Fix corrupted DB on networks where the first slot is skipped (Holesky)

[jimmygchen]

Issue Addressed

#4943 (co-authored with @michaelsproul)

Proposed Changes

There was a bug in earlier versions of Lighthouse where zero block roots are incorrectly stored before the first block slot. This happens on nodes that were checkpoint sync'd on a network that has skipped slot(s) before the first block. The additional consequence is that Lighthouse BN could return duplicate genesis blocks in BlocksByRange responses.

This bug was fixed in #4820, so it should not be an issue for nodes that are sync'd using v4.6.0 (next release) on Holesky. This PR contains migration script to heal the database on nodes that were checkpoint sync'd using 4.5.0, so they would no longer serve duplicate genesis blocks.

See @michaelsproul's comment here for more details.

[michaelsproul]

Reproduced the bug by backfilling a Holesky node with v4.5.0:

$ lighthouse db inspect --network holesky --freezer --column bbr --skip 1 --limit 1 --output values
Dec 07 03:31:43.183 INFO Running database manager for holesky network
Dec 07 03:31:43.266 INFO Hot-Cold DB initialized                 split_state: 0xb1aee59b844da3b1b8e71556bc10782345250db35f436b7dcb6db118dc661218, split_slot: 501376
Dec 07 03:31:43.266 INFO Blob DB initialized                     oldest_blob_slot: None, path: "/home/michael/.lighthouse/holesky/beacon/blobs_db"
Successfully saved values to file: "bbr_0000000000000001.ssz"
Num keys: 1
Total: 4096 bytes

$ xxd -len 96 bbr_0000000000000001.ssz
00000000: ab09 edd9 380f 8451 c3ff 5c80 9821 174a  ....8..Q..\..!.J
00000010: 36dc e606 fea8 b5ea 35ea 9369 15db f889  6.......5..i....
00000020: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000030: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000040: 1298 bea7 6ef3 7014 9e65 35e7 3617 fcfb  ....n.p..e5.6...
00000050: 2dcb bb29 601c f951 5ad9 2e55 7e52 acaa  -..)`..QZ..U~R..

There's that 0x0 block root!

After running this PR and healing block roots we get:

$ xxd -len 96 bbr_0000000000000001.ssz
00000000: ab09 edd9 380f 8451 c3ff 5c80 9821 174a  ....8..Q..\..!.J
00000010: 36dc e606 fea8 b5ea 35ea 9369 15db f889  6.......5..i....
00000020: ab09 edd9 380f 8451 c3ff 5c80 9821 174a  ....8..Q..\..!.J
00000030: 36dc e606 fea8 b5ea 35ea 9369 15db f889  6.......5..i....
00000040: 1298 bea7 6ef3 7014 9e65 35e7 3617 fcfb  ....n.p..e5.6...
00000050: 2dcb bb29 601c f951 5ad9 2e55 7e52 acaa  -..)`..QZ..U~R..

Fixed!

[michaelsproul]

Nice!!

[michaelsproul]

lets delete this println before merging