Use `git subtree` to manage LLVM libraries and musl

I only recently discover this features of git but apparently it has some advantages over `git submodule` for our use case.

1. It allows us to pull in just a sub-directory with the upstream repo (e.g. just compiler-rt and not the whole llvm)
2. We can maintain patches in-tree.
3. We can make changes the sub-tree in the same commit out changes to emscripten itself.

- No need to for a separate repo to keep in sync
- No need to manage `.gitmodules` metadata.
- No need to multi-step commits. We can commit a patch to mus land and immediately use & test it in emscripten.

See https://github.com/WebAssembly/wasi-libc/pull/797 for how this was done in wasi-libc.

Start by reviewing the referenced wasi-libc pull request 797 and the repository's current .gitmodules metadata. Determine how git subtree could manage the LLVM libraries and musl while preserving in-tree patches and same-commit changes. Done means the dependencies are migrated without requiring a separate synchronization repository or multi-step commits.

Written by the indexing model from the issue text.