Hello, after doing some research it's not clear to me whether or not there's a substantial way to interact with the taxonomy_index table.
My thought is that modules that do field level permissions should be able to prevent some nodes from being placed in a term's index is some level of privacy is desired.
This could get a little tricky, since it is possible for a node to have references to the same term. My thought is that each should have a chance to alter the index - if there is a private reference, it would be supressed, and if there is a public field it would be allowed.
So here are three examples:
1) private reference - deny indexing
2) public reference - allow indexing
3) public reference and private reference - allow indexing (public would trump private).
This issue was generated while working on another one: https://drupal.org/node/2027941
Perhaps I've overlooked some way to do this through an API? I feel like this should be a capability of the taxonomy module, since a none-core module would have a difficult time determining whether a node/term should be indexed or not on its own.