Once it's borked like this, you have to manually switch the SHAs back:

1. Go into JavaScriptCodeHints/thirdparty/acorn
2. `git checkout c152be4a2e8383a21c573ba0b2495afc9ae84643`
3. Go into JavaScriptCodeHints/thirdparty/tern
4. `git checkout 21c9f963b94f6ad077f95d182e9b4568c0d3874d`
5. Go back to the main Brackets src folder
6. `git add .` (though maybe do `git status` first to make sure you're not adding any _other_ unexpected diffs at the same time :-)