Deleting a nested submodule (and updating its URL) chdir'd the whole
process into the parent module, ran its git commands there, and chdir'd
back. Only those commands need to run there, and a process-wide chdir
leaks the parent module's directory into any command another goroutine
spawns during that window (e.g. a background refresh's). Set the
directory on the commands themselves instead.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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