It seems like there are so many problems with the OP code that the replies so far simply haven't been able to cover them all. There are still a couple whoppers that no one has pointed out yet. The first OP snippet starts out like this:

$dir= shift || '.';

opendir DIR, $dir or die "Can't open directory $dir: $!\n";

while ($file= readdir DIR) {
    next if $file=~/^\./;
        open (FH, ">", "$file") or die "Can't open file $file: $!\n";
        my @file_lines=<FH>;
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You truncate/open a file for output and then try to read from it? I hope you made a backup of the directory before you ran that script with $dir set to "." because the script would have obliterated all the data files. (Running it with some directory name in @ARGV would have saved your input data from oblivion, but wouldn't have gotten anything done.)

The second snippet avoids that problem, but still shares another problem with the first version: if $dir is set to something other than "." (i.e. via @ARGV), the open statement would need to be like this in order to do what you want:

     open (FH, "$dir/$file") ...
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Luckily, when you do it that way, it still works when $dir is set to "."

Put all that together with the other replies, and you should get pretty close to a working script.