On each PHP request (cli, cgi or apache module), this script will detect to which project the file belongs and log it.

time-spender-logger.php

<?php
/**
 * On each PHP request (cli, cgi or apache module), 
 * this script will detect to which project the file belongs and log it.
 * It also features a threshold so a couple consecutive minutes without a request
 * doesn't stop your timer, see below.
 * 
 * To install, configure the roots (see below) add this line to your php.ini:
 * auto_prepend_file=/path/to/file/time-spender-logger.php
 * 
 * Call this file directly to output your data so far.
 * 
 * This was done to track my time on each of my projects.
 * 
 * The weird class name is to ensure no name collision will occur.
 * 
 * @link http://blog.lavoie.sl/2013/01/track-your-time-working-on-php-projects.html
 */
class __TimeSpenderLogger
{
    private $script;
    private $datadir;

    /**
     * Number of minutes that are consired continuous
     * For example, if a script runs at:
     *  - 5:10
     *  - 5:12
     *  - 5:45
     *  - 5:50
     * it will be counted as (12 - 10 + 1) + (50 - 45 + 1) = 9 minutes
     */
    public $threshold = 10;

    /**
     * Roots are folders that contain your projects.
     * All the folders directly below are considered project names
     * You can specify multiple roots for different project groups
     * Must be an absolute path.
     * They are checked in order so you may have a path that is inside another
     * Ex: array(
     *  'dev'     => '/var/www/dev'
     *  'general' => '/var/www'
     * )
     * 
     * For example, if script /var/www/my-project/foo/bar.php is ran, it will be logged as:
     * group: general   project: my-project
     */
    public $roots = array(
        'Sites' => '/Users/seb/Sites',
    );

    public function __construct()
    {
        $this->script   = realpath($_SERVER['SCRIPT_FILENAME']);
        $this->datadir  = dirname(__FILE__) . '/data';
    }

    private static function startsWith($haystack, $needle)
    {
        return !strncmp($haystack, $needle, strlen($needle));
    }

    /**
     * @return array containing [group, project]
     */
    private function getProject()
    {
        foreach ($this->roots as $group => $root) {
            if (self::startsWith($this->script, $root)) {
                $project = substr($this->script, strlen($root) + 1);

                $trim = strpos($project, '/');
                if ($trim > 1) {
                    // If a slash was not found, it is because the script is directly under the root.
                    // The project will therefore be the filename itself. ie: index.php
                    $project = substr($project, 0, $trim);
                }
                if (empty($project)) {
                    // This is just to prevent further errors, shouldn't happen
                    $project = 'none';
                }

                return array($group, $project);
            }
        }

        return false;
    }

    /**
     * Touches a file at $datadir/$group/$project/Y-m-d/H-i
     * This is the critical function because it does I/O
     */
    public function log()
    {
        $project = $this->getProject();
        if (empty($project)) return;

        $date = date('Y-m-d');
        $time = date('H-i');
        $folder = "{$this->datadir}/{$project[0]}/{$project[1]}/$date";

        is_dir($folder) || mkdir($folder, 0777, true);
        touch("$folder/$time");
    }

    /**
     * Loops through all the folder and compiles the minutes spent on each project
     */
    public function getData()
    {
        if (!is_dir($this->datadir)) return array();

        $data = array();

        foreach (scandir($this->datadir) as $group) {
            if ($group[0] == '.') continue;

            foreach (scandir("{$this->datadir}/$group") as $project) {
                if ($project[0] == '.') continue;

                foreach (scandir("{$this->datadir}/$group/$project") as $date) {
                    if ($date[0] == '.') continue;

                    $minutes = 0; // total minutes for this day, first is not counted, so add one
                    $counter = 0; // total consecutive minutes
                    $last = null; // last minute that was checked

                    foreach (scandir("{$this->datadir}/$group/$project/$date") as $time) {
                        if ($time[0] == '.') continue;

                        list($hour, $minute) = explode('-', $time);
                        $m = $hour * 60 + $minute;
                        $diff = (null == $last) ? 1 : $m - $last;

                        if ($diff <= $this->threshold) {
                            // increment counter
                            $counter += $diff;
                        } else {
                            // add the counter and reset
                            $minutes += $counter;
                            $counter = 1;
                            $last = null;
                        }

                        $last = $m;
                    }
                    $minutes += $counter;

                    $data[$date][$group][$project] = $minutes;
                }
            }
        }

        return $data;
    }

    /**
     * Displays the data in 4 neatly formatted columns: date, group, project and time
     * Note that projects and projects group have a max of 20 chars
     */
    public function show($data)
    {
        header('Content-Type: text/plain');
        printf("%-15s %-20s %-20s %5s\n", 'DATE', 'GROUP', 'PROJECT', 'TIME');
        $line = str_repeat('-', 15 + 1 + 20 + 1 + 20 + 1 + 5) . "\n";
        echo $line;

        foreach ($data as $date => $groups) {
            foreach ($groups as $group => $projects) {
                foreach ($projects as $project => $minutes) {
                    $hours = floor($minutes / 60);
                    $minutes -= $hours * 60;
                    printf("%-15s %-20s %-20s %2d:%02d\n", $date, $group, $project, $hours, $minutes);
                }
            }
            echo $line;
        }
    }

    /**
     * Runs the logger
     * If the script is directly called, prints the data instead
     */
    public static function run()
    {
        $instance = new self();

        if ($instance->script == __FILE__) {
            $instance->show($instance->getData());

            // Ensure we won't re-run this file a second file 
            // Happens if you are using auto_prepend_file
            die();
        } else {
            $instance->log();
        }
    }
}

__TimeSpenderLogger::run();