Align to spec v0.9.3

[terencechain]

With the release of spec v0.9.3. This issue tracks to the overall progress to align Prysm codebase to spec v.0.9.3

The v0.9.3 release contains of the following:

Beacon chain

• remove signing_root and add explicit signed message containers (rm signing root (fixes #1487) ethereum/consensus-specs#1491)
• ensure attestation slot and target epoch are coherent (ensure that epoch of attestation slot matches the target epoch ethereum/consensus-specs#1509)
• fix activation queue rate and enforce only activate upon finality (Fix queue rate and only activate upon finality ethereum/consensus-specs#1514)
• disallow duplicate indices in indexed attestation (Fixes #1486: disallow duplicate indices in indexed attestation ethereum/consensus-specs#1516)
• additional proposer tests for increased coverage (Two tests for proposer indices being off because of (in)active validators ethereum/consensus-specs#1518)

Fork choice

• remove duplicate validation in on_attestation (Remove duplicated attestation target root check ethereum/consensus-specs#1492)
• filter out non-viable branches when call to get_head (filter viable branches in fork choice ethereum/consensus-specs#1495)
• clean up handle of slots (explicit use of GENESIS_SLOT in fork choice  ethereum/consensus-specs#1510)
• ensure best_justified_checkpoint updates to the best available (ensure the best better-justification is stored in fork choice ethereum/consensus-specs#1508)
• ensure attestation slot and target epoch are coherent(ensure that epoch of attestation slot matches the target epoch ethereum/consensus-specs#1509)

Simple Serialize

• remove signing_root (rm signing root (fixes #1487) ethereum/consensus-specs#1491)

[rauljordan]

This can be closed as well as all items are complete