apache.conf

<VirtualHost *:80>
    # ....
    php_value auto_prepend_file /etc/apache2/local/coverage-start.php
    php_value auto_append_file /etc/apache2/local/coverage-stop.php
    # ....
</VirtualHost>

coverage-start.php

<?php
if (isset($_GET['coverage'])) {
  setcookie('coverage', $_GET['coverage']);
}
if ((isset($_GET['coverage']) && $_GET['coverage'] == '1') 
  || (isset($_COOKIE['coverage']) && $_COOKIE['coverage'] == '1')){
require 'PHP/CodeCoverage/Autoload.php';
$_____coverage = new PHP_CodeCoverage;
$_____coverage->start('apache');
}

coverage-stop.php

<?php
if (isset($_____coverage)){
  $_____coverage->stop();
  $writer = new PHP_CodeCoverage_Report_PHP;
  $COVERAGE_DIRECTORY = '/tmp/coverage';
  if (!file_exists($COVERAGE_DIRECTORY)){
    mkdir($COVERAGE_DIRECTORY);
  }
  $writer->process($_____coverage, tempnam($COVERAGE_DIRECTORY, 'coverage'));
}

cd /tmp/coverage chown -R a+r . for f in *; do mv basename $f .cov $f.cov; done phpcov --html /tmp/cov-html/ --merge