Renan,
Your module folder tree looks correct for the query view. I tested it locally, and it looks like you might be missing part of the string for the xmlns attribute of the customView element in your XML. If I set the xmlns="http://labkey.org/data/xml/queryCustomView" the study_pubinfo view appears in the views menu of the study_pubmed query for me and was filtered as expected.

Give that a try.
-Cory


<customView xmlns="http://labkey.org/data/xml/queryCustomView">
        <filters>
                <filter column="study_accession" operator="eq" value="SDY61"/>
        </filters>
</customView>