Reorganize rust crates into a flat crates directory, simplify some CI steps (#4496)

* Move all rust crates (except lib) into crates dir, w/o nesting

* Remove stale path from .gitattributes

* Rename lib.rs files for easier navigation

* Rename mod.rs file for easier navigation

* Fix emscripten-version path

* Fix fixtures dir paths

* Use the default rustfmt settings

* Don't use nightly on CI

.github/workflows/build.yml

@@ -73,7 +73,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Read Emscripten version
-      run: printf 'EMSCRIPTEN_VERSION=%s\n' "$(<cli/loader/emscripten-version)" >> $GITHUB_ENV
+      run: printf 'EMSCRIPTEN_VERSION=%s\n' "$(<crates/loader/emscripten-version)" >> $GITHUB_ENV
 
     - name: Install Emscripten
       if: ${{ !matrix.no-run && !matrix.use-cross }}