Remove "TODO: Review uses of command substitution $() and decide whether we should clone their stderr to the log file.":
I've looked at all of them closely and they all check for exit-failure of the subshell and make perfect-flac-encode die with an error message to the log file if it had failed. So their stderr output is OK to not be in the log file as the log file will be terminated with an ERROR anyway. Most of those conditions are weird error cases anyway, so they will likely produce cryptic error messages which are more suitable for stderr than the log file. If such a problem happens, the user should just report whats on stderr in addition to the log file.