Merge branch 'dt/submodule-diff-fixes'

"git diff --submodule=diff" showed failure from run_command() when trying to run diff inside a submodule, when the user manually removes the submodule directory. * dt/submodule-diff-fixes: diff --submodule=diff: don't print failure message twice diff --submodule=diff: do not fail on ever-initialied deleted submodules t4060: remove unused variable