The main advantage of placing it in the
<head> is that you will track the
pageview even if they leave the page before it has been fully loaded.
Here's a handy quote from Mathias Bynens about our placement choice.
I should point out that it’s Google — not me — recommending to place this script before all other scripts in the document. The only real advantage is to catch a pageView call if your page fails to load completely (for example, if the user aborts loading, or quickly closes the page, etc.). Personally, I wouldn’t count that as a page view, so I actually prefer to place this script at the bottom, after all other scripts. This keeps all the scripts together and reinforces that scripts at the bottom are the right move. (Usually I concatenate and minify all my scripts into one .js file — the GA snippet being the suffix.)
Here's Nicolas Gallagher writing about how HTML5 Boilerplate and Bootstrap complement each other.
No, same as you don't normally replace the foundation of a house once it was built. However, there is nothing stopping you from trying to work in the latest changes, but you'll have to assess the costs/benefits of doing so.
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