[ghanja]

eqemu_update.pl
replace sub quest_files_fetch subroutine with the following:

sub quest_files_fetch{
	if (!-e "updates_staged/Quests-Plugins-master/quests/") {
		print "\n --- Fetching Latest Quests --- \n";
		get_remote_file("https://github.com/EQEmu/Quests-Plugins/archive/master.zip", "updates_staged/Quests-Plugins-master.zip", 1);
		print "\nFetched latest quests...\n";
		mkdir('updates_staged');
		unzip('updates_staged/Quests-Plugins-master.zip', 'updates_staged/');
	}
	$updateall = false;
	$fc = 0;
	use File::Find;
	use File::Compare;
	
	my @files;
	my $start_dir = "updates_staged/Quests-Plugins-master/quests/";
	find( 
		sub { push @files, $File::Find::name unless -d; }, 
		$start_dir
	);
	for my $file (@files) {
		if($file=~/\.pl|\.lua|\.ext/i){
			$staged_file = $file;
			$dest_file = $file;
			$dest_file =~s/updates_staged\/Quests-Plugins-master\///g;
			
			if (!-e $dest_file) {
				copy_file($staged_file, $dest_file);
				print "Installing :: '" . $dest_file . "'\n";
				$fc++;
			}
			
			else{
				$diff = do_file_diff($dest_file, $staged_file);
				$backup_dest = "updates_backups/" . $time_stamp . "/" . $dest_file;
				if($diff ne ""){
					if ($updateall){
						#::: Make a backup
						copy_file($dest_file, $backup_dest);
						#::: Copy staged to running
						copy($staged_file, $dest_file);
						print "Installing :: '" . $dest_file . "'\n\n";
					}
					else{
						print $diff . "\n";
						print "\nFile Different :: '" . $dest_file . "'\n";
						print "\nDo you wish to update this Quest? '" . $dest_file . "' [Yes (Enter) - No (N) - Update All (A)] \nA backup will be found in '" . $backup_dest . "'\n";
						my $input = <STDIN>;
						if($input=~/Y/i){
							#::: Make a backup
							copy_file($dest_file, $backup_dest);
							#::: Copy staged to running
							copy($staged_file, $dest_file);
							print "Installing :: '" . $dest_file . "'\n\n";
						}
						elsif($input=~/A/i){
							print "\nChoosing this option will overwrite ALL quests different from master (i.e. overwrite custom quests) [Type YES if certain] \n";
							my $input = <STDIN>;
							if($input=~/YES/i){$updateall = true;}
							#::: Make a backup
							copy_file($dest_file, $backup_dest);
							#::: Copy staged to running
							copy($staged_file, $dest_file);
							print "Installing :: '" . $dest_file . "'\n\n";
						}
						else{
						}
					}
				$fc++;
				}
			}
		}
	}
	rmtree('updates_staged');
	if($fc == 0){
		print "\nNo Quest Updates found... \n\n";
	}
}

Not the prettiest thing and I didn't check output (print) syntax format, but, in the case you just want to make a pot of coffee or something while it updates ALL quests files that are different from master (including custom quests by the same name), then there ya go.