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Ignore options are all now all behind a single flag, --ignore. For example, to ignore case and nonalpha characters you would previously have written --ignore-case --ignore-nonalpha, or -ia for short. Now you should write --ignore case nonalpha or -i c na. Some of the ignores have been renamed too -- see --help for details.
The option to ignore letter order has been removed, it wasn't useful.
Various deprecated aliases for ignore options have now been removed: --filter (use ignore regex), --filter-titles (use ignore titles), --as-latin (use ignore nonlatin), and --sort-words (use ignore words order).
The fuzzy method flag has been renamed from --fuzzy to --method. It now defaults to an exact match.
The short option for --threshold was previously -r, but it is now -t.
Input is no longer accepted from STDIN.
Output now defaults to including all fields from both input files, instead of only the fields used for the match.