Added comments

process.pl

@@ -5,35 +5,52 @@ use warnings;
 use File::Compare;
 use File::Basename;
 no warnings 'once';
-
+# For every argument (file)
 foreach my $file (@ARGV) {
+  # If it exists
   if (-e $file) {
+    # Load the autoformatted data into $data
     my $data = process_file($file);
     open(MYOUTPUTFILE, "+>$file.bak") or die "Error opening output file $!";
+    # Write the data to $file.bak
+    #TODO: This could be done with no .bak
     print MYOUTPUTFILE $data;
     close(MYOUTPUTFILE);
     if (compare($file, "$file.bak") != 0) {
+      # If there were changes, then tell the user
       print "Processed $file\n";
     }
+    # Replace the original file with this file
+    # Delete it
     unlink $file;
+    # Overwrite the old one
     rename "$file.bak", $file;
   }
-  
 }
+# Creates the automatically formatted file
 sub process_file {
   my($filename) = "$_[0]";
   open(MYINPUTFILE, "<$filename") or die "x $!";
+  # The formatted file
   my($data) = "";
+  # Loop through every line in the file
   while(<MYINPUTFILE>) {
+    # Get rid of trailing whitespace
     s/\s*$//;
     my($line) = $_;
+    # If it is not a whitespace only line, append it to $data
     if($line !~ /^\s*$/) {
       $data = $data . "$line\n";
     }
   }
   close(MYINPUTFILE);
+  # Get rid of final newline
   chomp($data);
   if ($data !~ /^\s*\/\*\*/) {
+    # Get the basename of the file, this prevents making the block comment say:
+    # @file src/folders/code.c
+    # And instead uses
+    # @file code.c
     my $basename = basename($filename);
     $data = "/**\n * \@file $basename\n * \@author Austen Adler (agadler)\n * TODO: Description\n */\n$data";
   }