Really simple, you are almost there:
<input ng-model="query">
<div ng-repeat="item in items | filter:query">{{item}}</div>
This way you have only one ng-model to filter.
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Edit:
If you have more properties in your object that don't want to be filtered, you can use a function or a custom filter, from the documentation:
{{ filter_expression | filter : expression : comparator}}
Expression can be: string, Object or function()
I've updated the fiddle to demonstrate how you can filter using both a function and a custom filter: fiddle.