight" icons from the left to the right on the titlebar of the window, and also make them a few pixels larger?

Using a Mac Air 13", I still have trouble clicking those tiny icons, and it's frustrating because often I leave my mouse cursor on the right side, and so I have to sweep across a form to the left to click those things. It's really bad engineering, in my opinion.

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Is there an alternative window manager for OS X (…)?

It depends on what you define as window manager. If you mean the entire framework that draws the windows, then no. This has always been the Window Server in conjunction with Quartz. If you mean apps that enhance some of the window switching and layouting behavior, there are plenty of those, but none of them really replaces anything.

Have a look at the following projects or tools if you want to tweak the window behavior, mostly with respect to resizing automatically:

Can I move the "stoplight" icons from the left to the right on the titlebar of the window, and also make them a few pixels larger?

There is no way to move the buttons somewhere else, as this is hardwired into the operating system. You also can't make them larger.

The only possible "customization" in the title bar is removing window buttons entirely, showing a subset of them, or making them smaller (i.e. Inspector windows).

It's really bad engineering, in my opinion.

This is Mac OS X, not Windows, and not Linux. It is what it is—you'll just have to get used to it. Mac people will probably take a week or two to get used to the inverse when sitting on a PC. And others might leave their cursor resting on the left.

OS X offers you tons of shortcuts to close or minimize a window without needing the mouse. If you have your left hand available, all you need to do is press ⌘W to close the window, or ⌘M to minimize it.

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As well, for Spotlight, ⌘Spacebar to access Spotlight search – Canadian Luke Jan 15 '13 at 6:58
The OP was talking about the red/yellow/green "stoplight" buttons, not Spotlight, but I had to read that twice myself :) – slhck Jan 15 '13 at 7:01
Ahhh... never mind then – Canadian Luke Jan 15 '13 at 7:19
@Volomike That's how they've always been—to be honest it's a wonder they let users install Linux and Windows on Macs and allow you to install software that's not from the App Store (although that's even disabled by default on Mountain Lion). That's a policy you have to live with. Apart from that, depending on what you do, you'll embrace OS X for its stability, Unix background and automation features. – slhck Jan 15 '13 at 19:47
@slhck Saying "you'll just have to get used to it" and "that's a policy you'll just have to get used to" as a rebuttal to "It's really bad engineering" is a really poor form of reasoning. The fact remains that it is very poor engineering. There is absolutely no excuses, and should you find yourself trying to convince others that they are wrong for pointing out the short comings, then I would hope that others see the twisted madness in your reasoning. – airtonix Jul 19 '13 at 14:14

You can change some of the look and feel with an app called Flavours.

You can't do much about the min, max and restore buttons (in terms of location or size) You can modify them a little and you'll see on their website some themes that do this. You can change the foreground and background colors (which was something I found annoying about Mavericks. I couldn't really tell what window had focus!) You can also change the look and feel of some of the standard widgits (Buttons, checkboxes, etc.)

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