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I stumbled upon the phrase focusing on the warts in a blog post. The post is about a programming tool git.

Following is the context of the phrase:

Rather than focusing on the warts, I hope this post will explain to newcomers the Places Model that will help motivate Git is complicated (and yet amazing).

I've searched ODO and UrbanDictionary with no luck.

Also, I found it's a widely used phrase with a Google search. I can guess its meaning was focus on the difficult, ugly part of sth. But I'm not sure my understanding is accurate.

Hope someone could give me a definite explanation.

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Your instinct is correct. It's based on the idiom "X, warts and all" (referring to taking some thing X as a whole, the good parts along with the bad parts). It's not (as far as I know) really an independent set phrase, but the sort of coinage that will be recognized on sight.

In essence, the quote is saying that, while not denying that there may be some ugly parts to git, the post isn't going to spend time attacking or defending those, but rather focus on an interesting (and presumably unique or powerful or otherwise praiseworthy) aspect, one that's not one of those ugly parts.

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