perl -pi -e's/(-----------step\s+)(\d+)\./$h{$2}||=$2;$h{$2}+=.1;$1.$h{$2}/ge' foo.txt; cat foo.txt
-----------step 1.1
-----------step 1.2
-----------step 1.3
-----------step 2.1
-----------step 1.4
-----------step 1.5
-----------step 1.6
-----------step 2.2
-----------step 2.3
-----------step 2.4
-----------step 3.1
-----------step 3.2
-----------step 2.5
-----------step 2.6
-----------step 3.3
-----------step 3.4