A index has to be named as "primary" to be detected Doctrine\ORM\Mapping\Driver\DatabaseDriver::loadMetadataForClass()

Condition

if (isset($indexes['primary']) && in_array($column->getName(), $indexes['primary']->getColumns())) {

needs the primary key to be named as primary. Discovered this when reverse engineering an existing database.

Fix, that worked for me:

Replace:

if (isset($indexes['primary']) && in_array($column->getName(), $indexes['primary']->getColumns())) {
$fieldMapping['id'] = true;

With:

$primary = false;

foreach ($indexes as $index)
{
if ($index->isPrimary())
{
if (in_array($column->getName(), $index->getColumns()))

}
}

if ($primary){
$fieldMapping['id'] = true;