I think I understand why this is happening. This is not an issue that argument parsing in git goes wrong. But instead, the `--upload-pack=` instructs git to run certain command in the remote server. In my above example (`system "git", "ls-remote", "--upload-pack=$(whoami)", "HEAD"`), HEAD is interpreted as a local file based git server. As such, the command is executed in the same machine.
I don't think so, you just forgot to add the remote server address. If you run `system "git", "ls-remote", " --upload-pack=$(touch hello) git@github.com:torvalds/linux.git", "HEAD"` it will fetch the remote server but still create the file on the local machine.
In your example, `HEAD` is the server address, which is interpreted as a local file. `$(touch hello) git@github.com:torvalds/linux.git` is the command to be run in the remote (locally in this case). It will not connect to the server in GitHub.
P.S. it seems that you have an extra space before `--upload-pack`.