No, there is a way to do this without editing you're php files using .htaccess and ini directives.
Assuming you're on Apache, you can put an auto_prepend call into you're .htaccess (which assumes you have AllowOverride for it).
php_value auto_prepend_file /path/to/autoprependfile.php
Use a full path to keep from crazyness happening, or you can put it in a known include_path.
With autoprependfile.php containing:
You won't need to auto append though, output buffering should flush itself at script termination.
May I inquire as to why so many php files though? I mean, I've moved pretty much exclusively to OOP in PHP, yet my library itself is now about 107 class files. Even when I was procedural, I think the most files I've ever created for an entire site was 24 excluding configuration files. Management of that alone was a horrid task - I had known PHP for maybe 3 years at that point, so there was still a lot I didn't know about it (such as OO hah).