This is not something that we can address, but first of all, you are making a few incorrect assumptions:

<?php
$m = new MongoClient();
$c = $m->phpunit->test;
$c->remove();
$c->insert( array( 0, 1, 1, 2, 3, 5 ) );
$c->update( array(), array( '$set' => array( "0" => 'zero int' ) ) );

This does not work - but you only see that when you have safe mode turned on:

MongoCursorException: localhost:27017: Invalid modifier specified: $set in /tmp/php-606.phpt on line 7

What happens is that when serializing arrays from PHP to BSON, the driver checks the field names. As you know, in PHP you can have numerically indexed array keys, and associative array keys. These types need to be converted differently into BSON.

A BSON array has *no* keys, and in PHP we will only create a BSON array out of a PHP array if:

 - There are no string keys, or:
 - The first key in the array is != 0, or:
 - The keys in the array are not consecutive (ie, have gaps), such as in
   array( 0, 1, 3, 4 ).

In all other cases, we create a BSON object.

If you supply an object from PHP (any class), then we will always convert it to a BSON object.

Now lets have a look at your updates:

array( '$set' => ( 0 => 'zero int' ) );

This gets converted into the following JSON/BSON if we follow the above guidelines.

{ '$set' : [ 'zero int'] }

 - The first level is an object {} because there is a string key ($set).
 - The nested PHP array is an array [] because: there are no string keys, the first key is a 0 and the keys are consecutive.

Conclusion: This creates an incorrect $set for MongoDB.

The same is true for the array('0' => 'zero str') case, as PHP converts string keys that look like numbers to numbers.

These two cases will work:

	array(1 => 'one int'),
	array('2' => 'two str'),

Both get converted to a BSON object.

Then the last array method:

	array(
		'0' => 'multi 0',
		'1' => 'multi 1',
		'2' => 'multi 2'
	)

Will create in JSON/BSON:

{ $set: [ 'multi 0', 'multi 1', 'multi 2' ] }

Which again is incorrect.

When you use $updClass in your example, then things work because objects are always converted to BSON objects.

Conclusion:
 - Don't use numerical field names (BSON requires *string* field names, but in PHP, you can't have one that looks like a number due to syntax restrictions.
 - If you do use numerical field names, you *have* to use an object from the PHP side to do updates, just like you do with:

$updClass = new stdClass;
$updClass->{0} = 'class 0';
$c->update( array(), array( '$set' => $updClass ) );

Thanks Derick,

You already gave me an answer here: http://stackoverflow.com/q/9297495/599857 (I 
even discussed this with you quickly at PHPNW!), you're a busy guy, so I'll let 
you off for not remembering :)