Does running git clean have some type of permanent effect for future checkouts?
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I have a very simple git repository that I've been using to learn git.  I have two branches in addition to `master`; `javafx`, `netty`.  I created a new project module within each branch.  For the `netty` branch, the project layout looks like this:

    sandbox
      netty

For the `javafx` branch, the project layout looks like this:

    sandbox
      javafx

Whenever I used to switch between branches, I would still have the directory from the other branch in my working directory.  I switched branches a lot and it the extra directory was never deleted.  I decided I should learn to clean up my working directory properly and, while on the `netty` branch, I ran:

    git clean -fd

It did exactly what I expected, but now Git's checkout behavior seems different.  When I switch from the `netty` branch to the `javafx` branch it's just like it used to be; the extra `netty` directory stays in my working directory.  However, now when I switch from the `javafx` branch to the `netty` branch, the `javafx` directory gets deleted / cleaned automatically.

However, if I clone the repo on another machine it still works the way it used to; all the untracked files get left in my working directory.  Does `git clean -fd` have some type of permanent effect?