Fix block backfill with genesis skip slots (#4820)

## Issue Addressed

Closes #4817.

## Proposed Changes

- Fill in the linear block roots array between 0 and the slot of the first block (e.g. slots 0 and 1 on Holesky).
- Backport the `--freezer`, `--skip` and `--limit` options for `lighthouse db inspect` from tree-states. This allows us to easily view the database corruption of 4817 using `lighthouse db inspect --network holesky --freezer --column bbr --output values --limit 2`.
- Backport the `iter_column_from` change and `MemoryStore` overhaul from tree-states. These are required to enable `lighthouse db inspect`.
- Rework `freezer_upper_limit` to allow state lookups for slots below the `state_lower_limit`. Currently state lookups will fail until state reconstruction completes entirely.

There is a new regression test for the main bug, but no test for the `freezer_upper_limit` fix because we don't currently support running state reconstruction partially (see #3026). This will be fixed once we merge `tree-states`! In lieu of an automated test, I've tested manually on a Holesky node while it was reconstructing.

## Additional Info

Users who backfilled Holesky to slot 0 (e.g. using `--reconstruct-historic-states`) need to either:

- Re-sync from genesis.
- Re-sync using checkpoint sync and the changes from this PR.

Due to the recency of the Holesky genesis, writing a custom pass to fix up broken databases (which would require its own thorough testing) was deemed unnecessary. This is the primary reason for this PR being marked `backwards-incompat`.

This will create few conflicts with Deneb, which I've already resolved on `tree-states-deneb` and will be happy to backport to Deneb once this PR is merged to unstable.

beacon_node/store/src/memory_store.rs

@@ -1,17 +1,17 @@
-use super::{Error, ItemStore, KeyValueStore, KeyValueStoreOp};
-use crate::{ColumnIter, DBColumn};
+use crate::{
+    get_key_for_col, leveldb_store::BytesKey, ColumnIter, ColumnKeyIter, DBColumn, Error,
+    ItemStore, Key, KeyValueStore, KeyValueStoreOp,
+};
 use parking_lot::{Mutex, MutexGuard, RwLock};
-use std::collections::{HashMap, HashSet};
+use std::collections::BTreeMap;
 use std::marker::PhantomData;
 use types::*;
 
-type DBHashMap = HashMap<Vec<u8>, Vec<u8>>;
-type DBKeyMap = HashMap<Vec<u8>, HashSet<Vec<u8>>>;
+type DBMap = BTreeMap<BytesKey, Vec<u8>>;
 
-/// A thread-safe `HashMap` wrapper.
+/// A thread-safe `BTreeMap` wrapper.
 pub struct MemoryStore<E: EthSpec> {
-    db: RwLock<DBHashMap>,
-    col_keys: RwLock<DBKeyMap>,
+    db: RwLock<DBMap>,
     transaction_mutex: Mutex<()>,
     _phantom: PhantomData<E>,
 }
@@ -20,36 +20,24 @@ impl<E: EthSpec> MemoryStore<E> {
     /// Create a new, empty database.
     pub fn open() -> Self {
         Self {
-            db: RwLock::new(HashMap::new()),
-            col_keys: RwLock::new(HashMap::new()),
+            db: RwLock::new(BTreeMap::new()),
             transaction_mutex: Mutex::new(()),
             _phantom: PhantomData,
         }
     }
-
-    fn get_key_for_col(col: &str, key: &[u8]) -> Vec<u8> {
-        let mut col = col.as_bytes().to_vec();
-        col.append(&mut key.to_vec());
-        col
-    }
 }
 
 impl<E: EthSpec> KeyValueStore<E> for MemoryStore<E> {
     /// Get the value of some key from the database. Returns `None` if the key does not exist.
     fn get_bytes(&self, col: &str, key: &[u8]) -> Result<Option<Vec<u8>>, Error> {
-        let column_key = Self::get_key_for_col(col, key);
+        let column_key = BytesKey::from_vec(get_key_for_col(col, key));
         Ok(self.db.read().get(&column_key).cloned())
     }
 
     /// Puts a key in the database.
     fn put_bytes(&self, col: &str, key: &[u8], val: &[u8]) -> Result<(), Error> {
-        let column_key = Self::get_key_for_col(col, key);
+        let column_key = BytesKey::from_vec(get_key_for_col(col, key));
         self.db.write().insert(column_key, val.to_vec());
-        self.col_keys
-            .write()
-            .entry(col.as_bytes().to_vec())
-            .or_default()
-            .insert(key.to_vec());
         Ok(())
     }
 
@@ -64,18 +52,14 @@ impl<E: EthSpec> KeyValueStore<E> for MemoryStore<E> {
 
     /// Return true if some key exists in some column.
     fn key_exists(&self, col: &str, key: &[u8]) -> Result<bool, Error> {
-        let column_key = Self::get_key_for_col(col, key);
+        let column_key = BytesKey::from_vec(get_key_for_col(col, key));
         Ok(self.db.read().contains_key(&column_key))
     }
 
     /// Delete some key from the database.
     fn key_delete(&self, col: &str, key: &[u8]) -> Result<(), Error> {
-        let column_key = Self::get_key_for_col(col, key);
+        let column_key = BytesKey::from_vec(get_key_for_col(col, key));
         self.db.write().remove(&column_key);
-        self.col_keys
-            .write()
-            .get_mut(&col.as_bytes().to_vec())
-            .map(|set| set.remove(key));
         Ok(())
     }
 
@@ -83,35 +67,41 @@ impl<E: EthSpec> KeyValueStore<E> for MemoryStore<E> {
         for op in batch {
             match op {
                 KeyValueStoreOp::PutKeyValue(key, value) => {
-                    self.db.write().insert(key, value);
+                    self.db.write().insert(BytesKey::from_vec(key), value);
                 }
 
-                KeyValueStoreOp::DeleteKey(hash) => {
-                    self.db.write().remove(&hash);
+                KeyValueStoreOp::DeleteKey(key) => {
+                    self.db.write().remove(&BytesKey::from_vec(key));
                 }
             }
         }
         Ok(())
     }
 
-    // pub type ColumnIter<'a> = Box<dyn Iterator<Item = Result<(Hash256, Vec<u8>), Error>> + 'a>;
-    fn iter_column(&self, column: DBColumn) -> ColumnIter {
+    fn iter_column_from<K: Key>(&self, column: DBColumn, from: &[u8]) -> ColumnIter<K> {
+        // We use this awkward pattern because we can't lock the `self.db` field *and* maintain a
+        // reference to the lock guard across calls to `.next()`. This would be require a
+        // struct with a field (the iterator) which references another field (the lock guard).
+        let start_key = BytesKey::from_vec(get_key_for_col(column.as_str(), from));
         let col = column.as_str();
-        if let Some(keys) = self
-            .col_keys
+        let keys = self
+            .db
             .read()
-            .get(col.as_bytes())
-            .map(|set| set.iter().cloned().collect::<Vec<_>>())
-        {
-            Box::new(keys.into_iter().filter_map(move |key| {
-                let hash = Hash256::from_slice(&key);
-                self.get_bytes(col, &key)
-                    .transpose()
-                    .map(|res| res.map(|bytes| (hash, bytes)))
-            }))
-        } else {
-            Box::new(std::iter::empty())
-        }
+            .range(start_key..)
+            .take_while(|(k, _)| k.remove_column_variable(column).is_some())
+            .filter_map(|(k, _)| k.remove_column_variable(column).map(|k| k.to_vec()))
+            .collect::<Vec<_>>();
+        Box::new(keys.into_iter().filter_map(move |key| {
+            self.get_bytes(col, &key).transpose().map(|res| {
+                let k = K::from_bytes(&key)?;
+                let v = res?;
+                Ok((k, v))
+            })
+        }))
+    }
+
+    fn iter_column_keys(&self, column: DBColumn) -> ColumnKeyIter {
+        Box::new(self.iter_column(column).map(|res| res.map(|(k, _)| k)))
     }
 
     fn begin_rw_transaction(&self) -> MutexGuard<()> {