Can not build if LLVM is a work-tree.

Hi, `emsdk` depends on some other `git` repositories. Such as `binaryen`, `emscripten` or `llvm`. The `llvm` repository especially is very huuuge. When building `emsdk` I don't want to download `llvm` if I already have it somewhere else for different purposes. I would like to use the `work-tree` technology of `git`.

So, instead of downloading the entirety of `lllvm`, I "just" create a new `git` `work-tree` instead.

But the `python` script in `emsdk` is not ready for this eventuality. It is not prepared for this scenario. It behaves as-if `git` `work-tree` functionality never existed, was never invented.

In this issue I propose to teach your `python` script about this eventuality, this would save me a lot of useless downloading.