Here's another solution, somewhat more elegant than my previous one.

s{<code>(.+?)</ code>|\[(.+?)\]|(<!--.+?-->)}
 {defined $1 ? "$GREEN$1$RESET" :
  defined $2 ? "$RED$2$RESET"   :
  defined $3 ? "$YELLOW$3$RESET"
  : warn "Broken with $+\n"
 }ge;
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