In a standard $lookup operation involving a local and a foreign collection, index usage can be specified for the foreign collection using query settings.

Consider an example with two collections, mainColl and secondaryColl, both having indexes {a:1} and {a:1, b:1}. The following pipeline is applied to mainColl:

[
  {
    "$match": { "a": 1, "b": 5 }
  },
  {
    "$lookup":
    {    
        "from": "secondaryColl",
        localField": "a",
        "foreignField": "a",
        "as": "output"     
    }
  }
]

Case 1: Specifying an index for the local collection (mainColl)

If the query settings are set as follows:

"settings": {
    "indexHints": {
        "ns": { "db": "test", "coll": "mainColl" },
        "allowedIndexes": [
            { "a": 1, "b": 1 }
        ]
    }
}

The index {a:1, b:1} on mainColl will be used for the $match filter stage.

Case 2: Specifying an index for the foreign collection (secondaryColl)
 
If the query settings are set as follows:

"settings": {
    "indexHints": {
        "ns": { "db": "test", "coll": "secondaryColl" },
        "allowedIndexes": [
            { "a": 1, "b": 1 }
        ]
    }
}

The index {a:1, b:1} on secondaryColl will be used when executing the $lookup stage.

Issue in Self-Lookups
 
A self-lookup occurs when the foreign collection is the same as the local collection, as shown below:

[
  {
    "$match": { "a": 1, "b": 5 }
  },
  {
    "$lookup":
    {    
        "from": "mainColl",
        localField": "a",
        "foreignField": "a",
        "as": "output"     
    }
  }
]

If the query settings specify an index for mainColl:

"settings": {
    "indexHints": {
        "ns": { "db": "test", "coll": "mainColl" },
        "allowedIndexes": [
            { "a": 1, "b": 1 }
        ]
    }
}

One would expect the index {a:1, b:1} to be used for both the $match and the $lookup stages. However, this is not currently the case. While the index {a:1, b:1} is correctly used for the filter stage, the index used for the $lookup stage is the {a:1}.

Solution : To ensure the specified index hint is respected in self-lookups, the query settings index hints for the main collection should be applied when computing index information for the secondary collections.

Reproduction : buildscripts/resmoke.py run --suites=replica_sets_jscore_passthrough --runAllFeatureFlagTests qs-repro.js