queryManager.uris does not honor additional-query in search options

Start at the QueryManager.search and QueryBatcher entry points, using the provided Java reproduction and the all.xml options content. Compare how the options name and its and-not-query collection filter are applied in simple search versus QueryBatcher. Done means both paths return the same collection-filtered results, including excluding ignoredCollection.

Version of MarkLogic Java Client API

6.5.0

Version of MarkLogic Server

11.0.2

Java version

JDK 17

OS and version

ProductName: macOS
ProductVersion: 13.5
BuildVersion: 22G74

Input: Some code to illustrate the problem, preferably in a state that can be independently reproduced on our end

The current issue is a follow-up of this one: https://github.com/marklogic/java-client-api/issues/1640

In the last issue you correctly mentioned that the correct format for search positive/negative is: positive-query and negative-query

However, the way I created the last issue is not 1:1 with the issue that we actually had. Our issue is actually the following:
executing a search query and passing an options name parameter (where the options contains an and-not-query looking for a collection is simply ignored in QueryBatcher, but it works for a simple search).

Let me help you a bit with a piece of code:

QueryManager queryManager= markLogicDatabaseClient.newQueryManager();
        final RawCombinedQueryDefinition structQueryDef = queryManager
            .newRawCombinedQueryDefinition(new StringHandle(
                "<search xmlns=\"http://marklogic.com/appservices/search\">\n" +
			"  <query>\n" +
			"    <and-query>\n" +
			"      <term-query>\n" +
			"        <text>world</text>\n" +
			"      </term-query>\n" +
			"    </and-query>\n" +
			"  </query>\n" +
			"</search>"), "all");

        final SearchHandle result = queryManager.search(structQueryDef, new SearchHandle());
        result.getMatchResults();

The content of "all.xml" contains (between other stuff):

<cts:and-not-query>
	  <cts:annotation type="searchable-collections"/>
	  <cts:positive>
	    <cts:collection-query>
	      <cts:uri>collection1</cts:uri>
	      <cts:uri>collection2</cts:uri>
	    </cts:collection-query>
	  </cts:positive>
	  <cts:negative>
	      <cts:collection-query>
		<cts:uri>ignoredCollection</cts:uri>
	      </cts:collection-query>
	  </cts:negative>
	</cts:and-not-query>

Actual output: What did you observe? What errors did you see? Can you attach the logs? (Java logs, MarkLogic logs)

The output is correct for a simple search, the collections are filtered, but for QueryBatcher they are not.

Expected output: What specifically did you expect to happen?

The output is the same for both search and QueryBatcher (collections are taken into account)

Alternatives: What else have you tried, actual/expected?