Address search/index issues

This PR attempts to address the search and index problems described in Sanger RT#374851 and RT#372269, in particular:
- indexing issues with *E. multilocularis*, *T. brucei brucei 927* and *P. chabaudi* where adding previously missing feature classes prevents mysterious exceptions during the indexing (via PopulateLuceneIndices tool), causing indexing batches to fail and therefore creating 'holes' in the indexed annotation coverage
- search/autosuggest issues w.r.t. gap features, where gaps would be suggested as hits but could not be displayed