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Support --version/-V flag on the command-line
Support the file_filter per-tool config (in the config-file only), for filtering the appropriate paths for particular tools with a regex
Add more consistent configuration-file keys, to better match the arguments accepted by the command-line. Specifically, support annotate alongside annotator, and at global and tool level support all_files and unfiltered alongside changed_files and filter_messages (with reversed meanings, of course)
When no tool names are supplied on the command-line and no config file exists (or the config file doesn't specify default_tools), exit with a failing status and explain, instead of just running all of the tools. That's rarely a useful thing to do anymore.