diff --git a/apps/chat2/chat2.nim b/apps/chat2/chat2.nim
index 347c4b10b..45de2e262 100644
--- a/apps/chat2/chat2.nim
+++ b/apps/chat2/chat2.nim
@@ -23,12 +23,12 @@ import libp2p/[switch,                   # manage transports, a single entry poi
                protocols/secure/secio,   # define the protocol of secure input / output, allows encrypted communication that uses public keys to validate signed messages instead of a certificate authority like in TLS
                nameresolving/dnsresolver]# define DNS resolution
 import
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_lightpush,
-  ../../waku/v2/protocol/waku_lightpush/rpc,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_store,
-  ../../waku/v2/protocol/waku_dnsdisc,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_lightpush,
+  ../../waku/v2/waku_lightpush/rpc,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_store,
+  ../../waku/v2/waku_dnsdisc,
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_metrics,
   ../../waku/v2/node/peer_manager,
@@ -43,7 +43,7 @@ when defined(rln):
     libp2p/protocols/pubsub/rpc/messages,
     libp2p/protocols/pubsub/pubsub
   import
-    ../../waku/v2/protocol/waku_rln_relay
+    ../../waku/v2/waku_rln_relay
 
 const Help = """
   Commands: /[?|help|connect|nick|exit]
diff --git a/apps/chat2/config_chat2.nim b/apps/chat2/config_chat2.nim
index 7db502891..579ef09c9 100644
--- a/apps/chat2/config_chat2.nim
+++ b/apps/chat2/config_chat2.nim
@@ -7,7 +7,7 @@ import
   nimcrypto/utils,
   eth/keys
 import
-  ../../../waku/v2/protocol/waku_message
+  ../../../waku/v2/waku_message
 
 type
   Fleet* =  enum
diff --git a/apps/chat2bridge/chat2bridge.nim b/apps/chat2bridge/chat2bridge.nim
index 3370905a9..8c84b5730 100644
--- a/apps/chat2bridge/chat2bridge.nim
+++ b/apps/chat2bridge/chat2bridge.nim
@@ -14,12 +14,12 @@ import
   # Waku v2 imports
   libp2p/crypto/crypto,
   libp2p/errors,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_message,
   ../../../waku/v2/waku_node,
   ../../../waku/v2/utils/peers,
   ../../../waku/v2/node/peer_manager,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_store,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_store,
   # Chat 2 imports
   ../chat2/chat2,
   # Common cli config
diff --git a/apps/wakubridge/message_compat.nim b/apps/wakubridge/message_compat.nim
index f6b229761..a4e63610d 100644
--- a/apps/wakubridge/message_compat.nim
+++ b/apps/wakubridge/message_compat.nim
@@ -8,7 +8,7 @@ import
   libp2p/crypto/crypto
 import
   ../../waku/v1/protocol/waku_protocol,
-  ../../waku/v2/protocol/waku_message
+  ../../waku/v2/waku_message
 
 
 const
diff --git a/apps/wakubridge/wakubridge.nim b/apps/wakubridge/wakubridge.nim
index c6db7f775..38b07437a 100644
--- a/apps/wakubridge/wakubridge.nim
+++ b/apps/wakubridge/wakubridge.nim
@@ -25,9 +25,9 @@ import
   libp2p/crypto/crypto,
   libp2p/nameresolving/nameresolver,
   ../../waku/v2/utils/time,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_store,
-  ../../waku/v2/protocol/waku_filter,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_store,
+  ../../waku/v2/waku_filter,
   ../../waku/v2/node/message_cache,
   ../../waku/v2/waku_node,
   ../../waku/v2/node/peer_manager,
diff --git a/apps/wakunode2/wakunode2.nim b/apps/wakunode2/wakunode2.nim
index 81d7e4808..2290053f8 100644
--- a/apps/wakunode2/wakunode2.nim
+++ b/apps/wakunode2/wakunode2.nim
@@ -30,22 +30,22 @@ import
   ../../waku/v2/node/peer_manager/peer_store/migrations as peer_store_sqlite_migrations,
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_metrics,
-  ../../waku/v2/protocol/waku_archive,
-  ../../waku/v2/protocol/waku_archive/driver/queue_driver,
-  ../../waku/v2/protocol/waku_archive/driver/sqlite_driver,
-  ../../waku/v2/protocol/waku_archive/driver/sqlite_driver/migrations as archive_driver_sqlite_migrations,
-  ../../waku/v2/protocol/waku_archive/retention_policy,
-  ../../waku/v2/protocol/waku_archive/retention_policy/retention_policy_capacity,
-  ../../waku/v2/protocol/waku_archive/retention_policy/retention_policy_time,
-  ../../waku/v2/protocol/waku_store,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_lightpush,
-  ../../waku/v2/protocol/waku_enr,
-  ../../waku/v2/protocol/waku_dnsdisc,
-  ../../waku/v2/protocol/waku_discv5,
-  ../../waku/v2/protocol/waku_message/topics/pubsub_topic,
-  ../../waku/v2/protocol/waku_peer_exchange,
-  ../../waku/v2/protocol/waku_relay/validators,
+  ../../waku/v2/waku_archive,
+  ../../waku/v2/waku_archive/driver/queue_driver,
+  ../../waku/v2/waku_archive/driver/sqlite_driver,
+  ../../waku/v2/waku_archive/driver/sqlite_driver/migrations as archive_driver_sqlite_migrations,
+  ../../waku/v2/waku_archive/retention_policy,
+  ../../waku/v2/waku_archive/retention_policy/retention_policy_capacity,
+  ../../waku/v2/waku_archive/retention_policy/retention_policy_time,
+  ../../waku/v2/waku_store,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_lightpush,
+  ../../waku/v2/waku_enr,
+  ../../waku/v2/waku_dnsdisc,
+  ../../waku/v2/waku_discv5,
+  ../../waku/v2/waku_message/topics/pubsub_topic,
+  ../../waku/v2/waku_peer_exchange,
+  ../../waku/v2/waku_relay/validators,
   ../../waku/v2/utils/peers,
   ./wakunode2_setup_rest,
   ./wakunode2_setup_rpc,
@@ -53,7 +53,7 @@ import
 
 when defined(rln):
   import
-    ../../waku/v2/protocol/waku_rln_relay
+    ../../waku/v2/waku_rln_relay
 
 
 logScope:
diff --git a/examples/v2/publisher.nim b/examples/v2/publisher.nim
index e19b46965..0efd6154f 100644
--- a/examples/v2/publisher.nim
+++ b/examples/v2/publisher.nim
@@ -13,9 +13,9 @@ import
   ../../../waku/common/logging,
   ../../../waku/v2/node/peer_manager,
   ../../../waku/v2/waku_node,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_enr,
-  ../../../waku/v2/protocol/waku_discv5,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_enr,
+  ../../../waku/v2/waku_discv5,
   ../../../waku/v2/utils/time
 
 proc now*(): Timestamp =
diff --git a/examples/v2/subscriber.nim b/examples/v2/subscriber.nim
index f9b135bdb..1662e06a6 100644
--- a/examples/v2/subscriber.nim
+++ b/examples/v2/subscriber.nim
@@ -13,9 +13,9 @@ import
   ../../../waku/common/logging,
   ../../../waku/v2/node/peer_manager,
   ../../../waku/v2/waku_node,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_enr,
-  ../../../waku/v2/protocol/waku_discv5
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_enr,
+  ../../../waku/v2/waku_discv5
 
 # An accesible bootstrap node. See wakuv2.prod fleets.status.im
 const bootstrapNode = "enr:-Nm4QOdTOKZJKTUUZ4O_W932CXIET-M9NamewDnL78P5u9DOGnZl" &
diff --git a/tests/v2/test_message_cache.nim b/tests/v2/test_message_cache.nim
index 20e452754..326a8b77f 100644
--- a/tests/v2/test_message_cache.nim
+++ b/tests/v2/test_message_cache.nim
@@ -5,7 +5,7 @@ import
   testutils/unittests,
   chronicles
 import
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_message,
   ../../waku/v2/node/message_cache,
   ./testlib/common,
   ./testlib/wakucore
diff --git a/tests/v2/test_peer_manager.nim b/tests/v2/test_peer_manager.nim
index 3c4354192..dbdbfbd76 100644
--- a/tests/v2/test_peer_manager.nim
+++ b/tests/v2/test_peer_manager.nim
@@ -21,11 +21,11 @@ import
   ../../waku/v2/node/peer_manager/peer_manager,
   ../../waku/v2/node/peer_manager/peer_store/waku_peer_storage,
   ../../waku/v2/waku_node,
-  ../../waku/v2/protocol/waku_relay,
-  ../../waku/v2/protocol/waku_store,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_lightpush,
-  ../../waku/v2/protocol/waku_peer_exchange,
+  ../../waku/v2/waku_relay,
+  ../../waku/v2/waku_store,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_lightpush,
+  ../../waku/v2/waku_peer_exchange,
   ./testlib/common,
   ./testlib/testutils,
   ./testlib/wakucore,
diff --git a/tests/v2/test_utils_compat.nim b/tests/v2/test_utils_compat.nim
index 8047d797b..aa69c6eeb 100644
--- a/tests/v2/test_utils_compat.nim
+++ b/tests/v2/test_utils_compat.nim
@@ -3,7 +3,7 @@
 import
   testutils/unittests
 import
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_message,
   ../../waku/v2/utils/compat,
   ../../waku/v2/utils/time,
   ./testlib/common
diff --git a/tests/v2/test_waku_discv5.nim b/tests/v2/test_waku_discv5.nim
index e3e00b39c..71d020090 100644
--- a/tests/v2/test_waku_discv5.nim
+++ b/tests/v2/test_waku_discv5.nim
@@ -11,8 +11,8 @@ import
   eth/p2p/discoveryv5/enr
 import
   ../../waku/v2/waku_node,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_discv5,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_discv5,
   ./testlib/common,
   ./testlib/wakucore,
   ./testlib/wakunode
diff --git a/tests/v2/test_waku_dnsdisc.nim b/tests/v2/test_waku_dnsdisc.nim
index 2ff28680a..4b5e09258 100644
--- a/tests/v2/test_waku_dnsdisc.nim
+++ b/tests/v2/test_waku_dnsdisc.nim
@@ -13,7 +13,7 @@ import
 import
   ../../waku/v2/node/peer_manager,
   ../../waku/v2/waku_node,
-  ../../waku/v2/protocol/waku_dnsdisc,
+  ../../waku/v2/waku_dnsdisc,
   ./testlib/common,
   ./testlib/wakucore,
   ./testlib/wakunode
diff --git a/tests/v2/test_waku_enr.nim b/tests/v2/test_waku_enr.nim
index 86c014441..9472eb90a 100644
--- a/tests/v2/test_waku_enr.nim
+++ b/tests/v2/test_waku_enr.nim
@@ -5,8 +5,8 @@ import
   stew/results,
   testutils/unittests
 import
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_enr,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_enr,
   ./testlib/wakucore
 
 
diff --git a/tests/v2/test_waku_filter.nim b/tests/v2/test_waku_filter.nim
index 051cbb85f..9e08c751d 100644
--- a/tests/v2/test_waku_filter.nim
+++ b/tests/v2/test_waku_filter.nim
@@ -8,9 +8,9 @@ import
   libp2p/crypto/crypto
 import
   ../../waku/v2/node/peer_manager,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_filter/client,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_filter/client,
   ./testlib/common,
   ./testlib/wakucore
 
diff --git a/tests/v2/test_waku_keystore.nim b/tests/v2/test_waku_keystore.nim
index 218333529..75f57930f 100644
--- a/tests/v2/test_waku_keystore.nim
+++ b/tests/v2/test_waku_keystore.nim
@@ -4,10 +4,10 @@ import
   std/[algorithm, json, options, os],
   testutils/unittests, chronos, stint
 import
-  ../../waku/v2/protocol/waku_keystore,
+  ../../waku/v2/waku_keystore,
   ./testlib/common
 
-from  ../../waku/v2/protocol/waku_noise/noise_utils import randomSeqByte
+from  ../../waku/v2/waku_noise/noise_utils import randomSeqByte
 
 procSuite "Credentials test suite":
 
diff --git a/tests/v2/test_waku_keystore_keyfile.nim b/tests/v2/test_waku_keystore_keyfile.nim
index 7e8b2d962..d5357ff3c 100644
--- a/tests/v2/test_waku_keystore_keyfile.nim
+++ b/tests/v2/test_waku_keystore_keyfile.nim
@@ -6,10 +6,10 @@ import
   testutils/unittests, chronos,
   eth/keys
 import
-  ../../waku/v2/protocol/waku_keystore,
+  ../../waku/v2/waku_keystore,
   ./testlib/common
 
-from ../../waku/v2/protocol/waku_noise/noise_utils import randomSeqByte
+from ../../waku/v2/waku_noise/noise_utils import randomSeqByte
 
 suite "KeyFile test suite":
 
diff --git a/tests/v2/test_waku_lightpush.nim b/tests/v2/test_waku_lightpush.nim
index 9d168fbf7..b8920afe4 100644
--- a/tests/v2/test_waku_lightpush.nim
+++ b/tests/v2/test_waku_lightpush.nim
@@ -7,9 +7,9 @@ import
   libp2p/crypto/crypto
 import
   ../../waku/v2/node/peer_manager,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_lightpush,
-  ../../waku/v2/protocol/waku_lightpush/client,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_lightpush,
+  ../../waku/v2/waku_lightpush/client,
   ./testlib/common,
   ./testlib/wakucore
 
diff --git a/tests/v2/test_waku_message_digest.nim b/tests/v2/test_waku_message_digest.nim
index d24c0743c..b4d1330c5 100644
--- a/tests/v2/test_waku_message_digest.nim
+++ b/tests/v2/test_waku_message_digest.nim
@@ -5,9 +5,9 @@ import
   stew/byteutils,
   testutils/unittests
 import
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_message/codec,
-  ../../waku/v2/protocol/waku_message/digest,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_message/codec,
+  ../../waku/v2/waku_message/digest,
   ./testlib/wakucore
 
 suite "Waku Message - Deterministic hashing":
diff --git a/tests/v2/test_waku_message_topics.nim b/tests/v2/test_waku_message_topics.nim
index 30f6710d9..f0675d487 100644
--- a/tests/v2/test_waku_message_topics.nim
+++ b/tests/v2/test_waku_message_topics.nim
@@ -4,7 +4,7 @@ import
   stew/results,
   testutils/unittests
 import
-  ../../waku/v2/protocol/waku_message/topics
+  ../../waku/v2/waku_message/topics
 
 suite "Waku Message - Content topics namespacing":
 
diff --git a/tests/v2/test_waku_noise.nim b/tests/v2/test_waku_noise.nim
index c06097f0b..6f2e88ac4 100644
--- a/tests/v2/test_waku_noise.nim
+++ b/tests/v2/test_waku_noise.nim
@@ -10,11 +10,11 @@ import
   stew/endians2
 import
   ../../waku/v2/utils/noise as waku_message_utils,
-  ../../waku/v2/protocol/waku_noise/noise_types,
-  ../../waku/v2/protocol/waku_noise/noise_utils,
-  ../../waku/v2/protocol/waku_noise/noise,
-  ../../waku/v2/protocol/waku_noise/noise_handshake_processing,
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_noise/noise_types,
+  ../../waku/v2/waku_noise/noise_utils,
+  ../../waku/v2/waku_noise/noise,
+  ../../waku/v2/waku_noise/noise_handshake_processing,
+  ../../waku/v2/waku_message,
   ./testlib/common
 
 
diff --git a/tests/v2/test_waku_noise_sessions.nim b/tests/v2/test_waku_noise_sessions.nim
index 5cfbdc4cb..d10604ac4 100644
--- a/tests/v2/test_waku_noise_sessions.nim
+++ b/tests/v2/test_waku_noise_sessions.nim
@@ -7,10 +7,10 @@ import
 import
   ../../waku/common/protobuf,
   ../../waku/v2/utils/noise as waku_message_utils,
-  ../../waku/v2/protocol/waku_noise/noise_types,
-  ../../waku/v2/protocol/waku_noise/noise_utils,
-  ../../waku/v2/protocol/waku_noise/noise_handshake_processing,
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_noise/noise_types,
+  ../../waku/v2/waku_noise/noise_utils,
+  ../../waku/v2/waku_noise/noise_handshake_processing,
+  ../../waku/v2/waku_message,
   ./testlib/common
 
 procSuite "Waku Noise Sessions":
diff --git a/tests/v2/test_waku_peer_exchange.nim b/tests/v2/test_waku_peer_exchange.nim
index 9acc7bbe6..7b9b5e851 100644
--- a/tests/v2/test_waku_peer_exchange.nim
+++ b/tests/v2/test_waku_peer_exchange.nim
@@ -14,10 +14,10 @@ import
 import
   ../../waku/v2/waku_node,
   ../../waku/v2/node/peer_manager,
-  ../../waku/v2/protocol/waku_discv5,
-  ../../waku/v2/protocol/waku_peer_exchange,
-  ../../waku/v2/protocol/waku_peer_exchange/rpc,
-  ../../waku/v2/protocol/waku_peer_exchange/rpc_codec,
+  ../../waku/v2/waku_discv5,
+  ../../waku/v2/waku_peer_exchange,
+  ../../waku/v2/waku_peer_exchange/rpc,
+  ../../waku/v2/waku_peer_exchange/rpc_codec,
   ./testlib/wakucore,
   ./testlib/wakunode
 
diff --git a/tests/v2/test_wakunode.nim b/tests/v2/test_wakunode.nim
index 8bc69c0f8..cded0ad0c 100644
--- a/tests/v2/test_wakunode.nim
+++ b/tests/v2/test_wakunode.nim
@@ -19,9 +19,9 @@ import
 import
   ../../waku/v2/waku_node,
   ../../waku/v2/node/peer_manager,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_relay,
-  ../../waku/v2/protocol/waku_peer_exchange,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_relay,
+  ../../waku/v2/waku_peer_exchange,
   ../../waku/v2/utils/peers,
   ./testlib/wakucore,
   ./testlib/wakunode
diff --git a/tests/v2/test_wakunode_filter.nim b/tests/v2/test_wakunode_filter.nim
index a4331f333..e14411acf 100644
--- a/tests/v2/test_wakunode_filter.nim
+++ b/tests/v2/test_wakunode_filter.nim
@@ -9,7 +9,7 @@ import
 import
   ../../waku/v2/node/peer_manager,
   ../../waku/v2/waku_node,
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_message,
   ../../waku/v2/utils/peers,
   ./testlib/common,
   ./testlib/wakucore,
diff --git a/tests/v2/test_wakunode_lightpush.nim b/tests/v2/test_wakunode_lightpush.nim
index b15ac0a33..d88bcbb8b 100644
--- a/tests/v2/test_wakunode_lightpush.nim
+++ b/tests/v2/test_wakunode_lightpush.nim
@@ -8,8 +8,8 @@ import
   libp2p/crypto/crypto,
   libp2p/switch
 import
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_lightpush,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_lightpush,
   ../../waku/v2/node/peer_manager,
   ../../waku/v2/utils/peers,
   ../../waku/v2/waku_node,
diff --git a/tests/v2/testlib/wakucore.nim b/tests/v2/testlib/wakucore.nim
index 91878f820..bd86910b3 100644
--- a/tests/v2/testlib/wakucore.nim
+++ b/tests/v2/testlib/wakucore.nim
@@ -8,7 +8,7 @@ import
   libp2p/crypto/crypto as libp2p_keys,
   eth/keys as eth_keys
 import
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_message,
   ./common
 
 export switch
diff --git a/tests/v2/testlib/wakunode.nim b/tests/v2/testlib/wakunode.nim
index 9ab520939..96fdd8dd0 100644
--- a/tests/v2/testlib/wakunode.nim
+++ b/tests/v2/testlib/wakunode.nim
@@ -11,8 +11,8 @@ import
 import
   ../../../waku/v2/waku_node,
   ../../../waku/v2/node/peer_manager,
-  ../../../waku/v2/protocol/waku_enr,
-  ../../../waku/v2/protocol/waku_discv5,
+  ../../../waku/v2/waku_enr,
+  ../../../waku/v2/waku_discv5,
   ./common
 
 
diff --git a/tests/v2/waku_archive/test_driver_queue.nim b/tests/v2/waku_archive/test_driver_queue.nim
index 0aedc4b4b..9e59fa5f5 100644
--- a/tests/v2/waku_archive/test_driver_queue.nim
+++ b/tests/v2/waku_archive/test_driver_queue.nim
@@ -5,10 +5,10 @@ import
   stew/results,
   testutils/unittests
 import
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver/queue_driver {.all.},
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver/index,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/queue_driver/queue_driver {.all.},
+  ../../../waku/v2/waku_archive/driver/queue_driver/index,
+  ../../../waku/v2/waku_message,
   ../../../waku/v2/utils/time
 
 
diff --git a/tests/v2/waku_archive/test_driver_queue_index.nim b/tests/v2/waku_archive/test_driver_queue_index.nim
index 727643be7..a63b0a577 100644
--- a/tests/v2/waku_archive/test_driver_queue_index.nim
+++ b/tests/v2/waku_archive/test_driver_queue_index.nim
@@ -6,8 +6,8 @@ import
   testutils/unittests,
   nimcrypto
 import
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver/index,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_archive/driver/queue_driver/index,
   ../../../waku/v2/utils/time
 
 
diff --git a/tests/v2/waku_archive/test_driver_queue_pagination.nim b/tests/v2/waku_archive/test_driver_queue_pagination.nim
index adefff626..12ed2c43d 100644
--- a/tests/v2/waku_archive/test_driver_queue_pagination.nim
+++ b/tests/v2/waku_archive/test_driver_queue_pagination.nim
@@ -5,10 +5,10 @@ import
   testutils/unittests,
   libp2p/protobuf/minprotobuf
 import
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver/queue_driver {.all.},
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver/index,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/queue_driver/queue_driver {.all.},
+  ../../../waku/v2/waku_archive/driver/queue_driver/index,
+  ../../../waku/v2/waku_message,
   ../../../waku/v2/utils/time,
   ../testlib/common,
   ../testlib/wakucore
diff --git a/tests/v2/waku_archive/test_driver_queue_query.nim b/tests/v2/waku_archive/test_driver_queue_query.nim
index fe5dbd062..1141a8f41 100644
--- a/tests/v2/waku_archive/test_driver_queue_query.nim
+++ b/tests/v2/waku_archive/test_driver_queue_query.nim
@@ -6,9 +6,9 @@ import
   chronos,
   chronicles
 import
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/queue_driver,
+  ../../../waku/v2/waku_message,
   ../testlib/common,
   ../testlib/wakucore
 
diff --git a/tests/v2/waku_archive/test_driver_sqlite.nim b/tests/v2/waku_archive/test_driver_sqlite.nim
index 89bba38a5..a39895cbe 100644
--- a/tests/v2/waku_archive/test_driver_sqlite.nim
+++ b/tests/v2/waku_archive/test_driver_sqlite.nim
@@ -6,9 +6,9 @@ import
   chronos
 import
   ../../../waku/common/sqlite,
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/sqlite_driver,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/sqlite_driver,
+  ../../../waku/v2/waku_message,
   ../testlib/common,
   ../testlib/wakucore
 
diff --git a/tests/v2/waku_archive/test_driver_sqlite_query.nim b/tests/v2/waku_archive/test_driver_sqlite_query.nim
index eea7fd497..7aae376e0 100644
--- a/tests/v2/waku_archive/test_driver_sqlite_query.nim
+++ b/tests/v2/waku_archive/test_driver_sqlite_query.nim
@@ -7,9 +7,9 @@ import
   chronicles
 import
   ../../../waku/common/sqlite,
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/sqlite_driver,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/sqlite_driver,
+  ../../../waku/v2/waku_message,
   ../testlib/common,
   ../testlib/wakucore
 
diff --git a/tests/v2/waku_archive/test_retention_policy.nim b/tests/v2/waku_archive/test_retention_policy.nim
index b6e1a2004..a4b331e91 100644
--- a/tests/v2/waku_archive/test_retention_policy.nim
+++ b/tests/v2/waku_archive/test_retention_policy.nim
@@ -7,11 +7,11 @@ import
   chronos
 import
   ../../../waku/common/sqlite,
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/sqlite_driver,
-  ../../../waku/v2/protocol/waku_archive/retention_policy,
-  ../../../waku/v2/protocol/waku_archive/retention_policy/retention_policy_capacity,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/sqlite_driver,
+  ../../../waku/v2/waku_archive/retention_policy,
+  ../../../waku/v2/waku_archive/retention_policy/retention_policy_capacity,
+  ../../../waku/v2/waku_message,
   ../../../waku/v2/utils/time,
   ../testlib/common,
   ../testlib/wakucore
diff --git a/tests/v2/waku_archive/test_waku_archive.nim b/tests/v2/waku_archive/test_waku_archive.nim
index e1f61e033..a24da0c92 100644
--- a/tests/v2/waku_archive/test_waku_archive.nim
+++ b/tests/v2/waku_archive/test_waku_archive.nim
@@ -7,9 +7,9 @@ import
   libp2p/crypto/crypto
 import
   ../../../waku/common/sqlite,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_archive/driver/sqlite_driver,
-  ../../../waku/v2/protocol/waku_archive,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_archive/driver/sqlite_driver,
+  ../../../waku/v2/waku_archive,
   ../../../waku/v2/utils/time,
   ../testlib/common,
   ../testlib/wakucore
diff --git a/tests/v2/waku_filter_v2/test_waku_filter.nim b/tests/v2/waku_filter_v2/test_waku_filter.nim
index 5f4824184..22368a047 100644
--- a/tests/v2/waku_filter_v2/test_waku_filter.nim
+++ b/tests/v2/waku_filter_v2/test_waku_filter.nim
@@ -8,10 +8,10 @@ import
   libp2p/peerstore
 import
   ../../../waku/v2/node/peer_manager,
-  ../../../waku/v2/protocol/waku_filter_v2,
-  ../../../waku/v2/protocol/waku_filter_v2/client,
-  ../../../waku/v2/protocol/waku_filter_v2/rpc,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_filter_v2,
+  ../../../waku/v2/waku_filter_v2/client,
+  ../../../waku/v2/waku_filter_v2/rpc,
+  ../../../waku/v2/waku_message,
   ../testlib/common,
   ../testlib/wakucore
 
diff --git a/tests/v2/waku_filter_v2/test_waku_filter_protocol.nim b/tests/v2/waku_filter_v2/test_waku_filter_protocol.nim
index 3ff12bc52..cb344d8f9 100644
--- a/tests/v2/waku_filter_v2/test_waku_filter_protocol.nim
+++ b/tests/v2/waku_filter_v2/test_waku_filter_protocol.nim
@@ -8,10 +8,10 @@ import
   libp2p/peerstore
 import
   ../../../waku/v2/node/peer_manager,
-  ../../../waku/v2/protocol/waku_filter_v2,
-  ../../../waku/v2/protocol/waku_filter_v2/rpc,
-  ../../../waku/v2/protocol/waku_filter_v2/subscriptions,
-  ../../../waku/v2/protocol/waku_message,
+  ../../../waku/v2/waku_filter_v2,
+  ../../../waku/v2/waku_filter_v2/rpc,
+  ../../../waku/v2/waku_filter_v2/subscriptions,
+  ../../../waku/v2/waku_message,
   ../testlib/common,
   ../testlib/wakucore
 
diff --git a/tests/v2/waku_relay/test_waku_relay.nim b/tests/v2/waku_relay/test_waku_relay.nim
index bb9a46bbb..32dbe0124 100644
--- a/tests/v2/waku_relay/test_waku_relay.nim
+++ b/tests/v2/waku_relay/test_waku_relay.nim
@@ -10,8 +10,8 @@ import
   libp2p/protocols/pubsub/rpc/messages
 import
   ../../../waku/v2/node/peer_manager,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_relay,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_relay,
   ../testlib/common,
   ../testlib/wakucore
 
diff --git a/tests/v2/waku_relay/test_wakunode_relay.nim b/tests/v2/waku_relay/test_wakunode_relay.nim
index 8dc08446f..f864012a2 100644
--- a/tests/v2/waku_relay/test_wakunode_relay.nim
+++ b/tests/v2/waku_relay/test_wakunode_relay.nim
@@ -18,12 +18,12 @@ import
   libp2p/multihash,
   secp256k1
 import
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_message,
   ../../waku/v2/node/peer_manager,
   ../../waku/v2/utils/peers,
   ../../waku/v2/waku_node,
-  ../../waku/v2/protocol/waku_relay,
-  ../../waku/v2/protocol/waku_relay/validators,
+  ../../waku/v2/waku_relay,
+  ../../waku/v2/waku_relay/validators,
   ../testlib/testutils,
   ../testlib/common,
   ../testlib/wakucore,
diff --git a/tests/v2/waku_rln_relay/test_rln_group_manager_onchain.nim b/tests/v2/waku_rln_relay/test_rln_group_manager_onchain.nim
index 9c1d11ff9..30ecd0cc9 100644
--- a/tests/v2/waku_rln_relay/test_rln_group_manager_onchain.nim
+++ b/tests/v2/waku_rln_relay/test_rln_group_manager_onchain.nim
@@ -18,12 +18,12 @@ import
   libp2p/crypto/crypto,
   eth/keys
 import
-  ../../../waku/v2/protocol/waku_rln_relay/protocol_types,
-  ../../../waku/v2/protocol/waku_rln_relay/constants,
-  ../../../waku/v2/protocol/waku_rln_relay/contract,
-  ../../../waku/v2/protocol/waku_rln_relay/rln,
-  ../../../waku/v2/protocol/waku_rln_relay/conversion_utils,
-  ../../../waku/v2/protocol/waku_rln_relay/group_manager/on_chain/group_manager,
+  ../../../waku/v2/waku_rln_relay/protocol_types,
+  ../../../waku/v2/waku_rln_relay/constants,
+  ../../../waku/v2/waku_rln_relay/contract,
+  ../../../waku/v2/waku_rln_relay/rln,
+  ../../../waku/v2/waku_rln_relay/conversion_utils,
+  ../../../waku/v2/waku_rln_relay/group_manager/on_chain/group_manager,
   ../testlib/common,
   ./utils
 
diff --git a/tests/v2/waku_rln_relay/test_rln_group_manager_static.nim b/tests/v2/waku_rln_relay/test_rln_group_manager_static.nim
index a6528fd0c..05887a85a 100644
--- a/tests/v2/waku_rln_relay/test_rln_group_manager_static.nim
+++ b/tests/v2/waku_rln_relay/test_rln_group_manager_static.nim
@@ -9,10 +9,10 @@ import
   testutils/unittests,
   stew/results,
   options,
-  ../../../waku/v2/protocol/waku_rln_relay/protocol_types,
-  ../../../waku/v2/protocol/waku_rln_relay/rln,
-  ../../../waku/v2/protocol/waku_rln_relay/conversion_utils,
-  ../../../waku/v2/protocol/waku_rln_relay/group_manager/static/group_manager
+  ../../../waku/v2/waku_rln_relay/protocol_types,
+  ../../../waku/v2/waku_rln_relay/rln,
+  ../../../waku/v2/waku_rln_relay/conversion_utils,
+  ../../../waku/v2/waku_rln_relay/group_manager/static/group_manager
 
 import
   stew/shims/net,
diff --git a/tests/v2/waku_rln_relay/test_waku_rln_relay.nim b/tests/v2/waku_rln_relay/test_waku_rln_relay.nim
index c1f8f180f..684443957 100644
--- a/tests/v2/waku_rln_relay/test_waku_rln_relay.nim
+++ b/tests/v2/waku_rln_relay/test_waku_rln_relay.nim
@@ -11,11 +11,11 @@ import
   stint,
   libp2p/crypto/crypto
 import
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_rln_relay,
-  ../../../waku/v2/protocol/waku_rln_relay/rln,
-  ../../../waku/v2/protocol/waku_rln_relay/protocol_metrics,
-  ../../../waku/v2/protocol/waku_keystore,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_rln_relay,
+  ../../../waku/v2/waku_rln_relay/rln,
+  ../../../waku/v2/waku_rln_relay/protocol_metrics,
+  ../../../waku/v2/waku_keystore,
   ../testlib/common
 
 const RlnRelayPubsubTopic = "waku/2/rlnrelay/proto"
diff --git a/tests/v2/waku_rln_relay/test_wakunode_rln_relay.nim b/tests/v2/waku_rln_relay/test_wakunode_rln_relay.nim
index 82e488a8f..1f2da7ab1 100644
--- a/tests/v2/waku_rln_relay/test_wakunode_rln_relay.nim
+++ b/tests/v2/waku_rln_relay/test_wakunode_rln_relay.nim
@@ -15,9 +15,9 @@ import
   eth/keys
 import
   ../../../waku/v2/waku_node,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_rln_relay,
-  ../../../waku/v2/protocol/waku_keystore,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_rln_relay,
+  ../../../waku/v2/waku_keystore,
   ../../../waku/v2/utils/peers,
   ../testlib/wakucore,
   ../testlib/wakunode
diff --git a/tests/v2/waku_store/test_resume.nim b/tests/v2/waku_store/test_resume.nim
index cec9ea1c8..71545b6e6 100644
--- a/tests/v2/waku_store/test_resume.nim
+++ b/tests/v2/waku_store/test_resume.nim
@@ -10,8 +10,8 @@ import
   ../../waku/common/sqlite,
   ../../waku/v2/node/message_store/sqlite_store,
   ../../waku/v2/node/peer_manager,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_store,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_store,
   ./testlib/common,
   ./testlib/switch
 
diff --git a/tests/v2/waku_store/test_rpc_codec.nim b/tests/v2/waku_store/test_rpc_codec.nim
index 417f5a016..784d0cb3c 100644
--- a/tests/v2/waku_store/test_rpc_codec.nim
+++ b/tests/v2/waku_store/test_rpc_codec.nim
@@ -6,8 +6,8 @@ import
   chronos
 import
   ../../../waku/common/protobuf,
-  ../../../waku/v2/protocol/waku_store/rpc,
-  ../../../waku/v2/protocol/waku_store/rpc_codec,
+  ../../../waku/v2/waku_store/rpc,
+  ../../../waku/v2/waku_store/rpc_codec,
   ../../../waku/v2/utils/time,
   ../testlib/common,
   ../testlib/wakucore
diff --git a/tests/v2/waku_store/test_waku_store.nim b/tests/v2/waku_store/test_waku_store.nim
index b9705e1da..323db8623 100644
--- a/tests/v2/waku_store/test_waku_store.nim
+++ b/tests/v2/waku_store/test_waku_store.nim
@@ -8,9 +8,9 @@ import
   libp2p/crypto/crypto
 import
   ../../../waku/v2/node/peer_manager,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_store,
-  ../../../waku/v2/protocol/waku_store/client,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_store,
+  ../../../waku/v2/waku_store/client,
   ../testlib/common,
   ../testlib/wakucore
 
diff --git a/tests/v2/waku_store/test_wakunode_store.nim b/tests/v2/waku_store/test_wakunode_store.nim
index 6d81130e9..864461202 100644
--- a/tests/v2/waku_store/test_wakunode_store.nim
+++ b/tests/v2/waku_store/test_wakunode_store.nim
@@ -15,11 +15,11 @@ import
 import
   ../../../waku/common/sqlite,
   ../../../waku/v2/node/peer_manager,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/sqlite_driver,
-  ../../../waku/v2/protocol/waku_store,
-  ../../../waku/v2/protocol/waku_filter,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/sqlite_driver,
+  ../../../waku/v2/waku_store,
+  ../../../waku/v2/waku_filter,
   ../../../waku/v2/utils/peers,
   ../../../waku/v2/waku_node,
   ../testlib/common,
diff --git a/tests/v2/wakunode_jsonrpc/test_jsonrpc_admin.nim b/tests/v2/wakunode_jsonrpc/test_jsonrpc_admin.nim
index dfc939284..39b01ccd2 100644
--- a/tests/v2/wakunode_jsonrpc/test_jsonrpc_admin.nim
+++ b/tests/v2/wakunode_jsonrpc/test_jsonrpc_admin.nim
@@ -14,11 +14,11 @@ import
   ../../../waku/v2/waku_node,
   ../../../waku/v2/node/jsonrpc/admin/handlers as admin_api,
   ../../../waku/v2/node/jsonrpc/admin/client as admin_api_client,
-  ../../../waku/v2/protocol/waku_relay,
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver,
-  ../../../waku/v2/protocol/waku_store,
-  ../../../waku/v2/protocol/waku_filter,
+  ../../../waku/v2/waku_relay,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/queue_driver,
+  ../../../waku/v2/waku_store,
+  ../../../waku/v2/waku_filter,
   ../../../waku/v2/utils/peers,
   ../testlib/wakucore,
   ../testlib/wakunode
diff --git a/tests/v2/wakunode_jsonrpc/test_jsonrpc_filter.nim b/tests/v2/wakunode_jsonrpc/test_jsonrpc_filter.nim
index abeb64679..a4fea5b8d 100644
--- a/tests/v2/wakunode_jsonrpc/test_jsonrpc_filter.nim
+++ b/tests/v2/wakunode_jsonrpc/test_jsonrpc_filter.nim
@@ -13,10 +13,10 @@ import
   ../../../waku/v2/node/message_cache,
   ../../../waku/v2/node/jsonrpc/filter/handlers as filter_api,
   ../../../waku/v2/node/jsonrpc/filter/client as filter_api_client,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_filter,
-  ../../../waku/v2/protocol/waku_filter/rpc,
-  ../../../waku/v2/protocol/waku_filter/client,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_filter,
+  ../../../waku/v2/waku_filter/rpc,
+  ../../../waku/v2/waku_filter/client,
   ../../../waku/v2/utils/peers,
   ../testlib/wakucore,
   ../testlib/wakunode
diff --git a/tests/v2/wakunode_jsonrpc/test_jsonrpc_relay.nim b/tests/v2/wakunode_jsonrpc/test_jsonrpc_relay.nim
index 1516677f7..569f39f43 100644
--- a/tests/v2/wakunode_jsonrpc/test_jsonrpc_relay.nim
+++ b/tests/v2/wakunode_jsonrpc/test_jsonrpc_relay.nim
@@ -14,8 +14,8 @@ import
   ../../../waku/v2/waku_node,
   ../../../waku/v2/node/jsonrpc/relay/handlers as relay_api,
   ../../../waku/v2/node/jsonrpc/relay/client as relay_api_client,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_relay,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_relay,
   ../../../waku/v2/utils/compat,
   ../../../waku/v2/utils/peers,
   ../testlib/common,
diff --git a/tests/v2/wakunode_jsonrpc/test_jsonrpc_store.nim b/tests/v2/wakunode_jsonrpc/test_jsonrpc_store.nim
index 35843fe85..5ab323863 100644
--- a/tests/v2/wakunode_jsonrpc/test_jsonrpc_store.nim
+++ b/tests/v2/wakunode_jsonrpc/test_jsonrpc_store.nim
@@ -12,11 +12,11 @@ import
   ../../../waku/v2/waku_node,
   ../../../waku/v2/node/jsonrpc/store/handlers as store_api,
   ../../../waku/v2/node/jsonrpc/store/client as store_api_client,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver,
-  ../../../waku/v2/protocol/waku_store,
-  ../../../waku/v2/protocol/waku_store/rpc,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/queue_driver,
+  ../../../waku/v2/waku_store,
+  ../../../waku/v2/waku_store/rpc,
   ../../../waku/v2/utils/peers,
   ../../../waku/v2/utils/time,
   ../../v2/testlib/common,
diff --git a/tests/v2/wakunode_rest/test_rest_relay.nim b/tests/v2/wakunode_rest/test_rest_relay.nim
index 694ca2edf..7e6e10f32 100644
--- a/tests/v2/wakunode_rest/test_rest_relay.nim
+++ b/tests/v2/wakunode_rest/test_rest_relay.nim
@@ -17,8 +17,8 @@ import
   ../../waku/v2/node/rest/relay/handlers as relay_api,
   ../../waku/v2/node/rest/relay/client as relay_api_client,
   ../../waku/v2/node/rest/relay/topic_cache,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_relay,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_relay,
   ../../waku/v2/utils/time,
   ../testlib/wakucore,
   ../testlib/wakunode
diff --git a/tests/v2/wakunode_rest/test_rest_relay_serdes.nim b/tests/v2/wakunode_rest/test_rest_relay_serdes.nim
index f656f1f7f..e503d0049 100644
--- a/tests/v2/wakunode_rest/test_rest_relay_serdes.nim
+++ b/tests/v2/wakunode_rest/test_rest_relay_serdes.nim
@@ -9,7 +9,7 @@ import
   ../../waku/common/base64,
   ../../waku/v2/node/rest/serdes,
   ../../waku/v2/node/rest/relay/types,
-  ../../waku/v2/protocol/waku_message
+  ../../waku/v2/waku_message
 
 
 
diff --git a/tests/v2/wakunode_rest/test_rest_store.nim b/tests/v2/wakunode_rest/test_rest_store.nim
index 86c1bf02d..455fd6e0c 100644
--- a/tests/v2/wakunode_rest/test_rest_store.nim
+++ b/tests/v2/wakunode_rest/test_rest_store.nim
@@ -17,10 +17,10 @@ import
   ../../../waku/v2/node/rest/store/handlers as store_api,
   ../../../waku/v2/node/rest/store/client as store_api_client,
   ../../../waku/v2/node/rest/store/types,
-  ../../../waku/v2/protocol/waku_message,
-  ../../../waku/v2/protocol/waku_archive,
-  ../../../waku/v2/protocol/waku_archive/driver/queue_driver,
-  ../../../waku/v2/protocol/waku_store as waku_store,
+  ../../../waku/v2/waku_message,
+  ../../../waku/v2/waku_archive,
+  ../../../waku/v2/waku_archive/driver/queue_driver,
+  ../../../waku/v2/waku_store as waku_store,
   ../../../waku/v2/utils/peers,
   ../../../waku/v2/utils/time,
   ../../v2/testlib/common,
diff --git a/tests/wakubridge/test_message_compat.nim b/tests/wakubridge/test_message_compat.nim
index 6be19e524..ced0e4af6 100644
--- a/tests/wakubridge/test_message_compat.nim
+++ b/tests/wakubridge/test_message_compat.nim
@@ -7,7 +7,7 @@ import
   chronos,
   libp2p/switch
 import
-  ../../waku/v2/protocol/waku_message
+  ../../waku/v2/waku_message
 
 import
   ../../apps/wakubridge/message_compat
diff --git a/tests/wakubridge/test_wakubridge.nim b/tests/wakubridge/test_wakubridge.nim
index f9dea74da..a59003f27 100644
--- a/tests/wakubridge/test_wakubridge.nim
+++ b/tests/wakubridge/test_wakubridge.nim
@@ -17,7 +17,7 @@ import
   eth/keys
 import
   ../../waku/v1/protocol/waku_protocol,
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_message,
   ../../waku/v2/waku_node,
   ../../waku/v2/utils/compat,
   ../../waku/v2/utils/peers,
diff --git a/tools/networkmonitor/networkmonitor.nim b/tools/networkmonitor/networkmonitor.nim
index a1cd3e440..a04963b58 100644
--- a/tools/networkmonitor/networkmonitor.nim
+++ b/tools/networkmonitor/networkmonitor.nim
@@ -22,10 +22,10 @@ import
   ../../apps/wakunode2/wakunode2,
   ../../waku/v2/node/peer_manager,
   ../../waku/v2/waku_node,
-  ../../waku/v2/protocol/waku_message,
-  ../../waku/v2/protocol/waku_enr,
-  ../../waku/v2/protocol/waku_discv5,
-  ../../waku/v2/protocol/waku_dnsdisc,
+  ../../waku/v2/waku_message,
+  ../../waku/v2/waku_enr,
+  ../../waku/v2/waku_discv5,
+  ../../waku/v2/waku_dnsdisc,
   ../../waku/v2/utils/peers,
   ./networkmonitor_metrics,
   ./networkmonitor_config,
diff --git a/tools/scripts/rpc_info.nim b/tools/scripts/rpc_info.nim
index 85ca5c321..386a9c4df 100644
--- a/tools/scripts/rpc_info.nim
+++ b/tools/scripts/rpc_info.nim
@@ -9,8 +9,8 @@ import
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_payload,
   ../../waku/v2/node/jsonrpc/jsonrpc_types,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_store,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_store,
   ../../waku/v1/node/rpc/hexstrings
 
 from strutils import rsplit
diff --git a/tools/scripts/rpc_publish.nim b/tools/scripts/rpc_publish.nim
index 74829efb5..46ac13c28 100644
--- a/tools/scripts/rpc_publish.nim
+++ b/tools/scripts/rpc_publish.nim
@@ -9,8 +9,8 @@ import
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_payload,
   ../../waku/v2/node/jsonrpc/jsonrpc_types,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_store,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_store,
   ../../waku/v1/node/rpc/hexstrings
 
 from strutils import rsplit
diff --git a/tools/scripts/rpc_query.nim b/tools/scripts/rpc_query.nim
index af34792a7..364778826 100644
--- a/tools/scripts/rpc_query.nim
+++ b/tools/scripts/rpc_query.nim
@@ -9,8 +9,8 @@ import
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_payload,
   ../../waku/v2/node/jsonrpc/jsonrpc_types,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_store/rpc,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_store/rpc,
   ../../waku/v1/node/rpc/hexstrings
 
 
diff --git a/tools/scripts/rpc_subscribe.nim b/tools/scripts/rpc_subscribe.nim
index 8bdbf19b2..f4795782c 100644
--- a/tools/scripts/rpc_subscribe.nim
+++ b/tools/scripts/rpc_subscribe.nim
@@ -8,8 +8,8 @@ import
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_payload,
   ../../waku/v2/node/jsonrpc/jsonrpc_types,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_store,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_store,
   ../../waku/v1/node/rpc/hexstrings
 
 
diff --git a/tools/scripts/rpc_subscribe_filter.nim b/tools/scripts/rpc_subscribe_filter.nim
index 555d8aacc..5996c81b3 100644
--- a/tools/scripts/rpc_subscribe_filter.nim
+++ b/tools/scripts/rpc_subscribe_filter.nim
@@ -9,8 +9,8 @@ import
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_payload,
   ../../waku/v2/node/jsonrpc/jsonrpc_types,
-  ../../waku/v2/protocol/waku_filter,
-  ../../waku/v2/protocol/waku_store,
+  ../../waku/v2/waku_filter,
+  ../../waku/v2/waku_store,
   ../../waku/v1/node/rpc/hexstrings
 
 from strutils import rsplit
diff --git a/tools/simulation/quicksim2.nim b/tools/simulation/quicksim2.nim
index bf914b12d..9c71c4055 100644
--- a/tools/simulation/quicksim2.nim
+++ b/tools/simulation/quicksim2.nim
@@ -6,9 +6,9 @@ import
   json_rpc/[rpcclient, rpcserver],
   libp2p/protobuf/minprotobuf
 import
-  ../../waku/v2/protocol/waku_filter/rpc,
-  ../../waku/v2/protocol/waku_store/rpc,
-  ../../waku/v2/protocol/waku_message,
+  ../../waku/v2/waku_filter/rpc,
+  ../../waku/v2/waku_store/rpc,
+  ../../waku/v2/waku_message,
   ../../waku/v2/utils/time,
   ../../waku/v2/waku_node,
   ../../waku/v2/node/waku_payload,
diff --git a/waku/v2/node/builder.nim b/waku/v2/node/builder.nim
index 5c7308cc2..baeaaee08 100644
--- a/waku/v2/node/builder.nim
+++ b/waku/v2/node/builder.nim
@@ -12,8 +12,8 @@ import
   libp2p/builders,
   libp2p/nameresolving/nameresolver
 import
-  ../protocol/waku_enr,
-  ../protocol/waku_discv5,
+  ../waku_enr,
+  ../waku_discv5,
   ./config,
   ./peer_manager,
   ./waku_node
diff --git a/waku/v2/node/config.nim b/waku/v2/node/config.nim
index 3f6f6ba81..5763e38c7 100644
--- a/waku/v2/node/config.nim
+++ b/waku/v2/node/config.nim
@@ -9,7 +9,7 @@ import
   stew/shims/net,
   libp2p/multiaddress
 import
-  ../protocol/waku_enr
+  ../waku_enr
 
 
 type NetConfig* = object
diff --git a/waku/v2/node/jsonrpc/admin/handlers.nim b/waku/v2/node/jsonrpc/admin/handlers.nim
index f32474e76..5c7f1a29d 100644
--- a/waku/v2/node/jsonrpc/admin/handlers.nim
+++ b/waku/v2/node/jsonrpc/admin/handlers.nim
@@ -9,9 +9,9 @@ import
   json_rpc/rpcserver,
   libp2p/[peerinfo, switch]
 import
-  ../../../protocol/waku_store,
-  ../../../protocol/waku_filter,
-  ../../../protocol/waku_relay,
+  ../../../waku_store,
+  ../../../waku_filter,
+  ../../../waku_relay,
   ../../peer_manager,
   ../../waku_node,
   ./types
diff --git a/waku/v2/node/jsonrpc/filter/client.nim b/waku/v2/node/jsonrpc/filter/client.nim
index 25f719578..17b9fb743 100644
--- a/waku/v2/node/jsonrpc/filter/client.nim
+++ b/waku/v2/node/jsonrpc/filter/client.nim
@@ -7,8 +7,8 @@ import
   std/[os, strutils],
   json_rpc/rpcclient
 import
-  ../../../protocol/waku_message,
-  ../../../protocol/waku_filter/rpc
+  ../../../waku_message,
+  ../../../waku_filter/rpc
 
 template sourceDir: string = currentSourcePath.rsplit(DirSep, 1)[0]
 
diff --git a/waku/v2/node/jsonrpc/filter/handlers.nim b/waku/v2/node/jsonrpc/filter/handlers.nim
index c676105cc..e05f3cd13 100644
--- a/waku/v2/node/jsonrpc/filter/handlers.nim
+++ b/waku/v2/node/jsonrpc/filter/handlers.nim
@@ -8,10 +8,10 @@ import
   chronicles,
   json_rpc/rpcserver
 import
-  ../../../protocol/waku_message,
-  ../../../protocol/waku_filter,
-  ../../../protocol/waku_filter/rpc,
-  ../../../protocol/waku_filter/client,
+  ../../../waku_message,
+  ../../../waku_filter,
+  ../../../waku_filter/rpc,
+  ../../../waku_filter/client,
   ../../message_cache,
   ../../peer_manager,
   ../../waku_node
diff --git a/waku/v2/node/jsonrpc/message.nim b/waku/v2/node/jsonrpc/message.nim
index c3ccdafee..07cefee7e 100644
--- a/waku/v2/node/jsonrpc/message.nim
+++ b/waku/v2/node/jsonrpc/message.nim
@@ -4,7 +4,7 @@ import
   json_rpc/rpcserver
 import
   ../../../common/base64,
-  ../../protocol/waku_message,
+  ../../waku_message,
   ../../utils/time
 
 
diff --git a/waku/v2/node/jsonrpc/relay/client.nim b/waku/v2/node/jsonrpc/relay/client.nim
index b38c005a0..830a3f75b 100644
--- a/waku/v2/node/jsonrpc/relay/client.nim
+++ b/waku/v2/node/jsonrpc/relay/client.nim
@@ -7,7 +7,7 @@ import
   std/[os, strutils],
   json_rpc/rpcclient
 import
-  ../../../protocol/waku_message,
+  ../../../waku_message,
   ../../../utils/compat,
   ./types
 
diff --git a/waku/v2/node/jsonrpc/relay/handlers.nim b/waku/v2/node/jsonrpc/relay/handlers.nim
index 32bd4520b..5d1f2f17e 100644
--- a/waku/v2/node/jsonrpc/relay/handlers.nim
+++ b/waku/v2/node/jsonrpc/relay/handlers.nim
@@ -11,8 +11,8 @@ import
   nimcrypto/sysrand
 import
   ../../../../common/base64,
-  ../../../protocol/waku_message,
-  ../../../protocol/waku_relay,
+  ../../../waku_message,
+  ../../../waku_relay,
   ../../../utils/compat,
   ../../../utils/time,
   ../../waku_node,
diff --git a/waku/v2/node/jsonrpc/store/client.nim b/waku/v2/node/jsonrpc/store/client.nim
index 296f5990a..8679ab201 100644
--- a/waku/v2/node/jsonrpc/store/client.nim
+++ b/waku/v2/node/jsonrpc/store/client.nim
@@ -7,7 +7,7 @@ import
   std/[os, strutils],
   json_rpc/rpcclient
 import
-  ../../../protocol/waku_store/rpc,
+  ../../../waku_store/rpc,
   ../../../utils/time,
   ./types
 
diff --git a/waku/v2/node/jsonrpc/store/handlers.nim b/waku/v2/node/jsonrpc/store/handlers.nim
index 0a74c5f7d..5ab7d2e23 100644
--- a/waku/v2/node/jsonrpc/store/handlers.nim
+++ b/waku/v2/node/jsonrpc/store/handlers.nim
@@ -8,8 +8,8 @@ import
   chronicles,
   json_rpc/rpcserver
 import
-  ../../../protocol/waku_store,
-  ../../../protocol/waku_store/rpc,
+  ../../../waku_store,
+  ../../../waku_store/rpc,
   ../../../utils/time,
   ../../waku_node,
   ../../peer_manager,
diff --git a/waku/v2/node/jsonrpc/store/types.nim b/waku/v2/node/jsonrpc/store/types.nim
index b22edd125..44341fe18 100644
--- a/waku/v2/node/jsonrpc/store/types.nim
+++ b/waku/v2/node/jsonrpc/store/types.nim
@@ -6,7 +6,7 @@ else:
 import
   std/options
 import
-  ../../../protocol/waku_store/rpc,
+  ../../../waku_store/rpc,
   ../message
 
 export message
diff --git a/waku/v2/node/message_cache.nim b/waku/v2/node/message_cache.nim
index 2d66ca793..9035f4a04 100644
--- a/waku/v2/node/message_cache.nim
+++ b/waku/v2/node/message_cache.nim
@@ -10,9 +10,9 @@ import
   chronos,
   libp2p/protocols/pubsub
 import
-  ../protocol/waku_message
+  ../waku_message
 
-logScope: 
+logScope:
   topics = "waku node message_cache"
 
 const DefaultMessageCacheCapacity*: uint = 30 # Max number of messages cached per topic @TODO make this configurable
@@ -27,7 +27,7 @@ type MessageCache*[K] = ref object
 func init*[K](T: type MessageCache[K], capacity=DefaultMessageCacheCapacity): T =
   MessageCache[K](
     capacity: capacity,
-    table: initTable[K, seq[WakuMessage]]() 
+    table: initTable[K, seq[WakuMessage]]()
   )
 
 
@@ -39,7 +39,7 @@ proc subscribe*[K](t: MessageCache[K], topic: K) =
     return
   t.table[topic] = @[]
 
-proc unsubscribe*[K](t: MessageCache[K], topic: K) = 
+proc unsubscribe*[K](t: MessageCache[K], topic: K) =
   if not t.isSubscribed(topic):
     return
   t.table.del(topic)
@@ -55,10 +55,10 @@ proc addMessage*[K](t: MessageCache, topic: K, msg: WakuMessage) =
   if messages.len >= t.capacity.int:
     trace "Topic cache capacity reached", topic=topic
     # Message cache on this topic exceeds maximum. Delete oldest.
-    # TODO: this may become a bottle neck if called as the norm rather than 
+    # TODO: this may become a bottle neck if called as the norm rather than
     #  exception when adding messages. Performance profile needed.
     messages.delete(0,0)
-  
+
   messages.add(msg)
 
   # Replace indexed entry with copy
diff --git a/waku/v2/node/peer_manager/peer_manager.nim b/waku/v2/node/peer_manager/peer_manager.nim
index 5e8397288..2e48ff27f 100644
--- a/waku/v2/node/peer_manager/peer_manager.nim
+++ b/waku/v2/node/peer_manager/peer_manager.nim
@@ -12,7 +12,7 @@ import
   libp2p/multistream,
   libp2p/muxers/muxer
 import
-  ../../protocol/waku_relay,
+  ../../waku_relay,
   ../../utils/peers,
   ../../utils/heartbeat,
   ./peer_store/peer_storage,
diff --git a/waku/v2/node/rest/relay/client.nim b/waku/v2/node/rest/relay/client.nim
index 07efc1a6f..48be881d9 100644
--- a/waku/v2/node/rest/relay/client.nim
+++ b/waku/v2/node/rest/relay/client.nim
@@ -11,7 +11,7 @@ import
   json_serialization/std/options,
   presto/[route, client, common]
 import
-  ../../../protocol/waku_message,
+  ../../../waku_message,
   ../serdes,
   ../responses,
   ./types
diff --git a/waku/v2/node/rest/relay/topic_cache.nim b/waku/v2/node/rest/relay/topic_cache.nim
index a56a08773..b8318ec86 100644
--- a/waku/v2/node/rest/relay/topic_cache.nim
+++ b/waku/v2/node/rest/relay/topic_cache.nim
@@ -7,8 +7,8 @@ import
   chronos,
   chronicles
 import
-  ../../../protocol/waku_relay,
-  ../../../protocol/waku_message,
+  ../../../waku_relay,
+  ../../../waku_message,
   ../../message_cache
 
 export message_cache
diff --git a/waku/v2/node/rest/relay/types.nim b/waku/v2/node/rest/relay/types.nim
index cc7e723bf..c6ebd46ea 100644
--- a/waku/v2/node/rest/relay/types.nim
+++ b/waku/v2/node/rest/relay/types.nim
@@ -11,7 +11,7 @@ import
   presto/[route, client, common]
 import
   ../../../../common/base64,
-  ../../../protocol/waku_message,
+  ../../../waku_message,
   ../serdes
 
 
diff --git a/waku/v2/node/rest/store/client.nim b/waku/v2/node/rest/store/client.nim
index a567489ff..71babc8e1 100644
--- a/waku/v2/node/rest/store/client.nim
+++ b/waku/v2/node/rest/store/client.nim
@@ -9,7 +9,7 @@ import
   json_serialization/std/options,
   presto/[route, client]
 import
-  ../../../protocol/waku_store/common,
+  ../../../waku_store/common,
   ../serdes,
   ../responses,
   ./types
diff --git a/waku/v2/node/rest/store/handlers.nim b/waku/v2/node/rest/store/handlers.nim
index 67bb6d340..3c845903f 100644
--- a/waku/v2/node/rest/store/handlers.nim
+++ b/waku/v2/node/rest/store/handlers.nim
@@ -11,8 +11,8 @@ import
   presto/route
 import
   ../../../../common/base64,
-  ../../../protocol/waku_message/topics/content_topic,
-  ../../../protocol/waku_store/common,
+  ../../../waku_message/topics/content_topic,
+  ../../../waku_store/common,
   ../../../utils/time,
   ../../waku_node,
   ../../peer_manager,
diff --git a/waku/v2/node/rest/store/types.nim b/waku/v2/node/rest/store/types.nim
index 811cd5b6c..a4291e222 100644
--- a/waku/v2/node/rest/store/types.nim
+++ b/waku/v2/node/rest/store/types.nim
@@ -11,12 +11,12 @@ import
   json_serialization/std/options,
   presto/[route, client, common]
 import
-  ../../../protocol/waku_store/common as waku_store_common,
+  ../../../waku_store/common as waku_store_common,
   ../../../../common/base64,
   ../../../utils/time,
-  ../../../protocol/waku_message/topics/content_topic,
-  ../../../protocol/waku_message/topics/pubsub_topic,
-  ../../../protocol/waku_message/message,
+  ../../../waku_message/topics/content_topic,
+  ../../../waku_message/topics/pubsub_topic,
+  ../../../waku_message/message,
   ../serdes
 
 
@@ -30,7 +30,7 @@ type
     digest*: MessageDigest
 
   StoreRequestRest* = object
-    # inspired by https://github.com/waku-org/nwaku/blob/f95147f5b7edfd45f914586f2d41cd18fb0e0d18/waku/v2/protocol/waku_store/common.nim#L52
+    # inspired by https://github.com/waku-org/nwaku/blob/f95147f5b7edfd45f914586f2d41cd18fb0e0d18/waku/v2//waku_store/common.nim#L52
     pubsubTopic*: Option[PubsubTopic]
     contentTopics*: seq[ContentTopic]
     cursor*: Option[HistoryCursorRest]
@@ -71,7 +71,7 @@ proc parseMsgDigest*(input: Option[string]):
     return err(base64Decoded.error)
 
   let base64DecodedArr = base64Decoded.get()
-  # Next snippet inspired by "nwaku/waku/v2/protocol/waku_archive/archive.nim"
+  # Next snippet inspired by "nwaku/waku/v2/waku_archive/archive.nim"
   # TODO: Improve coherence of MessageDigest type
   messageDigest = block:
       var data: array[32, byte]
diff --git a/waku/v2/node/waku_metrics.nim b/waku/v2/node/waku_metrics.nim
index 1986dee22..2a5fdf04b 100644
--- a/waku/v2/node/waku_metrics.nim
+++ b/waku/v2/node/waku_metrics.nim
@@ -10,13 +10,13 @@ import
   metrics,
   metrics/chronos_httpserver
 import
-  ../protocol/waku_filter/protocol_metrics as filter_metrics,
+  ../waku_filter/protocol_metrics as filter_metrics,
   ../utils/collector,
   ./peer_manager,
   ./waku_node
 
 when defined(rln):
-  import ../protocol/waku_rln_relay/protocol_metrics as rln_metrics
+  import ../waku_rln_relay/protocol_metrics as rln_metrics
 
 
 const LogInterval = 30.seconds
diff --git a/waku/v2/node/waku_node.nim b/waku/v2/node/waku_node.nim
index 510b8927a..4b8745820 100644
--- a/waku/v2/node/waku_node.nim
+++ b/waku/v2/node/waku_node.nim
@@ -24,20 +24,20 @@ import
   libp2p/transports/tcptransport,
   libp2p/transports/wstransport
 import
-  ../protocol/waku_message,
-  ../protocol/waku_relay,
-  ../protocol/waku_archive,
-  ../protocol/waku_store,
-  ../protocol/waku_store/client as store_client,
-  ../protocol/waku_filter as legacy_filter,  #TODO: support for legacy filter protocol will be removed
-  ../protocol/waku_filter/client as filter_client, #TODO: support for legacy filter protocol will be removed
-  ../protocol/waku_filter_v2,
-  ../protocol/waku_lightpush,
-  ../protocol/waku_lightpush/client as lightpush_client,
-  ../protocol/waku_enr,
-  ../protocol/waku_dnsdisc,
-  ../protocol/waku_discv5,
-  ../protocol/waku_peer_exchange,
+  ../waku_message,
+  ../waku_relay,
+  ../waku_archive,
+  ../waku_store,
+  ../waku_store/client as store_client,
+  ../waku_filter as legacy_filter,  #TODO: support for legacy filter protocol will be removed
+  ../waku_filter/client as filter_client, #TODO: support for legacy filter protocol will be removed
+  ../waku_filter_v2,
+  ../waku_lightpush,
+  ../waku_lightpush/client as lightpush_client,
+  ../waku_enr,
+  ../waku_dnsdisc,
+  ../waku_discv5,
+  ../waku_peer_exchange,
   ../utils/peers,
   ../utils/time,
   ./config,
@@ -46,7 +46,7 @@ import
 
 when defined(rln):
   import
-    ../protocol/waku_rln_relay
+    ../waku_rln_relay
 
 declarePublicGauge waku_version, "Waku version info (in git describe format)", ["version"]
 declarePublicCounter waku_node_messages, "number of messages received", ["type"]
diff --git a/waku/v2/protocol/README.md b/waku/v2/protocol/README.md
deleted file mode 100644
index 2474257af..000000000
--- a/waku/v2/protocol/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# Waku v2 protocol
-
-This folder contains implementations of [Waku v2 protocols](https://specs.vac.dev/specs/waku/v2/waku-v2.html).
diff --git a/waku/v2/utils/compat.nim b/waku/v2/utils/compat.nim
index 84d0d2adc..f3b7cf2fc 100644
--- a/waku/v2/utils/compat.nim
+++ b/waku/v2/utils/compat.nim
@@ -10,7 +10,7 @@ import
   eth/keys
 import
   ../../whisper/whisper_types,
-  ../protocol/waku_message
+  ../waku_message
 
 export whisper_types, keys, options
 
diff --git a/waku/v2/utils/noise.nim b/waku/v2/utils/noise.nim
index 37f9ef285..0e030ebce 100644
--- a/waku/v2/utils/noise.nim
+++ b/waku/v2/utils/noise.nim
@@ -6,9 +6,9 @@ else:
 import
   stew/results
 import
-  ../protocol/waku_message,
-  ../protocol/waku_noise/noise_types,
-  ../protocol/waku_noise/noise_utils
+  ../waku_message,
+  ../waku_noise/noise_types,
+  ../waku_noise/noise_utils
 
 
 # Decodes a WakuMessage to a PayloadV2
diff --git a/waku/v2/protocol/waku_archive.nim b/waku/v2/waku_archive.nim
similarity index 100%
rename from waku/v2/protocol/waku_archive.nim
rename to waku/v2/waku_archive.nim
diff --git a/waku/v2/protocol/waku_archive/archive.nim b/waku/v2/waku_archive/archive.nim
similarity index 99%
rename from waku/v2/protocol/waku_archive/archive.nim
rename to waku/v2/waku_archive/archive.nim
index 2d5f9e7c8..4837507ce 100644
--- a/waku/v2/protocol/waku_archive/archive.nim
+++ b/waku/v2/waku_archive/archive.nim
@@ -11,7 +11,7 @@ import
   chronos,
   metrics
 import
-  ../../utils/time,
+  ../utils/time,
   ../waku_message,
   ./common,
   ./archive_metrics,
diff --git a/waku/v2/protocol/waku_archive/archive_metrics.nim b/waku/v2/waku_archive/archive_metrics.nim
similarity index 100%
rename from waku/v2/protocol/waku_archive/archive_metrics.nim
rename to waku/v2/waku_archive/archive_metrics.nim
diff --git a/waku/v2/protocol/waku_archive/common.nim b/waku/v2/waku_archive/common.nim
similarity index 99%
rename from waku/v2/protocol/waku_archive/common.nim
rename to waku/v2/waku_archive/common.nim
index d6c4f56cc..70514df7b 100644
--- a/waku/v2/protocol/waku_archive/common.nim
+++ b/waku/v2/waku_archive/common.nim
@@ -9,7 +9,7 @@ import
   stew/byteutils,
   nimcrypto/sha2
 import
-  ../../utils/time,
+  ../utils/time,
   ../waku_message
 
 
diff --git a/waku/v2/protocol/waku_archive/driver.nim b/waku/v2/waku_archive/driver.nim
similarity index 98%
rename from waku/v2/protocol/waku_archive/driver.nim
rename to waku/v2/waku_archive/driver.nim
index 6f7c5cff5..d44061a99 100644
--- a/waku/v2/protocol/waku_archive/driver.nim
+++ b/waku/v2/waku_archive/driver.nim
@@ -7,7 +7,7 @@ import
   std/options,
   stew/results
 import
-  ../../utils/time,
+  ../utils/time,
   ../waku_message,
   ./common
 
diff --git a/waku/v2/protocol/waku_archive/driver/queue_driver.nim b/waku/v2/waku_archive/driver/queue_driver.nim
similarity index 100%
rename from waku/v2/protocol/waku_archive/driver/queue_driver.nim
rename to waku/v2/waku_archive/driver/queue_driver.nim
diff --git a/waku/v2/protocol/waku_archive/driver/queue_driver/index.nim b/waku/v2/waku_archive/driver/queue_driver/index.nim
similarity index 97%
rename from waku/v2/protocol/waku_archive/driver/queue_driver/index.nim
rename to waku/v2/waku_archive/driver/queue_driver/index.nim
index 8b2786191..68446092a 100644
--- a/waku/v2/protocol/waku_archive/driver/queue_driver/index.nim
+++ b/waku/v2/waku_archive/driver/queue_driver/index.nim
@@ -7,8 +7,8 @@ import
   stew/byteutils,
   nimcrypto/sha2
 import
-  ../../../../protocol/waku_message,
-  ../../../../utils/time,
+  ../../../waku_message,
+  ../../../utils/time,
   ../../common
 
 
diff --git a/waku/v2/protocol/waku_archive/driver/queue_driver/queue_driver.nim b/waku/v2/waku_archive/driver/queue_driver/queue_driver.nim
similarity index 99%
rename from waku/v2/protocol/waku_archive/driver/queue_driver/queue_driver.nim
rename to waku/v2/waku_archive/driver/queue_driver/queue_driver.nim
index a756a59a2..6b9994d19 100644
--- a/waku/v2/protocol/waku_archive/driver/queue_driver/queue_driver.nim
+++ b/waku/v2/waku_archive/driver/queue_driver/queue_driver.nim
@@ -9,8 +9,8 @@ import
   stew/sorted_set,
   chronicles
 import
-  ../../../../protocol/waku_message,
-  ../../../../utils/time,
+  ../../../waku_message,
+  ../../../utils/time,
   ../../common,
   ../../driver,
   ./index
diff --git a/waku/v2/protocol/waku_archive/driver/sqlite_driver.nim b/waku/v2/waku_archive/driver/sqlite_driver.nim
similarity index 100%
rename from waku/v2/protocol/waku_archive/driver/sqlite_driver.nim
rename to waku/v2/waku_archive/driver/sqlite_driver.nim
diff --git a/waku/v2/protocol/waku_archive/driver/sqlite_driver/cursor.nim b/waku/v2/waku_archive/driver/sqlite_driver/cursor.nim
similarity index 80%
rename from waku/v2/protocol/waku_archive/driver/sqlite_driver/cursor.nim
rename to waku/v2/waku_archive/driver/sqlite_driver/cursor.nim
index 696197c02..ce87f791a 100644
--- a/waku/v2/protocol/waku_archive/driver/sqlite_driver/cursor.nim
+++ b/waku/v2/waku_archive/driver/sqlite_driver/cursor.nim
@@ -5,8 +5,8 @@ else:
 
 
 import
-  ../../../../protocol/waku_message,
-  ../../../../utils/time,
+  ../../../waku_message,
+  ../../../utils/time,
   ../../common
 
 type DbCursor* = (Timestamp, seq[byte], PubsubTopic)
diff --git a/waku/v2/protocol/waku_archive/driver/sqlite_driver/migrations.nim b/waku/v2/waku_archive/driver/sqlite_driver/migrations.nim
similarity index 89%
rename from waku/v2/protocol/waku_archive/driver/sqlite_driver/migrations.nim
rename to waku/v2/waku_archive/driver/sqlite_driver/migrations.nim
index c094ae4f3..fe73834e9 100644
--- a/waku/v2/protocol/waku_archive/driver/sqlite_driver/migrations.nim
+++ b/waku/v2/waku_archive/driver/sqlite_driver/migrations.nim
@@ -5,17 +5,17 @@ import
   stew/results,
   chronicles
 import
-  ../../../../../common/sqlite,
-  ../../../../../common/sqlite/migrations
+  ../../../../common/sqlite,
+  ../../../../common/sqlite/migrations
 
 
 logScope:
-  topics = "message_store.migration"
+  topics = "waku archive migration"
 
 
 const SchemaVersion* = 7 # increase this when there is an update in the database schema
 
-template projectRoot: string = currentSourcePath.rsplit(DirSep, 1)[0] / ".." / ".." / ".." / ".." / ".."
+template projectRoot: string = currentSourcePath.rsplit(DirSep, 1)[0] / ".." / ".." / ".." / ".."
 const MessageStoreMigrationPath: string = projectRoot / "migrations" / "message_store"
 
 
diff --git a/waku/v2/protocol/waku_archive/driver/sqlite_driver/queries.nim b/waku/v2/waku_archive/driver/sqlite_driver/queries.nim
similarity index 99%
rename from waku/v2/protocol/waku_archive/driver/sqlite_driver/queries.nim
rename to waku/v2/waku_archive/driver/sqlite_driver/queries.nim
index ee915eac5..7fff1310d 100644
--- a/waku/v2/protocol/waku_archive/driver/sqlite_driver/queries.nim
+++ b/waku/v2/waku_archive/driver/sqlite_driver/queries.nim
@@ -9,9 +9,9 @@ import
   stew/[results, byteutils],
   sqlite3_abi
 import
-  ../../../../../common/sqlite,
-  ../../../../protocol/waku_message,
-  ../../../../utils/time,
+  ../../../../common/sqlite,
+  ../../../waku_message,
+  ../../../utils/time,
   ./cursor
 
 
diff --git a/waku/v2/protocol/waku_archive/driver/sqlite_driver/sqlite_driver.nim b/waku/v2/waku_archive/driver/sqlite_driver/sqlite_driver.nim
similarity index 97%
rename from waku/v2/protocol/waku_archive/driver/sqlite_driver/sqlite_driver.nim
rename to waku/v2/waku_archive/driver/sqlite_driver/sqlite_driver.nim
index 812ef9550..d72199365 100644
--- a/waku/v2/protocol/waku_archive/driver/sqlite_driver/sqlite_driver.nim
+++ b/waku/v2/waku_archive/driver/sqlite_driver/sqlite_driver.nim
@@ -10,9 +10,9 @@ import
   stew/[byteutils, results],
   chronicles
 import
-  ../../../../../common/sqlite,
-  ../../../../protocol/waku_message,
-  ../../../../utils/time,
+  ../../../../common/sqlite,
+  ../../../waku_message,
+  ../../../utils/time,
   ../../common,
   ../../driver,
   ./cursor,
diff --git a/waku/v2/protocol/waku_archive/retention_policy.nim b/waku/v2/waku_archive/retention_policy.nim
similarity index 100%
rename from waku/v2/protocol/waku_archive/retention_policy.nim
rename to waku/v2/waku_archive/retention_policy.nim
diff --git a/waku/v2/protocol/waku_archive/retention_policy/retention_policy_capacity.nim b/waku/v2/waku_archive/retention_policy/retention_policy_capacity.nim
similarity index 100%
rename from waku/v2/protocol/waku_archive/retention_policy/retention_policy_capacity.nim
rename to waku/v2/waku_archive/retention_policy/retention_policy_capacity.nim
diff --git a/waku/v2/protocol/waku_archive/retention_policy/retention_policy_time.nim b/waku/v2/waku_archive/retention_policy/retention_policy_time.nim
similarity index 98%
rename from waku/v2/protocol/waku_archive/retention_policy/retention_policy_time.nim
rename to waku/v2/waku_archive/retention_policy/retention_policy_time.nim
index f9985450c..0c9c8573e 100644
--- a/waku/v2/protocol/waku_archive/retention_policy/retention_policy_time.nim
+++ b/waku/v2/waku_archive/retention_policy/retention_policy_time.nim
@@ -9,7 +9,7 @@ import
   chronicles,
   chronos
 import
-  ../../../utils/time,
+  ../../utils/time,
   ../driver,
   ../retention_policy
 
diff --git a/waku/v2/protocol/waku_discv5.nim b/waku/v2/waku_discv5.nim
similarity index 99%
rename from waku/v2/protocol/waku_discv5.nim
rename to waku/v2/waku_discv5.nim
index 6561f0236..2a210d875 100644
--- a/waku/v2/protocol/waku_discv5.nim
+++ b/waku/v2/waku_discv5.nim
@@ -16,7 +16,7 @@ import
   eth/p2p/discoveryv5/node,
   eth/p2p/discoveryv5/protocol
 import
-  ../utils/peers,
+  ./utils/peers,
   ./waku_enr
 
 export protocol, waku_enr
diff --git a/waku/v2/protocol/waku_dnsdisc.nim b/waku/v2/waku_dnsdisc.nim
similarity index 99%
rename from waku/v2/protocol/waku_dnsdisc.nim
rename to waku/v2/waku_dnsdisc.nim
index 9cb79df12..5cc3db2a0 100644
--- a/waku/v2/protocol/waku_dnsdisc.nim
+++ b/waku/v2/waku_dnsdisc.nim
@@ -22,7 +22,7 @@ import
   libp2p/peerid,
   discovery/dnsdisc/client
 import
-  ../utils/peers
+  ./utils/peers
 
 export client
 
diff --git a/waku/v2/protocol/waku_enr.nim b/waku/v2/waku_enr.nim
similarity index 87%
rename from waku/v2/protocol/waku_enr.nim
rename to waku/v2/waku_enr.nim
index ba97cd066..913eda577 100644
--- a/waku/v2/protocol/waku_enr.nim
+++ b/waku/v2/waku_enr.nim
@@ -1,5 +1,5 @@
 import
-  ../../common/enr,
+  ../common/enr,
   ./waku_enr/capabilities,
   ./waku_enr/multiaddr,
   ./waku_enr/sharding
diff --git a/waku/v2/protocol/waku_enr/capabilities.nim b/waku/v2/waku_enr/capabilities.nim
similarity index 99%
rename from waku/v2/protocol/waku_enr/capabilities.nim
rename to waku/v2/waku_enr/capabilities.nim
index 5192294b1..a4dcc9301 100644
--- a/waku/v2/protocol/waku_enr/capabilities.nim
+++ b/waku/v2/waku_enr/capabilities.nim
@@ -10,7 +10,7 @@ import
   eth/keys,
   libp2p/crypto/crypto
 import
-  ../../../common/enr
+  ../../common/enr
 
 const
   CapabilitiesEnrField* = "waku2"
diff --git a/waku/v2/protocol/waku_enr/multiaddr.nim b/waku/v2/waku_enr/multiaddr.nim
similarity index 99%
rename from waku/v2/protocol/waku_enr/multiaddr.nim
rename to waku/v2/waku_enr/multiaddr.nim
index d2029d325..60df2d796 100644
--- a/waku/v2/protocol/waku_enr/multiaddr.nim
+++ b/waku/v2/waku_enr/multiaddr.nim
@@ -11,7 +11,7 @@ import
   libp2p/[multiaddress, multicodec],
   libp2p/crypto/crypto
 import
-  ../../../common/enr
+  ../../common/enr
 
 const
   MultiaddrEnrField* = "multiaddrs"
diff --git a/waku/v2/protocol/waku_enr/sharding.nim b/waku/v2/waku_enr/sharding.nim
similarity index 99%
rename from waku/v2/protocol/waku_enr/sharding.nim
rename to waku/v2/waku_enr/sharding.nim
index 6269bdd70..db2c768de 100644
--- a/waku/v2/protocol/waku_enr/sharding.nim
+++ b/waku/v2/waku_enr/sharding.nim
@@ -12,7 +12,7 @@ import
   libp2p/[multiaddress, multicodec],
   libp2p/crypto/crypto
 import
-  ../../../common/enr,
+  ../../common/enr,
   ../waku_message
 
 logScope:
diff --git a/waku/v2/protocol/waku_filter.nim b/waku/v2/waku_filter.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter.nim
rename to waku/v2/waku_filter.nim
diff --git a/waku/v2/protocol/waku_filter/README.md b/waku/v2/waku_filter/README.md
similarity index 100%
rename from waku/v2/protocol/waku_filter/README.md
rename to waku/v2/waku_filter/README.md
diff --git a/waku/v2/protocol/waku_filter/client.nim b/waku/v2/waku_filter/client.nim
similarity index 99%
rename from waku/v2/protocol/waku_filter/client.nim
rename to waku/v2/waku_filter/client.nim
index 4ab848de7..4beeaccb8 100644
--- a/waku/v2/protocol/waku_filter/client.nim
+++ b/waku/v2/waku_filter/client.nim
@@ -13,8 +13,8 @@ import
   libp2p/protocols/protocol as libp2p_protocol
 import
   ../waku_message,
-  ../../node/peer_manager,
-  ../../utils/requests,
+  ../node/peer_manager,
+  ../utils/requests,
   ./rpc,
   ./rpc_codec,
   ./protocol,
diff --git a/waku/v2/protocol/waku_filter/protocol.nim b/waku/v2/waku_filter/protocol.nim
similarity index 99%
rename from waku/v2/protocol/waku_filter/protocol.nim
rename to waku/v2/waku_filter/protocol.nim
index 6f9c3563c..2e5ef9ce0 100644
--- a/waku/v2/protocol/waku_filter/protocol.nim
+++ b/waku/v2/waku_filter/protocol.nim
@@ -9,7 +9,7 @@ import
   libp2p/crypto/crypto
 import
   ../waku_message,
-  ../../node/peer_manager,
+  ../node/peer_manager,
   ./rpc,
   ./rpc_codec,
   ./protocol_metrics
diff --git a/waku/v2/protocol/waku_filter/protocol_metrics.nim b/waku/v2/waku_filter/protocol_metrics.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter/protocol_metrics.nim
rename to waku/v2/waku_filter/protocol_metrics.nim
diff --git a/waku/v2/protocol/waku_filter/rpc.nim b/waku/v2/waku_filter/rpc.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter/rpc.nim
rename to waku/v2/waku_filter/rpc.nim
diff --git a/waku/v2/protocol/waku_filter/rpc_codec.nim b/waku/v2/waku_filter/rpc_codec.nim
similarity index 99%
rename from waku/v2/protocol/waku_filter/rpc_codec.nim
rename to waku/v2/waku_filter/rpc_codec.nim
index 69ef1ab62..94756d84b 100644
--- a/waku/v2/protocol/waku_filter/rpc_codec.nim
+++ b/waku/v2/waku_filter/rpc_codec.nim
@@ -6,7 +6,7 @@ else:
 import
   std/options
 import
-  ../../../common/protobuf,
+  ../../common/protobuf,
   ../waku_message,
   ./rpc
 
diff --git a/waku/v2/protocol/waku_filter_v2.nim b/waku/v2/waku_filter_v2.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter_v2.nim
rename to waku/v2/waku_filter_v2.nim
diff --git a/waku/v2/protocol/waku_filter_v2/client.nim b/waku/v2/waku_filter_v2/client.nim
similarity index 99%
rename from waku/v2/protocol/waku_filter_v2/client.nim
rename to waku/v2/waku_filter_v2/client.nim
index 310b603f7..8360b1a7f 100644
--- a/waku/v2/protocol/waku_filter_v2/client.nim
+++ b/waku/v2/waku_filter_v2/client.nim
@@ -12,7 +12,7 @@ import
   libp2p/protocols/protocol,
   bearssl/rand
 import
-  ../../node/peer_manager,
+  ../node/peer_manager,
   ../waku_message,
   ./common,
   ./protocol_metrics,
diff --git a/waku/v2/protocol/waku_filter_v2/common.nim b/waku/v2/waku_filter_v2/common.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter_v2/common.nim
rename to waku/v2/waku_filter_v2/common.nim
diff --git a/waku/v2/protocol/waku_filter_v2/protocol.nim b/waku/v2/waku_filter_v2/protocol.nim
similarity index 99%
rename from waku/v2/protocol/waku_filter_v2/protocol.nim
rename to waku/v2/waku_filter_v2/protocol.nim
index de1af7d30..42ef73ff5 100644
--- a/waku/v2/protocol/waku_filter_v2/protocol.nim
+++ b/waku/v2/waku_filter_v2/protocol.nim
@@ -12,7 +12,7 @@ import
   libp2p/peerid,
   libp2p/protocols/protocol
 import
-  ../../node/peer_manager,
+  ../node/peer_manager,
   ../waku_message,
   ./common,
   ./protocol_metrics,
diff --git a/waku/v2/protocol/waku_filter_v2/protocol_metrics.nim b/waku/v2/waku_filter_v2/protocol_metrics.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter_v2/protocol_metrics.nim
rename to waku/v2/waku_filter_v2/protocol_metrics.nim
diff --git a/waku/v2/protocol/waku_filter_v2/rpc.nim b/waku/v2/waku_filter_v2/rpc.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter_v2/rpc.nim
rename to waku/v2/waku_filter_v2/rpc.nim
diff --git a/waku/v2/protocol/waku_filter_v2/rpc_codec.nim b/waku/v2/waku_filter_v2/rpc_codec.nim
similarity index 99%
rename from waku/v2/protocol/waku_filter_v2/rpc_codec.nim
rename to waku/v2/waku_filter_v2/rpc_codec.nim
index 404c5128d..9be22a7d8 100644
--- a/waku/v2/protocol/waku_filter_v2/rpc_codec.nim
+++ b/waku/v2/waku_filter_v2/rpc_codec.nim
@@ -6,7 +6,7 @@ else:
 import
   std/options
 import
-  ../../../common/protobuf,
+  ../../common/protobuf,
   ../waku_message,
   ./rpc
 
diff --git a/waku/v2/protocol/waku_filter_v2/subscriptions.nim b/waku/v2/waku_filter_v2/subscriptions.nim
similarity index 100%
rename from waku/v2/protocol/waku_filter_v2/subscriptions.nim
rename to waku/v2/waku_filter_v2/subscriptions.nim
diff --git a/waku/v2/protocol/waku_keystore.nim b/waku/v2/waku_keystore.nim
similarity index 100%
rename from waku/v2/protocol/waku_keystore.nim
rename to waku/v2/waku_keystore.nim
diff --git a/waku/v2/protocol/waku_keystore/conversion_utils.nim b/waku/v2/waku_keystore/conversion_utils.nim
similarity index 100%
rename from waku/v2/protocol/waku_keystore/conversion_utils.nim
rename to waku/v2/waku_keystore/conversion_utils.nim
diff --git a/waku/v2/protocol/waku_keystore/keyfile.nim b/waku/v2/waku_keystore/keyfile.nim
similarity index 100%
rename from waku/v2/protocol/waku_keystore/keyfile.nim
rename to waku/v2/waku_keystore/keyfile.nim
diff --git a/waku/v2/protocol/waku_keystore/keystore.nim b/waku/v2/waku_keystore/keystore.nim
similarity index 100%
rename from waku/v2/protocol/waku_keystore/keystore.nim
rename to waku/v2/waku_keystore/keystore.nim
diff --git a/waku/v2/protocol/waku_keystore/protocol_types.nim b/waku/v2/waku_keystore/protocol_types.nim
similarity index 100%
rename from waku/v2/protocol/waku_keystore/protocol_types.nim
rename to waku/v2/waku_keystore/protocol_types.nim
diff --git a/waku/v2/protocol/waku_keystore/utils.nim b/waku/v2/waku_keystore/utils.nim
similarity index 100%
rename from waku/v2/protocol/waku_keystore/utils.nim
rename to waku/v2/waku_keystore/utils.nim
diff --git a/waku/v2/protocol/waku_lightpush.nim b/waku/v2/waku_lightpush.nim
similarity index 100%
rename from waku/v2/protocol/waku_lightpush.nim
rename to waku/v2/waku_lightpush.nim
diff --git a/waku/v2/protocol/waku_lightpush/README.md b/waku/v2/waku_lightpush/README.md
similarity index 100%
rename from waku/v2/protocol/waku_lightpush/README.md
rename to waku/v2/waku_lightpush/README.md
diff --git a/waku/v2/protocol/waku_lightpush/client.nim b/waku/v2/waku_lightpush/client.nim
similarity index 92%
rename from waku/v2/protocol/waku_lightpush/client.nim
rename to waku/v2/waku_lightpush/client.nim
index 115ff8dca..6dd01adae 100644
--- a/waku/v2/protocol/waku_lightpush/client.nim
+++ b/waku/v2/waku_lightpush/client.nim
@@ -11,8 +11,8 @@ import
   metrics,
   bearssl/rand
 import
-  ../../node/peer_manager,
-  ../../utils/requests,
+  ../node/peer_manager,
+  ../utils/requests,
   ../waku_message,
   ./protocol,
   ./protocol_metrics,
@@ -29,13 +29,13 @@ type WakuLightPushClient* = ref object
     rng*: ref rand.HmacDrbgContext
 
 
-proc new*(T: type WakuLightPushClient, 
-          peerManager: PeerManager, 
+proc new*(T: type WakuLightPushClient,
+          peerManager: PeerManager,
           rng: ref rand.HmacDrbgContext): T =
   WakuLightPushClient(peerManager: peerManager, rng: rng)
 
 
-proc sendPushRequest(wl: WakuLightPushClient, req: PushRequest, peer: PeerId|RemotePeerInfo): Future[WakuLightPushResult[void]] {.async, gcsafe.} = 
+proc sendPushRequest(wl: WakuLightPushClient, req: PushRequest, peer: PeerId|RemotePeerInfo): Future[WakuLightPushResult[void]] {.async, gcsafe.} =
   let connOpt = await wl.peerManager.dialPeer(peer, WakuLightPushCodec)
   if connOpt.isNone():
     waku_lightpush_errors.inc(labelValues = [dialFailure])
diff --git a/waku/v2/protocol/waku_lightpush/protocol.nim b/waku/v2/waku_lightpush/protocol.nim
similarity index 99%
rename from waku/v2/protocol/waku_lightpush/protocol.nim
rename to waku/v2/waku_lightpush/protocol.nim
index 094f81779..e3af16026 100644
--- a/waku/v2/protocol/waku_lightpush/protocol.nim
+++ b/waku/v2/waku_lightpush/protocol.nim
@@ -11,7 +11,7 @@ import
   metrics,
   bearssl/rand
 import
-  ../../node/peer_manager,
+  ../node/peer_manager,
   ../waku_message,
   ./rpc,
   ./rpc_codec,
diff --git a/waku/v2/protocol/waku_lightpush/protocol_metrics.nim b/waku/v2/waku_lightpush/protocol_metrics.nim
similarity index 100%
rename from waku/v2/protocol/waku_lightpush/protocol_metrics.nim
rename to waku/v2/waku_lightpush/protocol_metrics.nim
diff --git a/waku/v2/protocol/waku_lightpush/rpc.nim b/waku/v2/waku_lightpush/rpc.nim
similarity index 100%
rename from waku/v2/protocol/waku_lightpush/rpc.nim
rename to waku/v2/waku_lightpush/rpc.nim
diff --git a/waku/v2/protocol/waku_lightpush/rpc_codec.nim b/waku/v2/waku_lightpush/rpc_codec.nim
similarity index 98%
rename from waku/v2/protocol/waku_lightpush/rpc_codec.nim
rename to waku/v2/waku_lightpush/rpc_codec.nim
index 9db2c5c5c..4cb4ac8a7 100644
--- a/waku/v2/protocol/waku_lightpush/rpc_codec.nim
+++ b/waku/v2/waku_lightpush/rpc_codec.nim
@@ -7,7 +7,7 @@ else:
 import
   std/options
 import
-  ../../../common/protobuf,
+  ../../common/protobuf,
   ../waku_message,
   ./rpc
 
diff --git a/waku/v2/protocol/waku_message.nim b/waku/v2/waku_message.nim
similarity index 100%
rename from waku/v2/protocol/waku_message.nim
rename to waku/v2/waku_message.nim
diff --git a/waku/v2/protocol/waku_message/codec.nim b/waku/v2/waku_message/codec.nim
similarity index 97%
rename from waku/v2/protocol/waku_message/codec.nim
rename to waku/v2/waku_message/codec.nim
index b8e18deba..e46ad1c58 100644
--- a/waku/v2/protocol/waku_message/codec.nim
+++ b/waku/v2/waku_message/codec.nim
@@ -9,8 +9,8 @@ else:
 
 
 import
-  ../../../common/protobuf,
-  ../../utils/time,
+  ../../common/protobuf,
+  ../utils/time,
   ./topics,
   ./message
 
diff --git a/waku/v2/protocol/waku_message/digest.nim b/waku/v2/waku_message/digest.nim
similarity index 100%
rename from waku/v2/protocol/waku_message/digest.nim
rename to waku/v2/waku_message/digest.nim
diff --git a/waku/v2/protocol/waku_message/message.nim b/waku/v2/waku_message/message.nim
similarity index 98%
rename from waku/v2/protocol/waku_message/message.nim
rename to waku/v2/waku_message/message.nim
index 6ec6e234b..6cc9623cc 100644
--- a/waku/v2/protocol/waku_message/message.nim
+++ b/waku/v2/waku_message/message.nim
@@ -10,7 +10,7 @@ else:
 
 
 import
-  ../../utils/time,
+  ../utils/time,
   ./topics
 
 const
diff --git a/waku/v2/protocol/waku_message/topics.nim b/waku/v2/waku_message/topics.nim
similarity index 100%
rename from waku/v2/protocol/waku_message/topics.nim
rename to waku/v2/waku_message/topics.nim
diff --git a/waku/v2/protocol/waku_message/topics/content_topic.nim b/waku/v2/waku_message/topics/content_topic.nim
similarity index 100%
rename from waku/v2/protocol/waku_message/topics/content_topic.nim
rename to waku/v2/waku_message/topics/content_topic.nim
diff --git a/waku/v2/protocol/waku_message/topics/parsing.nim b/waku/v2/waku_message/topics/parsing.nim
similarity index 100%
rename from waku/v2/protocol/waku_message/topics/parsing.nim
rename to waku/v2/waku_message/topics/parsing.nim
diff --git a/waku/v2/protocol/waku_message/topics/pubsub_topic.nim b/waku/v2/waku_message/topics/pubsub_topic.nim
similarity index 100%
rename from waku/v2/protocol/waku_message/topics/pubsub_topic.nim
rename to waku/v2/waku_message/topics/pubsub_topic.nim
diff --git a/waku/v2/protocol/waku_noise/noise.nim b/waku/v2/waku_noise/noise.nim
similarity index 100%
rename from waku/v2/protocol/waku_noise/noise.nim
rename to waku/v2/waku_noise/noise.nim
diff --git a/waku/v2/protocol/waku_noise/noise_handshake_processing.nim b/waku/v2/waku_noise/noise_handshake_processing.nim
similarity index 100%
rename from waku/v2/protocol/waku_noise/noise_handshake_processing.nim
rename to waku/v2/waku_noise/noise_handshake_processing.nim
diff --git a/waku/v2/protocol/waku_noise/noise_types.nim b/waku/v2/waku_noise/noise_types.nim
similarity index 100%
rename from waku/v2/protocol/waku_noise/noise_types.nim
rename to waku/v2/waku_noise/noise_types.nim
diff --git a/waku/v2/protocol/waku_noise/noise_utils.nim b/waku/v2/waku_noise/noise_utils.nim
similarity index 100%
rename from waku/v2/protocol/waku_noise/noise_utils.nim
rename to waku/v2/waku_noise/noise_utils.nim
diff --git a/waku/v2/protocol/waku_peer_exchange.nim b/waku/v2/waku_peer_exchange.nim
similarity index 100%
rename from waku/v2/protocol/waku_peer_exchange.nim
rename to waku/v2/waku_peer_exchange.nim
diff --git a/waku/v2/protocol/waku_peer_exchange/README.md b/waku/v2/waku_peer_exchange/README.md
similarity index 100%
rename from waku/v2/protocol/waku_peer_exchange/README.md
rename to waku/v2/waku_peer_exchange/README.md
diff --git a/waku/v2/protocol/waku_peer_exchange/protocol.nim b/waku/v2/waku_peer_exchange/protocol.nim
similarity index 99%
rename from waku/v2/protocol/waku_peer_exchange/protocol.nim
rename to waku/v2/waku_peer_exchange/protocol.nim
index 42c376c7b..d3413683f 100644
--- a/waku/v2/protocol/waku_peer_exchange/protocol.nim
+++ b/waku/v2/waku_peer_exchange/protocol.nim
@@ -8,7 +8,7 @@ import
   libp2p/crypto/crypto,
   eth/p2p/discoveryv5/enr
 import
-  ../../node/peer_manager,
+  ../node/peer_manager,
   ../waku_message,
   ../waku_discv5,
   ./rpc,
diff --git a/waku/v2/protocol/waku_peer_exchange/rpc.nim b/waku/v2/waku_peer_exchange/rpc.nim
similarity index 100%
rename from waku/v2/protocol/waku_peer_exchange/rpc.nim
rename to waku/v2/waku_peer_exchange/rpc.nim
diff --git a/waku/v2/protocol/waku_peer_exchange/rpc_codec.nim b/waku/v2/waku_peer_exchange/rpc_codec.nim
similarity index 98%
rename from waku/v2/protocol/waku_peer_exchange/rpc_codec.nim
rename to waku/v2/waku_peer_exchange/rpc_codec.nim
index f8916185b..bfeac7b21 100644
--- a/waku/v2/protocol/waku_peer_exchange/rpc_codec.nim
+++ b/waku/v2/waku_peer_exchange/rpc_codec.nim
@@ -5,7 +5,7 @@ else:
 
 
 import
-  ../../../common/protobuf,
+  ../../common/protobuf,
   ./rpc
 
 
diff --git a/waku/v2/protocol/waku_relay.nim b/waku/v2/waku_relay.nim
similarity index 100%
rename from waku/v2/protocol/waku_relay.nim
rename to waku/v2/waku_relay.nim
diff --git a/waku/v2/protocol/waku_relay/message_id.nim b/waku/v2/waku_relay/message_id.nim
similarity index 100%
rename from waku/v2/protocol/waku_relay/message_id.nim
rename to waku/v2/waku_relay/message_id.nim
diff --git a/waku/v2/protocol/waku_relay/protocol.nim b/waku/v2/waku_relay/protocol.nim
similarity index 100%
rename from waku/v2/protocol/waku_relay/protocol.nim
rename to waku/v2/waku_relay/protocol.nim
diff --git a/waku/v2/protocol/waku_relay/validators.nim b/waku/v2/waku_relay/validators.nim
similarity index 100%
rename from waku/v2/protocol/waku_relay/validators.nim
rename to waku/v2/waku_relay/validators.nim
diff --git a/waku/v2/protocol/waku_rln_relay.nim b/waku/v2/waku_rln_relay.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay.nim
rename to waku/v2/waku_rln_relay.nim
diff --git a/waku/v2/protocol/waku_rln_relay/constants.nim b/waku/v2/waku_rln_relay/constants.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/constants.nim
rename to waku/v2/waku_rln_relay/constants.nim
diff --git a/waku/v2/protocol/waku_rln_relay/contract.nim b/waku/v2/waku_rln_relay/contract.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/contract.nim
rename to waku/v2/waku_rln_relay/contract.nim
diff --git a/waku/v2/protocol/waku_rln_relay/conversion_utils.nim b/waku/v2/waku_rln_relay/conversion_utils.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/conversion_utils.nim
rename to waku/v2/waku_rln_relay/conversion_utils.nim
diff --git a/waku/v2/protocol/waku_rln_relay/group_manager.nim b/waku/v2/waku_rln_relay/group_manager.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/group_manager.nim
rename to waku/v2/waku_rln_relay/group_manager.nim
diff --git a/waku/v2/protocol/waku_rln_relay/group_manager/group_manager_base.nim b/waku/v2/waku_rln_relay/group_manager/group_manager_base.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/group_manager/group_manager_base.nim
rename to waku/v2/waku_rln_relay/group_manager/group_manager_base.nim
diff --git a/waku/v2/protocol/waku_rln_relay/group_manager/on_chain.nim b/waku/v2/waku_rln_relay/group_manager/on_chain.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/group_manager/on_chain.nim
rename to waku/v2/waku_rln_relay/group_manager/on_chain.nim
diff --git a/waku/v2/protocol/waku_rln_relay/group_manager/on_chain/group_manager.nim b/waku/v2/waku_rln_relay/group_manager/on_chain/group_manager.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/group_manager/on_chain/group_manager.nim
rename to waku/v2/waku_rln_relay/group_manager/on_chain/group_manager.nim
diff --git a/waku/v2/protocol/waku_rln_relay/group_manager/static.nim b/waku/v2/waku_rln_relay/group_manager/static.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/group_manager/static.nim
rename to waku/v2/waku_rln_relay/group_manager/static.nim
diff --git a/waku/v2/protocol/waku_rln_relay/group_manager/static/group_manager.nim b/waku/v2/waku_rln_relay/group_manager/static/group_manager.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/group_manager/static/group_manager.nim
rename to waku/v2/waku_rln_relay/group_manager/static/group_manager.nim
diff --git a/waku/v2/protocol/waku_rln_relay/protocol_metrics.nim b/waku/v2/waku_rln_relay/protocol_metrics.nim
similarity index 97%
rename from waku/v2/protocol/waku_rln_relay/protocol_metrics.nim
rename to waku/v2/waku_rln_relay/protocol_metrics.nim
index b9b60586e..844aaab80 100644
--- a/waku/v2/protocol/waku_rln_relay/protocol_metrics.nim
+++ b/waku/v2/waku_rln_relay/protocol_metrics.nim
@@ -9,9 +9,9 @@ import
   metrics,
   metrics/chronos_httpserver,
   ./constants,
-  ../../utils/collector
+  ../utils/collector
 
-export 
+export
   metrics
 
 logScope:
@@ -30,8 +30,8 @@ declarePublicCounter(waku_rln_messages_total, "number of messages published on t
 declarePublicCounter(waku_rln_spam_messages_total, "number of spam messages detected")
 declarePublicCounter(waku_rln_invalid_messages_total, "number of invalid messages detected", ["type"])
 # This metric will be useful in detecting the index of the root in the acceptable window of roots
-declarePublicHistogram(identifier = waku_rln_valid_messages_total, 
-  help = "number of valid messages with their roots tracked", 
+declarePublicHistogram(identifier = waku_rln_valid_messages_total,
+  help = "number of valid messages with their roots tracked",
   buckets = generateBucketsForHistogram(AcceptableRootWindowSize))
 declarePublicCounter(waku_rln_errors_total, "number of errors detected while operating the rln relay", ["type"])
 declarePublicCounter(waku_rln_proof_verification_total, "number of times the rln proofs are verified")
@@ -74,7 +74,7 @@ proc getRlnMetricsLogger*(): RLNMetricsLogger =
       let freshProofCount = parseAndAccumulate(waku_rln_proof_verification_total,
                                                cumulativeProofs)
 
-      
+
       info "Total messages", count = freshMsgCount
       info "Total spam messages", count = freshSpamCount
       info "Total invalid messages", count = freshInvalidMsgCount
@@ -82,4 +82,4 @@ proc getRlnMetricsLogger*(): RLNMetricsLogger =
       info "Total errors", count = freshErrorCount
       info "Total proofs verified", count = freshProofCount
   return logMetrics
-  
+
diff --git a/waku/v2/protocol/waku_rln_relay/protocol_types.nim b/waku/v2/waku_rln_relay/protocol_types.nim
similarity index 99%
rename from waku/v2/protocol/waku_rln_relay/protocol_types.nim
rename to waku/v2/waku_rln_relay/protocol_types.nim
index e240cde3f..e617315c5 100644
--- a/waku/v2/protocol/waku_rln_relay/protocol_types.nim
+++ b/waku/v2/waku_rln_relay/protocol_types.nim
@@ -12,7 +12,7 @@ import
 import
   ../waku_message,
   ../waku_keystore,
-  ../../../common/protobuf
+  ../../common/protobuf
 
 export
   waku_keystore,
diff --git a/waku/v2/protocol/waku_rln_relay/rln.nim b/waku/v2/waku_rln_relay/rln.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/rln.nim
rename to waku/v2/waku_rln_relay/rln.nim
diff --git a/waku/v2/protocol/waku_rln_relay/rln/rln_interface.nim b/waku/v2/waku_rln_relay/rln/rln_interface.nim
similarity index 100%
rename from waku/v2/protocol/waku_rln_relay/rln/rln_interface.nim
rename to waku/v2/waku_rln_relay/rln/rln_interface.nim
diff --git a/waku/v2/protocol/waku_rln_relay/rln/wrappers.nim b/waku/v2/waku_rln_relay/rln/wrappers.nim
similarity index 99%
rename from waku/v2/protocol/waku_rln_relay/rln/wrappers.nim
rename to waku/v2/waku_rln_relay/rln/wrappers.nim
index d5698fc2d..bbef00e71 100644
--- a/waku/v2/protocol/waku_rln_relay/rln/wrappers.nim
+++ b/waku/v2/waku_rln_relay/rln/wrappers.nim
@@ -11,7 +11,7 @@ import
   ../protocol_metrics
 import
   ../../waku_keystore,
-  ../../../utils/time
+  ../../utils/time
 
 logScope:
   topics = "waku rln_relay ffi"
diff --git a/waku/v2/protocol/waku_rln_relay/rln_relay.nim b/waku/v2/waku_rln_relay/rln_relay.nim
similarity index 99%
rename from waku/v2/protocol/waku_rln_relay/rln_relay.nim
rename to waku/v2/waku_rln_relay/rln_relay.nim
index 3a572f582..415bfe2dc 100644
--- a/waku/v2/protocol/waku_rln_relay/rln_relay.nim
+++ b/waku/v2/waku_rln_relay/rln_relay.nim
@@ -22,7 +22,7 @@ import
   ./protocol_types,
   ./protocol_metrics
 import
-  ../../utils/time,
+  ../utils/time,
   ../waku_keystore
 
 logScope:
diff --git a/waku/v2/protocol/waku_store.nim b/waku/v2/waku_store.nim
similarity index 100%
rename from waku/v2/protocol/waku_store.nim
rename to waku/v2/waku_store.nim
diff --git a/waku/v2/protocol/waku_store/README.md b/waku/v2/waku_store/README.md
similarity index 100%
rename from waku/v2/protocol/waku_store/README.md
rename to waku/v2/waku_store/README.md
diff --git a/waku/v2/protocol/waku_store/client.nim b/waku/v2/waku_store/client.nim
similarity index 99%
rename from waku/v2/protocol/waku_store/client.nim
rename to waku/v2/waku_store/client.nim
index 419b64ae9..74f51fe7a 100644
--- a/waku/v2/protocol/waku_store/client.nim
+++ b/waku/v2/waku_store/client.nim
@@ -11,8 +11,8 @@ import
   metrics,
   bearssl/rand
 import
-  ../../node/peer_manager,
-  ../../utils/requests,
+  ../node/peer_manager,
+  ../utils/requests,
   ./protocol_metrics,
   ./common,
   ./rpc,
diff --git a/waku/v2/protocol/waku_store/common.nim b/waku/v2/waku_store/common.nim
similarity index 99%
rename from waku/v2/protocol/waku_store/common.nim
rename to waku/v2/waku_store/common.nim
index b6bef8abf..b95484912 100644
--- a/waku/v2/protocol/waku_store/common.nim
+++ b/waku/v2/waku_store/common.nim
@@ -9,7 +9,7 @@ import
   stew/byteutils,
   nimcrypto/sha2
 import
-  ../../utils/time,
+  ../utils/time,
   ../waku_message
 
 
diff --git a/waku/v2/protocol/waku_store/protocol.nim b/waku/v2/waku_store/protocol.nim
similarity index 98%
rename from waku/v2/protocol/waku_store/protocol.nim
rename to waku/v2/waku_store/protocol.nim
index 858bcdd45..e9567d3c5 100644
--- a/waku/v2/protocol/waku_store/protocol.nim
+++ b/waku/v2/waku_store/protocol.nim
@@ -18,8 +18,8 @@ import
   libp2p/stream/connection,
   metrics
 import
-  ../../node/peer_manager,
-  ../../utils/time,
+  ../node/peer_manager,
+  ../utils/time,
   ./common,
   ./rpc,
   ./rpc_codec,
diff --git a/waku/v2/protocol/waku_store/protocol_metrics.nim b/waku/v2/waku_store/protocol_metrics.nim
similarity index 100%
rename from waku/v2/protocol/waku_store/protocol_metrics.nim
rename to waku/v2/waku_store/protocol_metrics.nim
diff --git a/waku/v2/protocol/waku_store/rpc.nim b/waku/v2/waku_store/rpc.nim
similarity index 99%
rename from waku/v2/protocol/waku_store/rpc.nim
rename to waku/v2/waku_store/rpc.nim
index 0e7e2daed..e68ad38b8 100644
--- a/waku/v2/protocol/waku_store/rpc.nim
+++ b/waku/v2/waku_store/rpc.nim
@@ -7,7 +7,7 @@ import
   std/[options, sequtils],
   stew/results
 import
-  ../../utils/time,
+  ../utils/time,
   ../waku_message,
   ./common
 
diff --git a/waku/v2/protocol/waku_store/rpc_codec.nim b/waku/v2/waku_store/rpc_codec.nim
similarity index 99%
rename from waku/v2/protocol/waku_store/rpc_codec.nim
rename to waku/v2/waku_store/rpc_codec.nim
index 4a7276d1e..e9368bddd 100644
--- a/waku/v2/protocol/waku_store/rpc_codec.nim
+++ b/waku/v2/waku_store/rpc_codec.nim
@@ -7,7 +7,7 @@ import
   std/options,
   nimcrypto/hash
 import
-  ../../../common/protobuf,
+  ../../common/protobuf,
   ../waku_message,
   ./common,
   ./rpc