Add proto_array fork choice (#804)

* Start implementing proto_array

* Add progress

* Add unfinished progress

* Add further progress

* Add progress

* Add tree filtering

* Add half-finished modifications

* Add refactored version

* Tidy, add incomplete LmdGhost impl

* Move impls in LmdGhost trait def

* Remove old reduced_tree fork choice

* Combine two functions in to `compute_deltas`

* Start testing

* Add more compute_deltas tests

* Add fork choice testing

* Add more fork choice testing

* Add more fork choice tests

* Add more testing to proto-array

* Remove old tests

* Modify tests

* Add more tests

* Add more testing

* Add comments and fixes

* Re-organise crate

* Tidy, finish pruning tests

* Add ssz encoding, other pub fns

* Rename lmd_ghost > proto_array_fork_choice

* Integrate proto_array into lighthouse

* Add first pass at fixing filter

* Clean out old comments

* Add more comments

* Attempt to fix prune error

* Adjust TODO

* Fix test compile errors

* Add extra justification change check

* Update cargo.lock

* Fix fork choice test compile errors

* Most remove ffg_update_required

* Fix bug with epoch of attestation votes

* Start adding new test format

* Make fork choice tests declarative

* Create test def concept

* Move test defs into crate

* Add binary, re-org crate

* Shuffle files

* Start adding ffg tests

* Add more fork choice tests

* Add fork choice JSON dumping

* Add more detail to best node error

* Ensure fin+just checkpoints from from same block

* Rename JustificationManager

* Move checkpoint manager into own file

* Tidy

* Add targetted logging for sneaky sync bug

* Fix justified balances bug

* Add cache metrics

* Add metrics for log levels

* Fix bug in checkpoint manager

* Fix compile error in fork choice tests

* Ignore duplicate blocks in fork choice

* Add block to fock choice before db

* Rename on_new_block fn

* Fix spec inconsistency in `CheckpointManager`

* Remove BlockRootTree

* Remove old reduced_tree code fragment

* Add API endpoint for fork choice

* Add more ffg tests

* Remove block_root_tree reminents

* Ensure effective balances are used

* Remove old debugging code, fix API fault

* Add check to ensure parent block is in fork choice

* Update readme dates

* Fix readme

* Tidy checkpoint manager

* Remove fork choice yaml files from repo

* Remove fork choice yaml from repo

* General tidy

* Address majority of Michael's comments

* Tidy bin/lib business

* Remove dangling file

* Undo changes for rpc/handler from master

* Revert "Undo changes for rpc/handler from master"

This reverts commit 876edff0e4a501aafbb47113454852826dcc24e8.

Co-authored-by: Age Manning <Age@AgeManning.com>

beacon_node/network/src/sync/range_sync/batch_processing.rs

@@ -70,7 +70,7 @@ fn process_batch<T: BeaconChainTypes>(
                         );
                         successful_block_import = true;
                     }
-                    BlockProcessingOutcome::ParentUnknown { parent } => {
+                    BlockProcessingOutcome::ParentUnknown { parent, .. } => {
                         // blocks should be sequential and all parents should exist
                         warn!(
                             log, "Parent block is unknown";

beacon_node/network/src/sync/range_sync/chain_collection.rs

@@ -307,8 +307,8 @@ impl<T: BeaconChainTypes> ChainCollection<T> {
         self.finalized_chains.retain(|chain| {
             if chain.target_head_slot <= local_finalized_slot
                 || beacon_chain
-                    .block_root_tree
-                    .is_known_block_root(&chain.target_head_root)
+                    .fork_choice
+                    .contains_block(&chain.target_head_root)
             {
                 debug!(log, "Purging out of finalized chain"; "start_slot" => chain.start_slot, "end_slot" => chain.target_head_slot);
                 chain.status_peers(network);
@@ -320,8 +320,8 @@ impl<T: BeaconChainTypes> ChainCollection<T> {
         self.head_chains.retain(|chain| {
             if chain.target_head_slot <= local_finalized_slot
                 || beacon_chain
-                    .block_root_tree
-                    .is_known_block_root(&chain.target_head_root)
+                    .fork_choice
+                    .contains_block(&chain.target_head_root)
             {
                 debug!(log, "Purging out of date head chain"; "start_slot" => chain.start_slot, "end_slot" => chain.target_head_slot);
                 chain.status_peers(network);

beacon_node/network/src/sync/range_sync/range.rs

@@ -150,9 +150,7 @@ impl<T: BeaconChainTypes> RangeSync<T> {
         self.chains.purge_outdated_chains(network, &self.log);
 
         if remote_finalized_slot > local_info.head_slot
-            && !chain
-                .block_root_tree
-                .is_known_block_root(&remote.finalized_root)
+            && !chain.fork_choice.contains_block(&remote.finalized_root)
         {
             debug!(self.log, "Finalization sync peer joined"; "peer_id" => format!("{:?}", peer_id));
             // Finalized chain search