How to add square braces around subarray data inside of a json encoded string?

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You need to wrap things in another array:

$data = array("item" => array(array("id" => "123456", "name" => "adam")));

This will be more understandable if we use the equivalent PHP 5.4 array syntax:

$data = [ "item" => [ ["id" => "123456", "name" => "adam"] ] ];

Compare this with the JSON:

        { "item":   [ {"id":"123456", "name":"adam"      } ] }

The only thing to explain is why one of the PHP arrays remains an array [] in JSON while the other two get converted to an object {}. But the documentation already does so:

When encoding an array, if the keys are not a continuous numeric
sequence starting from 0, all keys are encoded as strings, and
specified explicitly for each key-value pair.

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