[Mega Tracking] Align Codebase to Spec v0.5

[terencechain]

Note: This is mainly a tracking issue and the items from here should not take precedent over priority tasks such as sync, run time and E2E test issues. Any potential PR from this issue list will have to go through E2E test before merge.

This issue tracks the overall progress of updating the current beacon chain implementation to spec v0.5 Here is what has been done so far and the missing steps:

Phase 0 Beacon Chain Spec

🍪 Features:

Descriptions	Eth2.0 spec PR	Prysm PR
make get_beacon_proposer_index safe for next epoch	694
utilize updated version of ssz signed_root	725
modify BeaconState and Deposit fields to utilize new ssz fixed length tuples	737
break LMD GHOST ties in favor of higher hash tree roots	674
epoch transition at start of epoch	732 741
remove merkle_root and instead use hash_tree_root everywhere	739
weaken criterion for attestation inclusion	752
disallow duplicate voluntary exits	751
validator cannot exit until 2048 epochs	746
proposer slashing based upon epoch rather than slot	762
fair proposer selection by using epoch	733
improve fork version/signature domain semantics	738

🐛 Bugs:

Descriptions	Eth2.0 spec PR	Prysm PR
fix out-of-bounds in get_shuffling	641
fix slot range for attestation inclusion	669	#1715
fix previous epoch logic	672	#1721
fix handling of bad proof of possession in deposit	689	N/A
minor bugs related to ordering/typos/var-mismatch/etc	648 650 654 656 664 661	#1723

🐘 Misc:

Descriptions	Eth2.0 spec PR	Prysm PR
validator slashed and initiated_exited to booleans	658
rename shard_block_root -> crosslink_data_root	662	#1743
minor formatting/typos/etc PRs	640 640 643 646 666	N/A

Phase 0 validator spec

Descriptions	Eth2.0 spec PR	Prysm PR
fix epoch start lookup	671	#1674
make getting assignments more generic	673	#1746

Simple Serialize

Descriptions	Eth2.0 spec PR	Prysm PR
unified method for signature hashing	625

[terencechain]

Closed for #2307