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Add a structured config file so common defaults can live in one place
instead of being repeated in aliases or shell wrappers. CLI flags keep
precedence, which keeps one-off overrides predictable.
Use tomlq only when a config file is present, and fail early on missing
dependencies or invalid TOML so configuration mistakes do not silently
change encode behavior.
Move the persistent skip-codec list from the legacy skip.conf file to
[skip] codecs in config.toml. Config codecs are merged with --skip-codec
so global defaults and per-run skips can be combined.
Document the new format in the README and man page, update dependency
notes, and extend bash completion for config-file paths and the new
negative boolean flags.
BREAKING CHANGE: skip.conf is no longer read for codec skips. Migrate
its entries to [skip] codecs in config.toml and remove the old file.
BREAKING CHANGE: --encodefile and --encodefile= are replaced by
--encode-file and --encode-file=. Update scripts, aliases, and
completion usage to use the hyphenated option name.
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