Tie::File is handy for that kind of thing.

use Tie::File;

for (glob '*.{c,h}') {
   tie my @file, 'Tie::File', $_ or warn $! and next;
   unshift @file, '#include something3.cfg';
}
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The problen with seek and friends is that you wind up overwriting the original first line, as you say.

Without Tie::File, the way to do this is to write the new first line to a temp file, then copy the rest of the original to temp and rename temp to original.