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* Implement some more CLI Next up is adding slog and slog options. Also adding unit tests for some of the options. This PR adds `--output`,`--overwrite`, `--stdout` and `--allow-empty` and implements each of them. There are some edge cases I need to cover with logging and the `stdout` option, but otherwise this is a first draft of the 'complete' CLI. * Move flags comment to somewhere more visible * Improve CLI general behaviour cmd.go now prints usage when a flag error occurs, and is structured so that it throws around fewer global variables.
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