I rather surprised that no one else has mentioned how to constrain variable interpolation to interpolate what you are really looking for. In this case, escaping the square brackets does the trick, but I feel that it is not straightforward as the square brackets are not meta-characters when on the right side of a substitution (on the left side, of course, they wrap a character class). Instead, wrap the variable in curly braces {} to force the correct interpolation.

s/.+/${bef}[${mid}]${aft}\n/;
s/.+/${bef}${mid}[${aft}]\n/;
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I have tested the above two regexes and they work fine without escaping the square brackets. While this may be a matter of style over substance, I often wrap regex vars in curly braces because I have been bit one too many times by what you've experienced.

Cheers,
Ovid