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copied!<p>I keep my dotfiles in a Git repository like you do—my home dir is a Git repository.</p> <ul> <li><p><code>git gui</code>: I rarely use it, so I'm not really sure how its performance is impacted by lots of untracked files. However, I do have a <code>~/.gitignore</code> file that simply contains <code>*</code>. Perhaps ignoring everything will speed up <code>git gui</code> for you.</p></li> <li><p>Accidentally adding files: Creating a <code>~/.gitignore</code> file that simply contains <code>*</code> also solves the problem of accidentally adding a file to your dotfiles repository when you forget to initialize a new project repository (it'll tell you to use <code>-f</code> if you really want to add the file).</p></li> <li><p>I've never had a problem with nested repositories.</p></li> </ul> <p>Some notes:</p> <ul> <li><p>The main reason why I set my <code>~/.gitignore</code> to <code>*</code> is so that <code>git status</code> doesn't show every file in my home directory. It forces me to use <code>git add -f</code> all the time, which is a bit annoying, but not that big of a deal.</p></li> <li><p>Get in the habit of using <code>git clean -dx</code> instead of <code>git clean -dxf</code>. You'll have to remember to run <code>git config clean.requireForce false</code> in new project repositories, but it'll prevent you from accidentally deleting all of your files in your home directory if you're not in the directory you think you're in.</p></li> <li><p>Git sometimes decides to reset file permissions. This can be bad if you want to keep sensitive files (<code>chmod og-rwx</code>) in your Git repository. I handle this via a <code>post-checkout</code> hook that fixes permissions of certain files and directories (e.g., <code>~/.ssh/authorized_keys</code>).</p></li> </ul>

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