Can you check your Doctrine/ORM/Version.php file?
========================================
Tried but that file doesn't exist for me. To make sure I was using the proper beta package I've started from scratch and downloaded Doctrine via http://www.doctrine-project.org/downloads/DoctrineORM-2.0.0-BETA1.tgz
The only Version.php file I found was Doctrine/Common/Version.php and the "VERSION" costants value is "2.0-DEV" (That's the same version that gets spit out using "php doctrine -V")
Also, did you try reproducing this in a simpler scenario? i.e. without Symfony?
============================================================
Yes. And everything worked. I used the SchemaTool class and didn't have any issues.
New Issues
=========
After starting over using the files located at the URL above the problem still exists however it's changed slightly. I still can't extend a class using another class located in a different file (same namespace). If I place both classes in the same file then the cli works. However, unlike my original post it's no longer limited to classes named "Module"; all class names fail now.
Just to make sure I had a clean version of Symfony I grabbed the latest from http://svn.symfony-project.com/branches/2.0 (Rev 29773) and nothing changed..same error.
Not sure if it will help but here's a stack trace:
> php doctrine -v orm:schema-tool:update
PHP Fatal error: Class 'App\Entities\Module' not found in [path] on line [line]
PHP Stack trace:
PHP 1. {main}() /srv/www/projects/test/scripts/doctrine/doctrine:0
PHP 2. include() /srv/www/projects/test/scripts/doctrine/doctrine:4
PHP 3. Symfony\Components\Console\Application->run() /srv/www/projects/test/scripts/doctrine/doctrine.php:41
PHP 4. Symfony\Components\Console\Application->doRun() /srv/www/projects/test/library/Symfony/Components/Console/Application.php:115
PHP 5. Symfony\Components\Console\Command\Command->run() /srv/www/projects/test/library/Symfony/Components/Console/Application.php:186
PHP 6. Doctrine\ORM\Tools\Console\Command\SchemaTool\AbstractCommand->execute() /srv/www/projects/test/library/Symfony/Components/Console/Command/Command.php:152
PHP 7. Doctrine\ORM\Mapping\ClassMetadataFactory->getAllMetadata() /srv/www/projects/test/library/Doctrine/ORM/Tools/Console/Command/SchemaTool/AbstractCommand.php:53
PHP 8. Doctrine\ORM\Mapping\Driver\AnnotationDriver->getAllClassNames() /srv/www/projects/test/library/Doctrine/ORM/Mapping/ClassMetadataFactory.php:99
PHP 9. require_once() /srv/www/projects/test/library/Doctrine/ORM/Mapping/Driver/AnnotationDriver.php:454
... I haven't changed the original Entities at all, they are still as described above.
That sounds weird. Are you using Symfony (2) with Doctrine2Bundle? There is no specific treatment of classes with certain names within Doctrine that I can think of.