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codeintel: add tests which cover sub-repo permissions filtering logic for references query

Administrator requested to merge ao/subrepo-perms-code-intel-references into main

Created by: sashaostrikov

Add tests which cover logic for references query

Sub-repo filtering itself is implemented here

Should be merged after https://github.com/sourcegraph/sourcegraph/pull/29328

Closes https://github.com/sourcegraph/sourcegraph/issues/29239

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