If a moderator does a mass retag it usually means that the two tags are synonym. Therefore a checkbox in the tag merge page should be added to automatically add those entries as synonyms.
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I agree with Grace Note's Answer in that a synonym should not be added automatically.
However, I think it would be reasonable and useful to add a checkbox to the moderator tag merging UI that would let the mod create a synonym at the same time if they checked the box (default would be unchecked to prevent screwups).
This probably wouldn't save a huge amount of time, but it makes a lot of sense to have the ability right there on the same page. It will make initial system input a lot easier, too.
Mistakes aren't the only time this would be hazardous. This is not a good idea when mass-retags occur during the disambiguation of a tag. For example, if we clear out a tag like [language] to catch all outlying situations and leave whatever currently has the largest count, then a mass-retag is more convenient for everyone. But it doesn't make [language] an exclusive synonym of whatever that final choice was. It's an extra step, but one that is vital. Otherwise, we'll need an extra step to undo the synonym setting. Disambiguation is just as important a job in cleaning our tag base as consolidating synonyms.