A stand alone script that can be used to compare and copy configuration from two different sub-sites into a default configuration.

Config Merge

<?php

require './vendor/autoload.php';

// Set up the directories needed.
$parentDirectory = 'config/siteone';
$siblingDirectory = 'config/sitetwo';

$destinationDirectory = 'config/default';

$parentConfigSplitFile = $destinationDirectory . '/config_split.config_split.siteone.yml';
$siblingConfigSplitFile = $destinationDirectory . '/config_split.config_split.sitetwo.yml';

// Name and clear out the log files.
$updateFile = 'configUpdate.txt';
file_put_contents($updateFile, '');

// Set up the config type lists.
$parentBlacklist = [];
$parentGraylist = [];
$siblingBlacklist = [];
$siblingGraylist = [];

// Load all of the files in the parent directory to check them.
$files = array_diff(scandir($parentDirectory), array('..', '.'));

foreach ($files as $filename) {
    // Check to see if we have a yml file.
    if (strstr($filename, '.yml') !== FALSE) {

        // Extract the configuration name.
        $configName = str_replace('.yml', '', $filename);

        if (file_exists($siblingDirectory . '/' . $filename)) {
            // File also exists in the sibling directory.
            // Get the contents of both of the files.
            $parentFileContents = file_get_contents($parentDirectory . '/' . $filename);
            $parentArray = \Drupal\Core\Serialization\Yaml::decode($parentFileContents);
            $siblingFileContents = file_get_contents($siblingDirectory . '/' . $filename);
            $siblingArray = \Drupal\Core\Serialization\Yaml::decode($siblingFileContents);

            // Calculate the difference between the two files.
            $difference = \Drupal\Component\Utility\DiffArray::diffAssocRecursive($parentArray, $siblingArray);

            if (count($difference) == 1 && isset($difference['uuid'])) {
                // If we have exactly 1 difference and that difference is the uuid then process it.
                // Extract the uuid from the parent and write this to a file.
                $uuid = $parentArray['uuid'];

                $output = "'" . $configName . "' => '" . $uuid . "'," . PHP_EOL;
                file_put_contents($updateFile, $output, FILE_APPEND);

                // Copy the parent file to the destination directory.
                copy($parentDirectory . '/' . $filename, $destinationDirectory . '/' . $filename);

                // Delete both of the files.
                unlink($parentDirectory . '/' . $filename);
                unlink($siblingDirectory . '/' . $filename);
            }
            elseif (count($difference) > 0  && !isset($difference['uuid'])) {
                // This is not a uuid change and as it's different we just need to gray list and copy this version to
                // the default config.
                $parentGraylist[] = $configName;
                $siblingGraylist[] = $configName;
                copy($parentDirectory . '/' . $filename, $destinationDirectory . '/' . $filename);
            }
            elseif (count($difference) == 0) {
                // If we have exactly no difference between the two files then just move it.
                // Copy the parent file to the destination directory.
                copy($parentDirectory . '/' . $filename, $destinationDirectory . '/' . $filename);

                // Delete both of the files.
                unlink($parentDirectory . '/' . $filename);
                unlink($siblingDirectory . '/' . $filename);
            }
        }
        else {
            // Config doesn't exist in sibling, make sure it doesn't also exist in the default configuration.
            if (!file_exists($destinationDirectory . '/' . $filename)) {
                // Add it to blacklist.
                $parentBlacklist[] = $configName;
            }
        }
    }
}

// Run the same checks on the sibling directory.
$files = array_diff(scandir($siblingDirectory), array('..', '.'));

foreach ($files as $filename) {
    // Check to see if we have a yml file.
    if (strstr($filename, '.yml') !== FALSE) {
        // Extract the configuration name.
        $configName = str_replace('.yml', '', $filename);

        if (!file_exists($parentDirectory . '/' . $filename)) {
            if (!file_exists($destinationDirectory . '/' . $filename)) {
                $siblingBlacklist[] = $configName;
            }
        }
    }
}

// Export the data to our config split files.
if (count($parentBlacklist) > 0 || count($parentGraylist) > 0) {
    $parentConfigSplitFileContents = file_get_contents($parentConfigSplitFile);
    $parentConfigSplit = \Drupal\Core\Serialization\Yaml::decode($parentConfigSplitFileContents);

    if (count($parentBlacklist) > 0) {
        $parentConfigSplit['blacklist'] = array_unique(array_merge($parentConfigSplit['blacklist'], $parentBlacklist));
        sort($parentConfigSplit['blacklist']);
    }

    if (count($parentGraylist) > 0) {
        $parentConfigSplit['graylist'] = array_unique(array_merge($parentConfigSplit['graylist'], $parentGraylist));
        sort($parentConfigSplit['graylist']);
    }
    $parentConfigSplitFileContents = \Drupal\Core\Serialization\Yaml::encode($parentConfigSplit);
    file_put_contents($parentConfigSplitFile, $parentConfigSplitFileContents);
}

if (count($siblingBlacklist) > 0 || count($siblingGraylist) > 0) {
    $siblingConfigSplitFileContents = file_get_contents($siblingConfigSplitFile);
    $siblingConfigSplit = \Drupal\Core\Serialization\Yaml::decode($siblingConfigSplitFileContents);

    if (count($parentBlacklist) > 0) {
        $siblingConfigSplit['blacklist'] = array_unique(array_merge($siblingConfigSplit['blacklist'], $siblingBlacklist));
        sort($siblingConfigSplit['blacklist']);
    }

    if (count($parentGraylist) > 0) {
        $siblingConfigSplit['graylist'] = array_unique(array_merge($siblingConfigSplit['graylist'], $siblingGraylist));
        sort($siblingConfigSplit['graylist']);
    }
    $siblingConfigSplitFileContents = \Drupal\Core\Serialization\Yaml::encode($siblingConfigSplit);
    file_put_contents($siblingConfigSplitFile, $siblingConfigSplitFileContents);
}

echo 'Done.' . PHP_EOL;