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$$file =~ 
s/<%[ ]*link_name[ ]*([^ ]*)[ ]*%>(?{push(@link_names,$1);})/<% link_n
+ame $1%>/g;
...
){
  push @link_names,$1
}

while($$file =~ 
  m{( <% \s* link_name \s* (\S*) \s* %> )}xg
...
     # you know the positions of your links and their 
     # length, so use substr(!) here
}