The foglight indexes aren't "missing", they're intentionally not there. Those tools are suggesting covering indexes for a lot of queries that have been run by the database. Adding those indexes might speed up certain queries, but they will also slow down inserts, and greatly increase the database size. The indexes that are currently on the table should have a good balance of read/write performance.
In the FMS 5.6.11 release, index-organized tables have been added, which should remove the need for a lot of covering indexes.
Also, not all the tables/indexes referred to in that report belong to Foglight.