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#!/usr/bin/perl

...
A line with_two_underscores.
~A line with an_underscore starting with a tilde.
~A line with_two_underscores starting with a tilde.

A line with an_underscore.
A line with_two_underscores.
~A line with an+underscore starting with a tilde.
~A line with+two_underscores starting with a tilde.

  s/( ^ ~ .*? )  _  /$1+/xg;