Make plain reaction format the default.
In section "Specifying the Input" of README, describe the plain format before the arrow format.
In README, (almost) never say "rule"; say "reaction" instead.
In readInput, use "reactions" instead of "rules".
Rewrite the explanation of the --format option.
Use "reactions" instead of "rules" everywhere in the usage information.
In Formatter, always use "reaction" instead of "rule".
In section Batch Mode put forward the plain format rather than the arrow format.
In section Interactive Mode, put forward the plain reaction format as well.