An SQL query relating to role override function is producing large combinatorial result sets in our installation of Moodle 1.7+ (2006101009). We've seen the query below return upwards of 400k rows (around 10mb of data). Due to the large result set, this query alone takes upwards of 40 seconds to complete, depending on how many contexts are associated with the user.

1. Query_time: 31 Lock_time: 0 Rows_sent: 334368 Rows_examined: 1340316
   SELECT rc.capability, c1.id as id1, c2.id as id2, (c1.contextlevel * 100 + c2.contextlevel) AS aggrlevel,
   rc.permission AS sum
   FROM
   mdl_role_assignments ra,
   mdl_role_capabilities rc,
   mdl_context c1,
   mdl_context c2
   WHERE
   ra.contextid=c1.id AND
   ra.roleid=rc.roleid AND
   ra.userid=22 AND
   rc.contextid=c2.id AND
   c1.id IN (54,35,83,102,107,75,172,203,69,389,223,219,257,383,291,298,512,302,366,363,378,217,316,457,456,431,362,319,361,345,58,354,385) AND
   rc.contextid != 1
   AND ((ra.timestart = 0 OR ra.timestart < 1168276177) AND (ra.timeend = 0 OR ra.timeend > 1168276177))
   GROUP BY
   rc.capability, (c1.contextlevel * 100 + c2.contextlevel), c1.id, c2.id, rc.permission
   ORDER BY
   aggrlevel ASC;

It appears that most of these rows are discarded in a subsequent function call that determines if c1 is a parent of c2. I understand that there have been other bug reports regarding missing INDEX after upgrading vs. installing fresh. We recently upgraded from 1.5.3+ to 1.7 (on 1/8).

Some sizes for the tables used in the above query:
mdl_role_assignments: 3907 rows
mdl_role_capabilities: 31318 rows
mdl_context: 9267 rows (and growing constantly)

If I can provide additional information that might be of use, please do not hesitate to let me know.