with keyword causes rule indexer lookups to fail in some cases

[tsandall]

Expected Behavior

The rule indexer should correctly incorporate input & data values overridden by the with keyword.

Actual Behavior

The rule indexer is not returning rules that ought to match given certain evaluation contexts.

Steps to Reproduce the Problem

Given the following rego and json, q and r should generate the same value, however, the indexer incorrectly determines that r does not have to be evaluated. As a result, data.foo.r is undefined.

{"bar": "baz"}

package foo

p = x {
    data.bar = x
}

q = x {
    p = x
}

r = x {
    p = x with input as {}
}

Additional Info

It looks like this issue was introduced in 986d82f