reorganize project structure and migrate source to src/

.clang-format

@@ -0,0 +1,62 @@
+# Generated from CLion C/C++ Code Style settings
+---
+Language: Cpp
+BasedOnStyle: LLVM
+AccessModifierOffset: -4
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignOperands: true
+AlignTrailingComments: false
+AlwaysBreakTemplateDeclarations: Yes
+BraceWrapping: 
+  AfterCaseLabel: false
+  AfterClass: false
+  AfterControlStatement: false
+  AfterEnum: false
+  AfterFunction: false
+  AfterNamespace: false
+  AfterStruct: false
+  AfterUnion: false
+  AfterExternBlock: false
+  BeforeCatch: false
+  BeforeElse: false
+  BeforeLambdaBody: false
+  BeforeWhile: false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBraces: Allman
+BreakConstructorInitializers: AfterColon
+BreakConstructorInitializersBeforeComma: false
+ColumnLimit: 0
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ContinuationIndentWidth: 0
+IncludeCategories: 
+  - Regex: '^<.*'
+    Priority: 1
+  - Regex: '^".*'
+    Priority: 2
+  - Regex: '.*'
+    Priority: 3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentWidth: 4
+InsertNewlineAtEOF: true
+MacroBlockBegin: ''
+MacroBlockEnd: ''
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: All
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeRangeBasedForLoopColon: false
+SpaceInEmptyParentheses: false
+SpacesInAngles: false
+SpacesInConditionalStatement: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+TabWidth: 4
+PointerAlignment: Right
+AlignAfterOpenBracket: DontAlign
+AllowShortLambdasOnASingleLine: None
+BinPackArguments: false
+...

CMakeLists.txt

@@ -125,51 +125,38 @@ if (NOT COMPILER_SUPPORTS_AVX2)
 	message(WARNING "AVX2 not supported by the compiler")
 endif ()
 
-# --- Project Sources ---
-SET(FILES
-		${CMAKE_SOURCE_DIR}/connection/connection.cpp
-		${CMAKE_SOURCE_DIR}/connection/connectionPool.cpp
-		${CMAKE_SOURCE_DIR}/connection/NodeIntroducer.cpp
-        ${CMAKE_SOURCE_DIR}/database/db.cpp
-		${CMAKE_SOURCE_DIR}/database/garbageCleaner.cpp
-		${CMAKE_SOURCE_DIR}/Logger.cpp
-		${CMAKE_SOURCE_DIR}/DataProcessors.cpp
-		${CMAKE_SOURCE_DIR}/IOProcessor.cpp
-		${CMAKE_SOURCE_DIR}/LoggingEventProcessor.cpp
-		${CMAKE_SOURCE_DIR}/QubicServer.cpp
-		${CMAKE_SOURCE_DIR}/QubicIndexer.cpp
-		${CMAKE_SOURCE_DIR}/Config.cpp
-		${CMAKE_SOURCE_DIR}/bob.cpp
-		${CMAKE_SOURCE_DIR}/GlobalVar.cpp
-		${CMAKE_SOURCE_DIR}/LogEvent.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/bobAPI.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/ApiHelpers.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/querySmartContract.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/RESTServer.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/LogSubscriptionManager.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/LogWebSocket.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/QubicRpcMapper.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/QubicRpcWebSocket.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/QubicRpcMethods.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/QubicSubscriptionManager.cpp
-		${CMAKE_SOURCE_DIR}/RESTAPI/QubicRpcHandler.cpp
-)
+# --- Collect sources from src/ and exclude executables/tools ---
+file(GLOB_RECURSE ALL_SRC CONFIGURE_DEPENDS ${CMAKE_SOURCE_DIR}/src/*.c ${CMAKE_SOURCE_DIR}/src/*.cpp)
+
+set(LIB_SOURCES)
+foreach(_f IN LISTS ALL_SRC)
+	# exclude main executables and optional single-file tools
+	if(_f MATCHES "/main\\.cpp$" OR _f MATCHES "/pop10\\.cpp$" OR _f MATCHES "/migrator\\.cpp$")
+		continue()
+	endif()
+	list(APPEND LIB_SOURCES ${_f})
+endforeach()
+
+# Fallback: if explicit sources are required, ensure at least some files exist
+if(NOT LIB_SOURCES)
+	message(FATAL_ERROR "No library sources found under src/.")
+endif()
 
-add_library(XKCP_avx2 STATIC XKCP/KangarooTwelve.c
-		XKCP/KeccakP-1600-AVX2.s
-		XKCP/KeccakP-1600-times4-AVX2.c
-		                     XKCP/TurboSHAKE.c
+add_library(XKCP_avx2 STATIC external/XKCP/KangarooTwelve.c
+        external/XKCP/KeccakP-1600-AVX2.s
+        external/XKCP/KeccakP-1600-times4-AVX2.c
+        external/XKCP/TurboSHAKE.c
 )
 
 # Create a library from the source files to be shared between the main executable and tests
-add_library(bob_lib STATIC ${FILES})
+add_library(bob_lib STATIC ${LIB_SOURCES})
 target_link_libraries(bob_lib PRIVATE redis++_static hiredis spdlog::spdlog cxxopts::cxxopts
 		${ZSTD_TARGET} XKCP_avx2 drogon ${JSONCPP_TARGET})
 
 
 # --- Executable and Linking ---
-ADD_EXECUTABLE(bob main.cpp)
-ADD_EXECUTABLE(pop10 pop10.cpp)
+ADD_EXECUTABLE(bob src/main.cpp)
+ADD_EXECUTABLE(pop10 src/pop10.cpp)
 target_link_libraries(bob PRIVATE bob_lib)
 target_link_libraries(pop10 PRIVATE bob_lib)
 
@@ -196,6 +183,6 @@ add_custom_command(
 add_custom_command(
 		TARGET bob POST_BUILD
 		COMMAND ${CMAKE_COMMAND} -E copy_if_different
-		${CMAKE_SOURCE_DIR}/RESTAPI/openapi.json
+		${CMAKE_SOURCE_DIR}/src/rest_api/openapi.json
 		${CMAKE_BINARY_DIR}/openapi.json
 )

README.md

@@ -91,9 +91,9 @@ sudo apt install -y vim net-tools tmux cmake git libjsoncpp-dev \
 
 #### 2. Install KeyDB
 
-KeyDB is a Redis-compatible database required by Bob. Follow the [KeyDB installation guide](KEYDB_INSTALL.md).
+KeyDB is a Redis-compatible database required by Bob. Follow the [KeyDB installation guide](doc/KEYDB_INSTALL.md).
 
-Optionally, install KVRocks for additional disk-based persistence: [KVRocks installation guide](KVROCKS_INSTALL.MD).
+Optionally, install KVRocks for additional disk-based persistence: [KVRocks installation guide](doc/KVROCKS_INSTALL.MD).
 
 #### 3. Build Bob
 
@@ -181,13 +181,13 @@ curl -s -X POST http://localhost:40420/qubic \
 ## Useful Resources
 
 ### Using Bob
-- [Ethereum-like JSON-RPC (HTTP/WS)](QUBIC_JSON_RPC.md)
-- [REST API Endpoints](REST_API.md)
-- [What is a Logging Event in Qubic?](LOGGING_IN_QUBIC.MD)
-- [Mastering the findlog Method](FINDLOG.MD)
-- [Dealing with Transactions and Logging](DEAL_WITH_TX.MD)
-- [Improve Stability via Kernel Buffer Size](KERN_BUF_SIZE.MD)
+- [Ethereum-like JSON-RPC (HTTP/WS)](doc/QUBIC_JSON_RPC.md)
+- [REST API Endpoints](doc/REST_API.md)
+- [What is a Logging Event in Qubic?](doc/LOGGING_IN_QUBIC.MD)
+- [Mastering the findlog Method](doc/FINDLOG.MD)
+- [Dealing with Transactions and Logging](doc/DEAL_WITH_TX.MD)
+- [Improve Stability via Kernel Buffer Size](doc/KERN_BUF_SIZE.MD)
 
 ### Inside Bob
-- [Anatomy of Bob](ANATOMY_OF_BOB.MD)
-- [How the Indexer Indexes Qubic Data](INDEXER_INDEXING_DATA.MD)
+- [Anatomy of Bob](doc/ANATOMY_OF_BOB.MD)
+- [How the Indexer Indexes Qubic Data](doc/INDEXER_INDEXING_DATA.MD)

QUBIC_JSON_RPC.md → doc/QUBIC_JSON_RPC.md

@@ -6,7 +6,7 @@ This guide is for exchange developers and integrators who want to connect to Qub
 > [!NOTE]
 > This documentation covers the Qubic JSON-RPC 2.0 API including WebSocket subscriptions.
 
-To have a playground, you can open [rpc_playground.html](rpc_playground.html) in your browser. Or use the published version [here on github gist](https://gistpreview.github.io/?6912d613bc27ae75126859447fca8acf).
+To have a playground, you can open [rpc_playground.html](../web/rpc_playground.html) in your browser. Or use the published version [here on github gist](https://gistpreview.github.io/?6912d613bc27ae75126859447fca8acf).
 
 ## Table of Contents
 

bob.cpp → src/bob.cpp

@@ -1,37 +1,36 @@
-#include "Config.h"
+#include "bob.h"
+#include "src/core/k12_and_key_util.h"
+#include "src/profiler/profiler.h"
+#include "config.h"
 #include "connection/connection.h"
-#include "structs.h"
-#include "Logger.h"
-#include "GlobalVar.h"
+#include "core/structs.h"
 #include "database/db.h"
-#include "Profiler.h"
+#include "global_var.h"
+#include "logger/logger.h"
+#include "shim.h"
+#include "version.h"
+#include <algorithm> // std::max
 #include <chrono>
-#include <cstring>   // memcpy
 #include <cstdlib>   // strtoull
+#include <cstring>   // memcpy
 #include <limits>    // std::numeric_limits
-#include <algorithm> // std::max
-#include <random>    // std::random_device, std::mt19937
-#include "K12AndKeyUtil.h"
 #include <pthread.h> // thread naming on POSIX
-#include "shim.h"
-#include "bob.h"
-#include "Version.h"
-void IOVerifyThread();
-void IORequestThread(ConnectionPool& conn_pool, std::chrono::milliseconds requestCycle, uint32_t futureOffset);
-void EventRequestFromTrustedNode(ConnectionPool& connPoolWithPwd, std::chrono::milliseconds request_logging_cycle_ms);
+#include <random>    // std::random_device, std::mt19937
+
+void tickingVerifyThread();
+void tickingDataRequestThread(ConnectionPool& conn_pool, std::chrono::milliseconds requestCycle, uint32_t futureOffset);
+void eventRequestFromTrustedNode(ConnectionPool& connPoolWithPwd, std::chrono::milliseconds request_logging_cycle_ms);
 void connReceiver(QCPtr conn, const bool isTrustedNode);
-void DataProcessorThread();
-void RequestProcessorThread();
+void dataProcessorThread();
+void requestProcessorThread();
 void verifyLoggingEvent();
 void indexVerifiedTicks();
 void querySmartContractThread(ConnectionPool& connPoolAll);
 // Public helpers from QubicServer.cpp
-bool StartQubicServer(ConnectionPool* cp, uint16_t port = 21842);
-void StopQubicServer();
+bool startQubicServer(ConnectionPool* cp, uint16_t port = 21842);
+void stopQubicServer();
 void garbageCleaner();
 
-
-
 static inline void set_this_thread_name(const char* name_in) {
     // Linux allows up to 16 bytes including null terminator
     char buf[16];
@@ -108,7 +107,6 @@ int runBob(int argc, char *argv[])
     // Put redis_url in REDIS_CONNECTION_STRING
     std::string KEYDB_CONNECTION_STRING = cfg.keydb_url;
 
-
     // Read server flags
     const bool run_server = cfg.run_server;
     unsigned int server_port_u = cfg.server_port;
@@ -150,14 +148,13 @@ int runBob(int argc, char *argv[])
             return -1;
         }
         const uint16_t server_port = static_cast<uint16_t>(server_port_u);
-        if (!StartQubicServer(&connPool, server_port)) {
+        if (!startQubicServer(&connPool, server_port)) {
             Logger::get()->critical("Failed to start embedded server on port {}", server_port);
             return -1;
         }
         Logger::get()->info("Embedded server enabled on port {}", server_port);
     }
 
-
     uint32_t initTick = 0;
     uint16_t initEpoch = 0;
     uint32_t endEpochTick = 0;
@@ -206,11 +203,10 @@ int runBob(int argc, char *argv[])
         }
     }
 
-
     auto request_thread = std::thread(
             [&](){
                 set_this_thread_name("io-req");
-                IORequestThread(
+                tickingDataRequestThread(
                         std::ref(connPool),
                         std::chrono::milliseconds(request_cycle_ms),
                         static_cast<uint32_t>(future_offset)
@@ -219,11 +215,11 @@ int runBob(int argc, char *argv[])
     );
     auto verify_thread = std::thread([&](){
         set_this_thread_name("verify");
-        IOVerifyThread();
+        tickingVerifyThread();
     });
     auto log_request_trusted_nodes_thread = std::thread([&](){
         set_this_thread_name("trusted-log-req");
-        EventRequestFromTrustedNode(std::ref(connPool),
+        eventRequestFromTrustedNode(std::ref(connPool),
                                     std::chrono::milliseconds(request_logging_cycle_ms));
     });
     auto indexer_thread = std::thread([&](){
@@ -263,13 +259,13 @@ int runBob(int argc, char *argv[])
     {
         v_data_thread.emplace_back([&](){
             set_this_thread_name("data");
-            DataProcessorThread();
+            dataProcessorThread();
         });
         v_data_thread.emplace_back([&, i](){
             char nm[16];
             std::snprintf(nm, sizeof(nm), "reqp-%d", i);
             set_this_thread_name(nm);
-            RequestProcessorThread();
+            requestProcessorThread();
         });
     }
     std::thread log_event_verifier_thread;
@@ -403,7 +399,7 @@ int runBob(int argc, char *argv[])
 
     if (run_server)
     {
-        StopQubicServer();
+        stopQubicServer();
         Logger::get()->info("Closed Qubic server at port 21842");
     }
 

Config.cpp → src/config.cpp

@@ -1,10 +1,10 @@
-#include "Config.h"
+#include "config.h"
 #include "json/reader.h"
-#include <json/json.h>
 #include <fstream>
+#include <json/json.h>
+#include <memory>
 #include <sstream>
 #include <string>
-#include <memory>
 #include <thread>
 
 bool LoadConfig(const std::string& path, AppConfig& out, std::string& error) {

Config.h → src/config.h

@@ -1,9 +1,9 @@
 #pragma once
 
+#include "core/m256i.h"
+#include <map>
 #include <string>
 #include <vector>
-#include <map>
-#include "m256i.h"
 
 // Add tick storage mode enum
 enum class TickStorageMode {

connection/connection.cpp → src/connection/connection.cpp

@@ -1,22 +1,23 @@
-#include "structs.h"
 #include <memory>
 #include <stdexcept>
 #include <algorithm> // For std::min
 #include <thread>
 
-#include <sys/socket.h>
-#include <netinet/in.h>
+#include "connection.h"
 #include <arpa/inet.h>
-#include <unistd.h>
+#include <cerrno> // for errno
 #include <cstring>
-#include <cerrno>  // for errno
 #include <fcntl.h>
+#include <netinet/in.h>
 #include <netinet/tcp.h>
-#include "database/db.h"
-#include "connection.h"
-#include "Logger.h"
-#include "GlobalVar.h"
-#include "shim.h"
+#include <sys/socket.h>
+#include <unistd.h>
+
+#include "src/database/db.h"
+#include "src/global_var.h"
+#include "src/shim.h"
+
+#include <src/logger/logger.h>
 static int do_connect(const char* nodeIp, int nodePort)
 {
     int serverSocket = socket(AF_INET, SOCK_STREAM, 0);