.gitignore

###################################################
# WHITELISTED FILES
#
# Because we found so much garbage in here
# that we cannot tell what is important, and
# because we don't want to track garbage, we
# have the `include_log.php` script automatically
# append included files here.
#
# DO NOT EDIT BELOW -- Put custom .gitignores above
###################################################

# ignore everything
*

# ... except directories, because ignoring them will
# ignore everything inside them
!*/

# ... now whitelist files

gitignore_whitelist_includes.php

<?php

/**
* Register a function to whitelist included files before execution ends
* 
* Assumes this script is in same directory as .gitignore. Adds whitelists to
* .gitignore for every file included. Doesn't add the same whitelist twice
*/
register_shutdown_function(function () {
    $gitignoreFile = __DIR__ . '/.gitignore';
    $gitignores = explode("\n", file_get_contents($gitignoreFile));
    $includes = array_unique(get_included_files());
    $includeToWhitelist = function ($file) {
        return '!' . str_replace(__DIR__, '', $file);
    };
    $whitelists = array_diff(array_map($includeToWhitelist, $includes), $gitignores);
    file_put_contents($gitignoreFile, implode("\n", $whitelists), FILE_APPEND);
});

index.php

<?php

include __DIR__ . '/gitignore_whitelist_includes.php';

// some code here ...