conditions currently create separate annotations

Conditions are attached to a specific annotation as a "group", but currently each condition creates a separate annotation:

This causes a problem for querying.

here:

If I filter on NOT standard temperature, I would still retain the phenotype annotation because the experiment was performed using YES media (even though the experiment was also performed at standard temperature, and so should be filtered )

@kimrutherford

The issue names no files, tests, or entry points; begin by locating annotation creation and condition-group handling, then trace the query and filtering path. Done means conditions attached to one annotation are queried as a group, so filtering on NOT standard temperature removes the related phenotype annotation when that condition applies.

Written by the indexing model from the issue text.