diff --git a/pcsx2/CDVD/IsoFS/IsoFSCDVD.cpp b/pcsx2/CDVD/IsoFS/IsoFSCDVD.cpp
index 370f683a4c..3df2c39dd0 100644
--- a/pcsx2/CDVD/IsoFS/IsoFSCDVD.cpp
+++ b/pcsx2/CDVD/IsoFS/IsoFSCDVD.cpp
@@ -17,7 +17,7 @@
 #include "PrecompiledHeader.h"
 
 #include "IsoFSCDVD.h"
-#include "../CDVDaccess.h"
+#include "CDVD/CDVDaccess.h"
 
 IsoFSCDVD::IsoFSCDVD()
 {
diff --git a/pcsx2/CDVD/Linux/DriveUtility.cpp b/pcsx2/CDVD/Linux/DriveUtility.cpp
index 28b448106d..9ba07d154f 100644
--- a/pcsx2/CDVD/Linux/DriveUtility.cpp
+++ b/pcsx2/CDVD/Linux/DriveUtility.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../CDVDdiscReader.h"
+#include "CDVD/CDVDdiscReader.h"
 
 #ifdef __linux__
 #include <libudev.h>
diff --git a/pcsx2/CDVD/Linux/IOCtlSrc.cpp b/pcsx2/CDVD/Linux/IOCtlSrc.cpp
index 319c05ff72..3cffd8180f 100644
--- a/pcsx2/CDVD/Linux/IOCtlSrc.cpp
+++ b/pcsx2/CDVD/Linux/IOCtlSrc.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../CDVDdiscReader.h"
+#include "CDVD/CDVDdiscReader.h"
 
 #ifdef __linux__
 #include <linux/cdrom.h>
diff --git a/pcsx2/CDVD/Windows/DriveUtility.cpp b/pcsx2/CDVD/Windows/DriveUtility.cpp
index c75c2a3245..5143f1c646 100644
--- a/pcsx2/CDVD/Windows/DriveUtility.cpp
+++ b/pcsx2/CDVD/Windows/DriveUtility.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../CDVDdiscReader.h"
+#include "CDVD/CDVDdiscReader.h"
 
 std::vector<std::wstring> GetOpticalDriveList()
 {
diff --git a/pcsx2/CDVD/Windows/IOCtlSrc.cpp b/pcsx2/CDVD/Windows/IOCtlSrc.cpp
index 3d3cb1c375..fe774ba94b 100644
--- a/pcsx2/CDVD/Windows/IOCtlSrc.cpp
+++ b/pcsx2/CDVD/Windows/IOCtlSrc.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../CDVDdiscReader.h"
+#include "CDVD/CDVDdiscReader.h"
 
 #include <winioctl.h>
 #include <ntddcdvd.h>
diff --git a/pcsx2/DEV9/ATA/ATA.h b/pcsx2/DEV9/ATA/ATA.h
index 3fe4ab5093..0c3c933fff 100644
--- a/pcsx2/DEV9/ATA/ATA.h
+++ b/pcsx2/DEV9/ATA/ATA.h
@@ -23,7 +23,7 @@
 #include "ghc/filesystem.h"
 #include <fstream>
 
-#include "../SimpleQueue.h"
+#include "DEV9/SimpleQueue.h"
 
 class ATA
 {
diff --git a/pcsx2/DEV9/ATA/ATA_Info.cpp b/pcsx2/DEV9/ATA/ATA_Info.cpp
index f788592bcd..a62ab3c36a 100644
--- a/pcsx2/DEV9/ATA/ATA_Info.cpp
+++ b/pcsx2/DEV9/ATA/ATA_Info.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "ATA.h"
-#include "../DEV9.h"
+#include "DEV9/DEV9.h"
 
 void ATA::WriteUInt16(u8* data, int* index, u16 value)
 {
diff --git a/pcsx2/DEV9/ATA/ATA_State.cpp b/pcsx2/DEV9/ATA/ATA_State.cpp
index 6a42aefbc7..4d2c5d8643 100644
--- a/pcsx2/DEV9/ATA/ATA_State.cpp
+++ b/pcsx2/DEV9/ATA/ATA_State.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "ATA.h"
-#include "../DEV9.h"
+#include "DEV9/DEV9.h"
 #include "HddCreate.h"
 
 ATA::ATA()
diff --git a/pcsx2/DEV9/ATA/ATA_Transfer.cpp b/pcsx2/DEV9/ATA/ATA_Transfer.cpp
index 500805a6e6..20a4acb66a 100644
--- a/pcsx2/DEV9/ATA/ATA_Transfer.cpp
+++ b/pcsx2/DEV9/ATA/ATA_Transfer.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "ATA.h"
-#include "../DEV9.h"
+#include "DEV9/DEV9.h"
 
 void ATA::IO_Thread()
 {
diff --git a/pcsx2/DEV9/ATA/Commands/ATA_CmdDMA.cpp b/pcsx2/DEV9/ATA/Commands/ATA_CmdDMA.cpp
index 9cb21a2345..8073956c2b 100644
--- a/pcsx2/DEV9/ATA/Commands/ATA_CmdDMA.cpp
+++ b/pcsx2/DEV9/ATA/Commands/ATA_CmdDMA.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../ATA.h"
-#include "../../DEV9.h"
+#include "DEV9/ATA/ATA.h"
+#include "DEV9/DEV9.h"
 
 void ATA::DRQCmdDMADataToHost()
 {
diff --git a/pcsx2/DEV9/ATA/Commands/ATA_CmdExecuteDeviceDiag.cpp b/pcsx2/DEV9/ATA/Commands/ATA_CmdExecuteDeviceDiag.cpp
index 2e7272807a..e8f5a54414 100644
--- a/pcsx2/DEV9/ATA/Commands/ATA_CmdExecuteDeviceDiag.cpp
+++ b/pcsx2/DEV9/ATA/Commands/ATA_CmdExecuteDeviceDiag.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../ATA.h"
-#include "../../DEV9.h"
+#include "DEV9/ATA/ATA.h"
+#include "DEV9/DEV9.h"
 
 void ATA::PreCmdExecuteDeviceDiag()
 {
diff --git a/pcsx2/DEV9/ATA/Commands/ATA_CmdNoData.cpp b/pcsx2/DEV9/ATA/Commands/ATA_CmdNoData.cpp
index b83827eedf..680625d9fe 100644
--- a/pcsx2/DEV9/ATA/Commands/ATA_CmdNoData.cpp
+++ b/pcsx2/DEV9/ATA/Commands/ATA_CmdNoData.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../ATA.h"
-#include "../../DEV9.h"
+#include "DEV9/ATA/ATA.h"
+#include "DEV9/DEV9.h"
 
 void ATA::PostCmdNoData()
 {
diff --git a/pcsx2/DEV9/ATA/Commands/ATA_CmdPIOData.cpp b/pcsx2/DEV9/ATA/Commands/ATA_CmdPIOData.cpp
index e3691cb025..be53fa617e 100644
--- a/pcsx2/DEV9/ATA/Commands/ATA_CmdPIOData.cpp
+++ b/pcsx2/DEV9/ATA/Commands/ATA_CmdPIOData.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../ATA.h"
-#include "../../DEV9.h"
+#include "DEV9/ATA/ATA.h"
+#include "DEV9/DEV9.h"
 
 void ATA::DRQCmdPIODataToHost(u8* buff, int buffLen, int buffIndex, int size, bool sendIRQ)
 {
diff --git a/pcsx2/DEV9/ATA/Commands/ATA_CmdSMART.cpp b/pcsx2/DEV9/ATA/Commands/ATA_CmdSMART.cpp
index 32e2bc8969..cf215f08b0 100644
--- a/pcsx2/DEV9/ATA/Commands/ATA_CmdSMART.cpp
+++ b/pcsx2/DEV9/ATA/Commands/ATA_CmdSMART.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../ATA.h"
-#include "../../DEV9.h"
+#include "DEV9/ATA/ATA.h"
+#include "DEV9/DEV9.h"
 
 void ATA::HDD_Smart()
 {
diff --git a/pcsx2/DEV9/ATA/Commands/ATA_Command.cpp b/pcsx2/DEV9/ATA/Commands/ATA_Command.cpp
index e60d5f4af3..01d1a1228c 100644
--- a/pcsx2/DEV9/ATA/Commands/ATA_Command.cpp
+++ b/pcsx2/DEV9/ATA/Commands/ATA_Command.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../ATA.h"
-#include "../../DEV9.h"
+#include "DEV9/ATA/ATA.h"
+#include "DEV9/DEV9.h"
 
 void ATA::IDE_ExecCmd(u16 value)
 {
diff --git a/pcsx2/DEV9/ATA/Commands/ATA_SCE.cpp b/pcsx2/DEV9/ATA/Commands/ATA_SCE.cpp
index b4aa6e90e7..230e4d5b04 100644
--- a/pcsx2/DEV9/ATA/Commands/ATA_SCE.cpp
+++ b/pcsx2/DEV9/ATA/Commands/ATA_SCE.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../ATA.h"
-#include "../../DEV9.h"
+#include "DEV9/ATA/ATA.h"
+#include "DEV9/DEV9.h"
 
 void ATA::HDD_SCE()
 {
diff --git a/pcsx2/DEV9/InternalServers/DHCP_Server.cpp b/pcsx2/DEV9/InternalServers/DHCP_Server.cpp
index 0dddaa1deb..849bd27b2a 100644
--- a/pcsx2/DEV9/InternalServers/DHCP_Server.cpp
+++ b/pcsx2/DEV9/InternalServers/DHCP_Server.cpp
@@ -24,10 +24,10 @@
 #endif
 
 #include "DHCP_Server.h"
-#include "../PacketReader/IP/UDP/UDP_Packet.h"
-#include "../PacketReader/IP/UDP/DHCP/DHCP_Packet.h"
+#include "DEV9/PacketReader/IP/UDP/UDP_Packet.h"
+#include "DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.h"
 
-#include "../DEV9.h"
+#include "DEV9/DEV9.h"
 
 using namespace PacketReader;
 using namespace PacketReader::IP;
diff --git a/pcsx2/DEV9/InternalServers/DHCP_Server.h b/pcsx2/DEV9/InternalServers/DHCP_Server.h
index afd16e47e4..ca9c5f9aa0 100644
--- a/pcsx2/DEV9/InternalServers/DHCP_Server.h
+++ b/pcsx2/DEV9/InternalServers/DHCP_Server.h
@@ -17,9 +17,9 @@
 
 #include <functional>
 
-#include "../SimpleQueue.h"
-#include "../PacketReader/IP/IP_Address.h"
-#include "../PacketReader/IP/UDP/UDP_Packet.h"
+#include "DEV9/SimpleQueue.h"
+#include "DEV9/PacketReader/IP/IP_Address.h"
+#include "DEV9/PacketReader/IP/UDP/UDP_Packet.h"
 
 #ifdef _WIN32
 #include <winsock2.h>
diff --git a/pcsx2/DEV9/Linux/Config.cpp b/pcsx2/DEV9/Linux/Config.cpp
index 03012d6024..84548eef89 100644
--- a/pcsx2/DEV9/Linux/Config.cpp
+++ b/pcsx2/DEV9/Linux/Config.cpp
@@ -18,7 +18,7 @@
 #include <stdlib.h>
 #include <arpa/inet.h>
 
-#include "../DEV9.h"
+#include "DEV9/DEV9.h"
 #include "AppConfig.h"
 
 #include <unistd.h>
diff --git a/pcsx2/DEV9/Linux/Linux.cpp b/pcsx2/DEV9/Linux/Linux.cpp
index f114e29021..cf8a7b9862 100644
--- a/pcsx2/DEV9/Linux/Linux.cpp
+++ b/pcsx2/DEV9/Linux/Linux.cpp
@@ -30,15 +30,15 @@
 #include <string>
 #include "ghc/filesystem.h"
 
-#include "../Config.h"
-#include "../DEV9.h"
+#include "DEV9/Config.h"
+#include "DEV9/DEV9.h"
 #include "pcap.h"
-#include "../pcap_io.h"
-#include "../net.h"
-#include "../PacketReader/IP/IP_Address.h"
+#include "DEV9/pcap_io.h"
+#include "DEV9/net.h"
+#include "DEV9/PacketReader/IP/IP_Address.h"
 #include "AppCoreThread.h"
 
-#include "../ATA/HddCreate.h"
+#include "DEV9/ATA/HddCreate.h"
 
 using PacketReader::IP::IP_Address;
 
diff --git a/pcsx2/DEV9/PacketReader/EthernetFrame.h b/pcsx2/DEV9/PacketReader/EthernetFrame.h
index d8958fadaa..a3e5ccb189 100644
--- a/pcsx2/DEV9/PacketReader/EthernetFrame.h
+++ b/pcsx2/DEV9/PacketReader/EthernetFrame.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../net.h"
+#include "DEV9/net.h"
 #include "Payload.h"
 
 namespace PacketReader
diff --git a/pcsx2/DEV9/PacketReader/IP/IP_Options.cpp b/pcsx2/DEV9/PacketReader/IP/IP_Options.cpp
index 9bcc474188..3ea86b0fc5 100644
--- a/pcsx2/DEV9/PacketReader/IP/IP_Options.cpp
+++ b/pcsx2/DEV9/PacketReader/IP/IP_Options.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "IP_Options.h"
-#include "../NetLib.h"
+#include "DEV9/PacketReader/NetLib.h"
 
 namespace PacketReader::IP
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/IP_Packet.cpp b/pcsx2/DEV9/PacketReader/IP/IP_Packet.cpp
index 65a2724337..ec7a9e3cb2 100644
--- a/pcsx2/DEV9/PacketReader/IP/IP_Packet.cpp
+++ b/pcsx2/DEV9/PacketReader/IP/IP_Packet.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "IP_Packet.h"
-#include "../NetLib.h"
+#include "DEV9/PacketReader/NetLib.h"
 
 namespace PacketReader::IP
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/IP_Packet.h b/pcsx2/DEV9/PacketReader/IP/IP_Packet.h
index 47f3f1f70a..0261a3e655 100644
--- a/pcsx2/DEV9/PacketReader/IP/IP_Packet.h
+++ b/pcsx2/DEV9/PacketReader/IP/IP_Packet.h
@@ -16,7 +16,7 @@
 #pragma once
 #include <vector>
 
-#include "../Payload.h"
+#include "DEV9/PacketReader/Payload.h"
 #include "IP_Address.h"
 #include "IP_Options.h"
 #include "IP_Payload.h"
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.cpp b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.cpp
index 91b37237d0..ef5ba135d5 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.cpp
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "DHCP_Options.h"
-#include "../../../NetLib.h"
+#include "DEV9/PacketReader/NetLib.h"
 
 namespace PacketReader::IP::UDP::DHCP
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.h b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.h
index 2a730bda48..dd4ae7b025 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.h
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Options.h
@@ -17,8 +17,8 @@
 #include <string>
 #include <vector>
 
-#include "../../IP_Packet.h"
-#include "../../IP_Options.h"
+#include "DEV9/PacketReader/IP/IP_Packet.h"
+#include "DEV9/PacketReader/IP/IP_Options.h"
 
 namespace PacketReader::IP::UDP::DHCP
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.cpp b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.cpp
index cbbac9b0d0..d969794deb 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.cpp
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.cpp
@@ -15,7 +15,7 @@
 
 #include "PrecompiledHeader.h"
 #include "DHCP_Packet.h"
-#include "../../../NetLib.h"
+#include "DEV9/PacketReader/NetLib.h"
 
 namespace PacketReader::IP::UDP::DHCP
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.h b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.h
index aeb6186333..b8e1e422e9 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.h
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/DHCP/DHCP_Packet.h
@@ -17,7 +17,7 @@
 #include <vector>
 
 #include "DHCP_Options.h"
-#include "../../IP_Packet.h"
+#include "DEV9/PacketReader/IP/IP_Packet.h"
 
 namespace PacketReader::IP::UDP::DHCP
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Classes.cpp b/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Classes.cpp
index 233809e6d7..dbcbf33187 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Classes.cpp
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Classes.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "DNS_Classes.h"
-#include "../../../NetLib.h"
+#include "DEV9/PacketReader/NetLib.h"
 
 namespace PacketReader::IP::UDP::DNS
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.cpp b/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.cpp
index 9c82ff37e5..56368b860b 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.cpp
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "DNS_Packet.h"
-#include "../../../NetLib.h"
+#include "DEV9/PacketReader/NetLib.h"
 
 namespace PacketReader::IP::UDP::DNS
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.h b/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.h
index 8e150f4423..a9bae2d542 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.h
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/DNS/DNS_Packet.h
@@ -18,7 +18,7 @@
 
 #include "DNS_Classes.h"
 #include "DNS_Enums.h"
-#include "../../../Payload.h"
+#include "DEV9/PacketReader/Payload.h"
 
 namespace PacketReader::IP::UDP::DNS
 {
@@ -78,4 +78,4 @@ namespace PacketReader::IP::UDP::DNS
 		virtual int GetLength();
 		virtual void WriteBytes(u8* buffer, int* offset);
 	};
-} // namespace PacketReader::IP::UDP::DNS
\ No newline at end of file
+} // namespace PacketReader::IP::UDP::DNS
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.cpp b/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.cpp
index e7cde8327e..d22570edb7 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.cpp
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 
 #include "UDP_Packet.h"
-#include "../../NetLib.h"
+#include "DEV9/PacketReader/NetLib.h"
 
 namespace PacketReader::IP::UDP
 {
diff --git a/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.h b/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.h
index e67f9f7602..618755989d 100644
--- a/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.h
+++ b/pcsx2/DEV9/PacketReader/IP/UDP/UDP_Packet.h
@@ -14,7 +14,7 @@
  */
 
 #pragma once
-#include "../IP_Packet.h"
+#include "DEV9/PacketReader/IP/IP_Packet.h"
 
 namespace PacketReader::IP::UDP
 {
diff --git a/pcsx2/DEV9/Win32/Win32.cpp b/pcsx2/DEV9/Win32/Win32.cpp
index 0e85c1b69a..e3c46608f2 100644
--- a/pcsx2/DEV9/Win32/Win32.cpp
+++ b/pcsx2/DEV9/Win32/Win32.cpp
@@ -30,7 +30,7 @@
 #include "tap.h"
 #include "AppCoreThread.h"
 
-#include "../ATA/HddCreate.h"
+#include "DEV9/ATA/HddCreate.h"
 
 using PacketReader::IP::IP_Address;
 
diff --git a/pcsx2/DEV9/Win32/pcap_io_win32.cpp b/pcsx2/DEV9/Win32/pcap_io_win32.cpp
index 2bc07f5421..690efaf5bc 100644
--- a/pcsx2/DEV9/Win32/pcap_io_win32.cpp
+++ b/pcsx2/DEV9/Win32/pcap_io_win32.cpp
@@ -15,7 +15,7 @@
 
 #include "PrecompiledHeader.h"
 
-#include "../pcap_io.h"
+#include "DEV9/pcap_io.h"
 
 HMODULE hpcap = nullptr;
 
diff --git a/pcsx2/DebugTools/BiosDebugData.cpp b/pcsx2/DebugTools/BiosDebugData.cpp
index b1cf87a713..8d240e6a1a 100644
--- a/pcsx2/DebugTools/BiosDebugData.cpp
+++ b/pcsx2/DebugTools/BiosDebugData.cpp
@@ -15,7 +15,7 @@
 
 #include "PrecompiledHeader.h"
 #include "BiosDebugData.h"
-#include "../Memory.h"
+#include "Memory.h"
 
 std::vector<EEThread> getEEThreads()
 {
diff --git a/pcsx2/DebugTools/BiosDebugData.h b/pcsx2/DebugTools/BiosDebugData.h
index 314e3a0fe2..4e3ec34509 100644
--- a/pcsx2/DebugTools/BiosDebugData.h
+++ b/pcsx2/DebugTools/BiosDebugData.h
@@ -15,7 +15,7 @@
 
 #pragma once
 #include "Pcsx2Types.h"
-#include "../ps2/BiosTools.h"
+#include "ps2/BiosTools.h"
 
 struct EEInternalThread { // internal struct
 	u32 prev;
diff --git a/pcsx2/DebugTools/Breakpoints.cpp b/pcsx2/DebugTools/Breakpoints.cpp
index 20e11b1604..605a71f7c2 100644
--- a/pcsx2/DebugTools/Breakpoints.cpp
+++ b/pcsx2/DebugTools/Breakpoints.cpp
@@ -18,8 +18,8 @@
 #include "SymbolMap.h"
 #include "MIPSAnalyst.h"
 #include <cstdio>
-#include "../R5900.h"
-#include "../System.h"
+#include "R5900.h"
+#include "System.h"
 
 std::vector<BreakPoint> CBreakPoints::breakPoints_;
 u32 CBreakPoints::breakSkipFirstAtEE_ = 0;
diff --git a/pcsx2/DebugTools/Debug.h b/pcsx2/DebugTools/Debug.h
index 0cad80d748..e5f09459b6 100644
--- a/pcsx2/DebugTools/Debug.h
+++ b/pcsx2/DebugTools/Debug.h
@@ -16,7 +16,7 @@
 #pragma once
 
 #include "Utilities/TraceLog.h"
-#include "../Memory.h"
+#include "Memory.h"
 
 extern FILE *emuLog;
 extern wxString emuLogName;
diff --git a/pcsx2/DebugTools/DebugInterface.cpp b/pcsx2/DebugTools/DebugInterface.cpp
index 5f549d166a..c2ad8c5cfb 100644
--- a/pcsx2/DebugTools/DebugInterface.cpp
+++ b/pcsx2/DebugTools/DebugInterface.cpp
@@ -20,12 +20,12 @@
 #include "R5900.h"
 #include "AppCoreThread.h"
 #include "Debug.h"
-#include "../VU.h"
-#include "../GS.h" // Required for gsNonMirroredRead()
+#include "VU.h"
+#include "GS.h" // Required for gsNonMirroredRead()
 #include "Counters.h"
 
-#include "../R3000A.h"
-#include "../IopMem.h"
+#include "R3000A.h"
+#include "IopMem.h"
 #include "SymbolMap.h"
 
 extern AppCoreThread CoreThread;
diff --git a/pcsx2/DebugTools/MIPSAnalyst.cpp b/pcsx2/DebugTools/MIPSAnalyst.cpp
index fadd8d3258..6f9bb9c86e 100644
--- a/pcsx2/DebugTools/MIPSAnalyst.cpp
+++ b/pcsx2/DebugTools/MIPSAnalyst.cpp
@@ -19,8 +19,8 @@
 #include "DebugInterface.h"
 #include "SymbolMap.h"
 #include "DebugInterface.h"
-#include "../R5900.h"
-#include "../R5900OpcodeTables.h"
+#include "R5900.h"
+#include "R5900OpcodeTables.h"
 
 static std::vector<MIPSAnalyst::AnalyzedFunction> functions;
 
diff --git a/pcsx2/DebugTools/MipsStackWalk.cpp b/pcsx2/DebugTools/MipsStackWalk.cpp
index 088dcc0971..bcf2c181af 100644
--- a/pcsx2/DebugTools/MipsStackWalk.cpp
+++ b/pcsx2/DebugTools/MipsStackWalk.cpp
@@ -23,7 +23,7 @@
 #include "SymbolMap.h"
 #include "MIPSAnalyst.h"
 #include "DebugInterface.h"
-#include "../R5900OpcodeTables.h"
+#include "R5900OpcodeTables.h"
 
 #define _RS ((rawOp >> 21) & 0x1F)
 #define _RT ((rawOp >> 16) & 0x1F)
diff --git a/pcsx2/GS/Renderers/Common/GSDevice.cpp b/pcsx2/GS/Renderers/Common/GSDevice.cpp
index 924ae86928..8d960b1734 100644
--- a/pcsx2/GS/Renderers/Common/GSDevice.cpp
+++ b/pcsx2/GS/Renderers/Common/GSDevice.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../GS.h"
+#include "GS/GS.h"
 #include "GSDevice.h"
 
 GSDevice::GSDevice()
diff --git a/pcsx2/GS/Renderers/Common/GSDevice.h b/pcsx2/GS/Renderers/Common/GSDevice.h
index a5873b1d96..c42d217097 100644
--- a/pcsx2/GS/Renderers/Common/GSDevice.h
+++ b/pcsx2/GS/Renderers/Common/GSDevice.h
@@ -16,10 +16,10 @@
 #pragma once
 
 #include "GSFastList.h"
-#include "../../Window/GSWnd.h"
+#include "GS/Window/GSWnd.h"
 #include "GSTexture.h"
 #include "GSVertex.h"
-#include "../../GSAlignedClass.h"
+#include "GS/GSAlignedClass.h"
 #include "GSOsdManager.h"
 
 enum ShaderConvert
diff --git a/pcsx2/GS/Renderers/Common/GSDirtyRect.h b/pcsx2/GS/Renderers/Common/GSDirtyRect.h
index e1c52e3157..24807c51c8 100644
--- a/pcsx2/GS/Renderers/Common/GSDirtyRect.h
+++ b/pcsx2/GS/Renderers/Common/GSDirtyRect.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../../GSLocalMemory.h"
+#include "GS/GSLocalMemory.h"
 
 class GSDirtyRect
 {
diff --git a/pcsx2/GS/Renderers/Common/GSFastList.h b/pcsx2/GS/Renderers/Common/GSFastList.h
index eb5b4c1bdb..184542aa47 100644
--- a/pcsx2/GS/Renderers/Common/GSFastList.h
+++ b/pcsx2/GS/Renderers/Common/GSFastList.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../../GS_types.h"
+#include "GS/GS_types.h"
 
 template <class T>
 struct Element
diff --git a/pcsx2/GS/Renderers/Common/GSFunctionMap.h b/pcsx2/GS/Renderers/Common/GSFunctionMap.h
index 19128cac0d..adb7adf13c 100644
--- a/pcsx2/GS/Renderers/Common/GSFunctionMap.h
+++ b/pcsx2/GS/Renderers/Common/GSFunctionMap.h
@@ -15,10 +15,10 @@
 
 #pragma once
 
-#include "../../GS.h"
-#include "../../GSCodeBuffer.h"
+#include "GS/GS.h"
+#include "GS/GSCodeBuffer.h"
 
-#include "../SW/GSScanlineEnvironment.h"
+#include "GS/Renderers/SW/GSScanlineEnvironment.h"
 
 template <class KEY, class VALUE>
 class GSFunctionMap
diff --git a/pcsx2/GS/Renderers/Common/GSOsdManager.cpp b/pcsx2/GS/Renderers/Common/GSOsdManager.cpp
index b7b31719ac..24a2429fa8 100644
--- a/pcsx2/GS/Renderers/Common/GSOsdManager.cpp
+++ b/pcsx2/GS/Renderers/Common/GSOsdManager.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../GS.h"
+#include "GS/GS.h"
 #include "GSOsdManager.h"
 #ifdef _WIN32
 #include "resource.h"
diff --git a/pcsx2/GS/Renderers/Common/GSOsdManager.h b/pcsx2/GS/Renderers/Common/GSOsdManager.h
index 29b331e702..281508d953 100644
--- a/pcsx2/GS/Renderers/Common/GSOsdManager.h
+++ b/pcsx2/GS/Renderers/Common/GSOsdManager.h
@@ -16,7 +16,7 @@
 #pragma once
 
 #include "PrecompiledHeader.h"
-#include "../../GSVector.h"
+#include "GS/GSVector.h"
 #include "GSVertex.h"
 #include "GSTexture.h"
 #include <ft2build.h>
diff --git a/pcsx2/GS/Renderers/Common/GSRenderer.h b/pcsx2/GS/Renderers/Common/GSRenderer.h
index 670bcb7158..e12853e659 100644
--- a/pcsx2/GS/Renderers/Common/GSRenderer.h
+++ b/pcsx2/GS/Renderers/Common/GSRenderer.h
@@ -15,10 +15,10 @@
 
 #pragma once
 
-#include "../../GS.h"
-#include "../../Window/GSWnd.h"
-#include "../../GSState.h"
-#include "../../GSCapture.h"
+#include "GS/GS.h"
+#include "GS/Window/GSWnd.h"
+#include "GS/GSState.h"
+#include "GS/GSCapture.h"
 
 class GSRenderer : public GSState
 {
diff --git a/pcsx2/GS/Renderers/Common/GSTexture.h b/pcsx2/GS/Renderers/Common/GSTexture.h
index a9a9a2d862..81a2046fb9 100644
--- a/pcsx2/GS/Renderers/Common/GSTexture.h
+++ b/pcsx2/GS/Renderers/Common/GSTexture.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../../GSVector.h"
+#include "GS/GSVector.h"
 
 class GSTexture
 {
diff --git a/pcsx2/GS/Renderers/Common/GSVertex.h b/pcsx2/GS/Renderers/Common/GSVertex.h
index 529ed22733..d38f72dbfd 100644
--- a/pcsx2/GS/Renderers/Common/GSVertex.h
+++ b/pcsx2/GS/Renderers/Common/GSVertex.h
@@ -15,10 +15,10 @@
 
 #pragma once
 
-#include "../../GS.h"
-#include "../../GSVector.h"
-#include "../HW/GSVertexHW.h"
-#include "../SW/GSVertexSW.h"
+#include "GS/GS.h"
+#include "GS/GSVector.h"
+#include "GS/Renderers/HW/GSVertexHW.h"
+#include "GS/Renderers/SW/GSVertexSW.h"
 
 #pragma pack(push, 1)
 
diff --git a/pcsx2/GS/Renderers/Common/GSVertexTrace.cpp b/pcsx2/GS/Renderers/Common/GSVertexTrace.cpp
index 6bd18ee9d8..306dffa316 100644
--- a/pcsx2/GS/Renderers/Common/GSVertexTrace.cpp
+++ b/pcsx2/GS/Renderers/Common/GSVertexTrace.cpp
@@ -15,8 +15,8 @@
 
 #include "PrecompiledHeader.h"
 #include "GSVertexTrace.h"
-#include "../../GSUtil.h"
-#include "../../GSState.h"
+#include "GS/GSUtil.h"
+#include "GS/GSState.h"
 
 CONSTINIT const GSVector4 GSVertexTrace::s_minmax = GSVector4::cxpr(FLT_MAX, -FLT_MAX, 0.f, 0.f);
 
diff --git a/pcsx2/GS/Renderers/Common/GSVertexTrace.h b/pcsx2/GS/Renderers/Common/GSVertexTrace.h
index a132e03dda..ba86ceb9c9 100644
--- a/pcsx2/GS/Renderers/Common/GSVertexTrace.h
+++ b/pcsx2/GS/Renderers/Common/GSVertexTrace.h
@@ -15,10 +15,10 @@
 
 #pragma once
 
-#include "../../GSDrawingContext.h"
+#include "GS/GSDrawingContext.h"
 #include "GSVertex.h"
-#include "../SW/GSVertexSW.h"
-#include "../HW/GSVertexHW.h"
+#include "GS/Renderers/SW/GSVertexSW.h"
+#include "GS/Renderers/HW/GSVertexHW.h"
 #include "GSFunctionMap.h"
 
 class GSState;
diff --git a/pcsx2/GS/Renderers/HW/GSHwHack.cpp b/pcsx2/GS/Renderers/HW/GSHwHack.cpp
index 647206250b..f229d0558d 100644
--- a/pcsx2/GS/Renderers/HW/GSHwHack.cpp
+++ b/pcsx2/GS/Renderers/HW/GSHwHack.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../../GSState.h"
+#include "GS/GSState.h"
 #include "GS.h"
 
 bool s_nativeres;
diff --git a/pcsx2/GS/Renderers/HW/GSRendererHW.h b/pcsx2/GS/Renderers/HW/GSRendererHW.h
index aeb121c692..bd050f9858 100644
--- a/pcsx2/GS/Renderers/HW/GSRendererHW.h
+++ b/pcsx2/GS/Renderers/HW/GSRendererHW.h
@@ -16,8 +16,8 @@
 #pragma once
 
 #include "GSTextureCache.h"
-#include "../Common/GSFunctionMap.h"
-#include "../../GSState.h"
+#include "GS/Renderers/Common/GSFunctionMap.h"
+#include "GS/GSState.h"
 
 class GSRendererHW : public GSRenderer
 {
diff --git a/pcsx2/GS/Renderers/HW/GSTextureCache.cpp b/pcsx2/GS/Renderers/HW/GSTextureCache.cpp
index 39177a3cb4..92f97d01c3 100644
--- a/pcsx2/GS/Renderers/HW/GSTextureCache.cpp
+++ b/pcsx2/GS/Renderers/HW/GSTextureCache.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSTextureCache.h"
 #include "GSRendererHW.h"
-#include "../../GSUtil.h"
+#include "GS/GSUtil.h"
 
 bool GSTextureCache::m_disable_partial_invalidation = false;
 bool GSTextureCache::m_wrap_gs_mem = false;
diff --git a/pcsx2/GS/Renderers/HW/GSTextureCache.h b/pcsx2/GS/Renderers/HW/GSTextureCache.h
index 28699dfc70..a4ada3bd8e 100644
--- a/pcsx2/GS/Renderers/HW/GSTextureCache.h
+++ b/pcsx2/GS/Renderers/HW/GSTextureCache.h
@@ -15,9 +15,9 @@
 
 #pragma once
 
-#include "../Common/GSRenderer.h"
-#include "../Common/GSFastList.h"
-#include "../Common/GSDirtyRect.h"
+#include "GS/Renderers/Common/GSRenderer.h"
+#include "GS/Renderers/Common/GSFastList.h"
+#include "GS/Renderers/Common/GSDirtyRect.h"
 
 class GSTextureCache
 {
diff --git a/pcsx2/GS/Renderers/HW/GSVertexHW.h b/pcsx2/GS/Renderers/HW/GSVertexHW.h
index f75a93f79c..efa8d2390d 100644
--- a/pcsx2/GS/Renderers/HW/GSVertexHW.h
+++ b/pcsx2/GS/Renderers/HW/GSVertexHW.h
@@ -15,8 +15,8 @@
 
 #pragma once
 
-#include "../../GS.h"
-#include "../../GSVector.h"
+#include "GS/GS.h"
+#include "GS/GSVector.h"
 
 #pragma pack(push, 1)
 
diff --git a/pcsx2/GS/Renderers/Null/GSDeviceNull.h b/pcsx2/GS/Renderers/Null/GSDeviceNull.h
index 613abfdc88..a831e79348 100644
--- a/pcsx2/GS/Renderers/Null/GSDeviceNull.h
+++ b/pcsx2/GS/Renderers/Null/GSDeviceNull.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../Common/GSDevice.h"
+#include "GS/Renderers/Common/GSDevice.h"
 #include "GSTextureNull.h"
 
 class GSDeviceNull : public GSDevice
diff --git a/pcsx2/GS/Renderers/Null/GSRendererNull.h b/pcsx2/GS/Renderers/Null/GSRendererNull.h
index b8010dee53..2169cc0d2d 100644
--- a/pcsx2/GS/Renderers/Null/GSRendererNull.h
+++ b/pcsx2/GS/Renderers/Null/GSRendererNull.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../Common/GSRenderer.h"
+#include "GS/Renderers/Common/GSRenderer.h"
 
 class GSRendererNull : public GSRenderer
 {
diff --git a/pcsx2/GS/Renderers/Null/GSTextureNull.h b/pcsx2/GS/Renderers/Null/GSTextureNull.h
index 0a55245503..9c4d4a8f96 100644
--- a/pcsx2/GS/Renderers/Null/GSTextureNull.h
+++ b/pcsx2/GS/Renderers/Null/GSTextureNull.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../Common/GSTexture.h"
+#include "GS/Renderers/Common/GSTexture.h"
 
 class GSTextureNull : public GSTexture
 {
diff --git a/pcsx2/GS/Renderers/OpenGL/GLState.h b/pcsx2/GS/Renderers/OpenGL/GLState.h
index 06ff9fbfab..c6d8abfa81 100644
--- a/pcsx2/GS/Renderers/OpenGL/GLState.h
+++ b/pcsx2/GS/Renderers/OpenGL/GLState.h
@@ -15,8 +15,8 @@
 
 #pragma once
 
-#include "../../GS.h"
-#include "../../GSVector.h"
+#include "GS/GS.h"
+#include "GS/GSVector.h"
 
 namespace GLState
 {
diff --git a/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.cpp b/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.cpp
index c0ebb87a8e..969ba1dcbd 100644
--- a/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.cpp
+++ b/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.cpp
@@ -14,10 +14,10 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../../GSState.h"
+#include "GS/GSState.h"
 #include "GSDeviceOGL.h"
 #include "GLState.h"
-#include "../../GSUtil.h"
+#include "GS/GSUtil.h"
 #include <fstream>
 
 //#define ONLY_LINES
diff --git a/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.h b/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.h
index 2f00735137..4c2b9e4577 100644
--- a/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.h
+++ b/pcsx2/GS/Renderers/OpenGL/GSDeviceOGL.h
@@ -15,9 +15,9 @@
 
 #pragma once
 
-#include "../Common/GSDevice.h"
+#include "GS/Renderers/Common/GSDevice.h"
 #include "GSTextureOGL.h"
-#include "../../GS.h"
+#include "GS/GS.h"
 #include "GSVertexArrayOGL.h"
 #include "GSUniformBufferOGL.h"
 #include "GSShaderOGL.h"
diff --git a/pcsx2/GS/Renderers/OpenGL/GSRendererOGL.h b/pcsx2/GS/Renderers/OpenGL/GSRendererOGL.h
index 0e142ce8d9..b48fca67eb 100644
--- a/pcsx2/GS/Renderers/OpenGL/GSRendererOGL.h
+++ b/pcsx2/GS/Renderers/OpenGL/GSRendererOGL.h
@@ -15,9 +15,9 @@
 
 #pragma once
 
-#include "../HW/GSRendererHW.h"
+#include "GS/Renderers/HW/GSRendererHW.h"
 #include "GSTextureCacheOGL.h"
-#include "../HW/GSVertexHW.h"
+#include "GS/Renderers/HW/GSVertexHW.h"
 
 class GSRendererOGL final : public GSRendererHW
 {
diff --git a/pcsx2/GS/Renderers/OpenGL/GSTextureCacheOGL.h b/pcsx2/GS/Renderers/OpenGL/GSTextureCacheOGL.h
index 23ea5de3c4..e4903a2a9a 100644
--- a/pcsx2/GS/Renderers/OpenGL/GSTextureCacheOGL.h
+++ b/pcsx2/GS/Renderers/OpenGL/GSTextureCacheOGL.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../HW/GSTextureCache.h"
+#include "GS/Renderers/HW/GSTextureCache.h"
 #include "GSDeviceOGL.h"
 
 class GSTextureCacheOGL final : public GSTextureCache
diff --git a/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.cpp b/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.cpp
index 1d60649c4e..efba2677dc 100644
--- a/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.cpp
+++ b/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.cpp
@@ -17,7 +17,7 @@
 #include <limits.h>
 #include "GSTextureOGL.h"
 #include "GLState.h"
-#include "../../GSPng.h"
+#include "GS/GSPng.h"
 
 #ifdef ENABLE_OGL_DEBUG_MEM_BW
 extern uint64 g_real_texture_upload_byte;
diff --git a/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.h b/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.h
index 1bf515e156..4fdc275f68 100644
--- a/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.h
+++ b/pcsx2/GS/Renderers/OpenGL/GSTextureOGL.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../Common/GSTexture.h"
+#include "GS/Renderers/Common/GSTexture.h"
 #include "GS.h"
 
 namespace PboPool
diff --git a/pcsx2/GS/Renderers/OpenGL/GSVertexArrayOGL.h b/pcsx2/GS/Renderers/OpenGL/GSVertexArrayOGL.h
index 178404777d..43a8d57736 100644
--- a/pcsx2/GS/Renderers/OpenGL/GSVertexArrayOGL.h
+++ b/pcsx2/GS/Renderers/OpenGL/GSVertexArrayOGL.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../../config.h"
+#include "GS/config.h"
 
 #ifdef ENABLE_OGL_DEBUG_MEM_BW
 extern uint64 g_vertex_upload_byte;
diff --git a/pcsx2/GS/Renderers/SW/GSDrawScanline.h b/pcsx2/GS/Renderers/SW/GSDrawScanline.h
index af59043a6a..7ec8354259 100644
--- a/pcsx2/GS/Renderers/SW/GSDrawScanline.h
+++ b/pcsx2/GS/Renderers/SW/GSDrawScanline.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../../GSState.h"
+#include "GS/GSState.h"
 #include "GSRasterizer.h"
 #include "GSScanlineEnvironment.h"
 #include "GSSetupPrimCodeGenerator.h"
diff --git a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.h b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.h
index 828b73bffc..3140546651 100644
--- a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.h
+++ b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.h
@@ -16,8 +16,8 @@
 #pragma once
 
 #include "GSScanlineEnvironment.h"
-#include "../Common/GSFunctionMap.h"
-#include "../../GSUtil.h"
+#include "GS/Renderers/Common/GSFunctionMap.h"
+#include "GS/GSUtil.h"
 
 #if defined(_M_AMD64) || defined(_WIN64)
 #define RegLong Xbyak::Reg64
diff --git a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx.cpp b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx.cpp
index a4354051c0..eb3be1a385 100644
--- a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx.cpp
+++ b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSDrawScanlineCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #undef _t
 
diff --git a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx2.cpp b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx2.cpp
index 7a866f1a8e..27ab2d8ce0 100644
--- a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx2.cpp
+++ b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x64.avx2.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSDrawScanlineCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #undef _t
 
diff --git a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx.cpp b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx.cpp
index a4683efe02..33c468f912 100644
--- a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx.cpp
+++ b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSDrawScanlineCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE < 0x501 && !(defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx2.cpp b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx2.cpp
index 2e7a8fcbc6..7c14c55d8f 100644
--- a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx2.cpp
+++ b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.avx2.cpp
@@ -16,8 +16,8 @@
 #include "PrecompiledHeader.h"
 #include "GSDrawScanlineCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
-#include "../../GSVector.h"
+#include "GS/GS_codegen.h"
+#include "GS/GSVector.h"
 
 #if _M_SSE >= 0x501 && !(defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.cpp b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.cpp
index c34290983c..fa0cccd76a 100644
--- a/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.cpp
+++ b/pcsx2/GS/Renderers/SW/GSDrawScanlineCodeGenerator.x86.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSDrawScanlineCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE < 0x501 && !(defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSRasterizer.h b/pcsx2/GS/Renderers/SW/GSRasterizer.h
index 40d8ecb141..be85d7b987 100644
--- a/pcsx2/GS/Renderers/SW/GSRasterizer.h
+++ b/pcsx2/GS/Renderers/SW/GSRasterizer.h
@@ -17,10 +17,10 @@
 
 #include "GS.h"
 #include "GSVertexSW.h"
-#include "../Common/GSFunctionMap.h"
-#include "../../GSAlignedClass.h"
-#include "../../GSPerfMon.h"
-#include "../../GSThread_CXX11.h"
+#include "GS/Renderers/Common/GSFunctionMap.h"
+#include "GS/GSAlignedClass.h"
+#include "GS/GSPerfMon.h"
+#include "GS/GSThread_CXX11.h"
 
 class alignas(32) GSRasterizerData : public GSAlignedClass<32>
 {
diff --git a/pcsx2/GS/Renderers/SW/GSScanlineEnvironment.h b/pcsx2/GS/Renderers/SW/GSScanlineEnvironment.h
index 34a0f9259a..65902a2f16 100644
--- a/pcsx2/GS/Renderers/SW/GSScanlineEnvironment.h
+++ b/pcsx2/GS/Renderers/SW/GSScanlineEnvironment.h
@@ -15,8 +15,8 @@
 
 #pragma once
 
-#include "../../GSLocalMemory.h"
-#include "../../GSVector.h"
+#include "GS/GSLocalMemory.h"
+#include "GS/GSVector.h"
 
 union GSScanlineSelector
 {
diff --git a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.h b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.h
index 7fbdad3c63..2bda1b0777 100644
--- a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.h
+++ b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.h
@@ -16,8 +16,8 @@
 #pragma once
 
 #include "GSScanlineEnvironment.h"
-#include "../Common/GSFunctionMap.h"
-#include "../../GSUtil.h"
+#include "GS/Renderers/Common/GSFunctionMap.h"
+#include "GS/GSUtil.h"
 
 class GSSetupPrimCodeGenerator : public GSCodeGenerator
 {
diff --git a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx.cpp b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx.cpp
index 33fd508b5b..d965b49bc8 100644
--- a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx.cpp
+++ b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSSetupPrimCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE < 0x501 && (defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx2.cpp b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx2.cpp
index 54b269f1fa..916f4e682b 100644
--- a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx2.cpp
+++ b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.avx2.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSSetupPrimCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE >= 0x501 && (defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.cpp b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.cpp
index 2839cde144..3a12b46106 100644
--- a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.cpp
+++ b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x64.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSSetupPrimCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE < 0x501 && (defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx.cpp b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx.cpp
index 3f02f90576..555abda7a7 100644
--- a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx.cpp
+++ b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSSetupPrimCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE < 0x501 && !(defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx2.cpp b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx2.cpp
index c7cd66ef5a..a3f9ee653d 100644
--- a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx2.cpp
+++ b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.avx2.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSSetupPrimCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE >= 0x501 && !(defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.cpp b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.cpp
index 01b5313ac5..0b70d8ffc7 100644
--- a/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.cpp
+++ b/pcsx2/GS/Renderers/SW/GSSetupPrimCodeGenerator.x86.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "GSSetupPrimCodeGenerator.h"
 #include "GSVertexSW.h"
-#include "../../GS_codegen.h"
+#include "GS/GS_codegen.h"
 
 #if _M_SSE < 0x501 && !(defined(_M_AMD64) || defined(_WIN64))
 
diff --git a/pcsx2/GS/Renderers/SW/GSTextureCacheSW.h b/pcsx2/GS/Renderers/SW/GSTextureCacheSW.h
index 2a873a44de..85e909b2d1 100644
--- a/pcsx2/GS/Renderers/SW/GSTextureCacheSW.h
+++ b/pcsx2/GS/Renderers/SW/GSTextureCacheSW.h
@@ -15,8 +15,8 @@
 
 #pragma once
 
-#include "../Common/GSRenderer.h"
-#include "../Common/GSFastList.h"
+#include "GS/Renderers/Common/GSRenderer.h"
+#include "GS/Renderers/Common/GSFastList.h"
 
 class GSTextureCacheSW
 {
diff --git a/pcsx2/GS/Renderers/SW/GSTextureSW.cpp b/pcsx2/GS/Renderers/SW/GSTextureSW.cpp
index e862369939..e072bf1832 100644
--- a/pcsx2/GS/Renderers/SW/GSTextureSW.cpp
+++ b/pcsx2/GS/Renderers/SW/GSTextureSW.cpp
@@ -15,7 +15,7 @@
 
 #include "PrecompiledHeader.h"
 #include "GSTextureSW.h"
-#include "../../GSPng.h"
+#include "GS/GSPng.h"
 
 GSTextureSW::GSTextureSW(int type, int width, int height)
 {
diff --git a/pcsx2/GS/Renderers/SW/GSTextureSW.h b/pcsx2/GS/Renderers/SW/GSTextureSW.h
index 562e1df074..34be679311 100644
--- a/pcsx2/GS/Renderers/SW/GSTextureSW.h
+++ b/pcsx2/GS/Renderers/SW/GSTextureSW.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../Common/GSTexture.h"
+#include "GS/Renderers/Common/GSTexture.h"
 
 class GSTextureSW final : public GSTexture
 {
diff --git a/pcsx2/GS/Renderers/SW/GSVertexSW.h b/pcsx2/GS/Renderers/SW/GSVertexSW.h
index cf7ba931a5..6b3d5a29dd 100644
--- a/pcsx2/GS/Renderers/SW/GSVertexSW.h
+++ b/pcsx2/GS/Renderers/SW/GSVertexSW.h
@@ -15,7 +15,7 @@
 
 #pragma once
 
-#include "../../GSVector.h"
+#include "GS/GSVector.h"
 
 struct alignas(32) GSVertexSW
 {
diff --git a/pcsx2/GS/Window/GSWnd.h b/pcsx2/GS/Window/GSWnd.h
index fc9fc11569..535b6cf99e 100644
--- a/pcsx2/GS/Window/GSWnd.h
+++ b/pcsx2/GS/Window/GSWnd.h
@@ -16,8 +16,8 @@
 #pragma once
 
 #include "PrecompiledHeader.h"
-#include "../GS.h"
-#include "../GSVector.h"
+#include "GS/GS.h"
+#include "GS/GSVector.h"
 
 class GSWnd
 {
diff --git a/pcsx2/Interpreter.cpp b/pcsx2/Interpreter.cpp
index 36e40ef621..1f51f12ff0 100644
--- a/pcsx2/Interpreter.cpp
+++ b/pcsx2/Interpreter.cpp
@@ -23,7 +23,7 @@
 
 #include "Elfheader.h"
 
-#include "../DebugTools/Breakpoints.h"
+#include "DebugTools/Breakpoints.h"
 
 #include <float.h>
 
diff --git a/pcsx2/Linux/LnxKeyCodes.cpp b/pcsx2/Linux/LnxKeyCodes.cpp
index 55f513ce81..5a2a834884 100644
--- a/pcsx2/Linux/LnxKeyCodes.cpp
+++ b/pcsx2/Linux/LnxKeyCodes.cpp
@@ -13,7 +13,7 @@
  *  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../PrecompiledHeader.h"
+#include "PrecompiledHeader.h"
 #include "ConsoleLogger.h"
 
 #include <gdk/gdkkeysyms.h>
diff --git a/pcsx2/PAD/Linux/SDL/joystick.h b/pcsx2/PAD/Linux/SDL/joystick.h
index d37a96c217..72ed99c2b3 100644
--- a/pcsx2/PAD/Linux/SDL/joystick.h
+++ b/pcsx2/PAD/Linux/SDL/joystick.h
@@ -18,9 +18,9 @@
 #include <SDL.h>
 #include <SDL_haptic.h>
 
-#include "../GamePad.h"
-#include "../PAD.h"
-#include "../controller.h"
+#include "PAD/Linux/GamePad.h"
+#include "PAD/Linux/PAD.h"
+#include "PAD/Linux/controller.h"
 #define NB_EFFECT 2 // Don't use more than two, ps2 only has one for big motor and one for small(like most systems)
 // holds all joystick info
 class JoystickInfo : public GamePad
diff --git a/pcsx2/PAD/Linux/wx_dialog/GamepadConfiguration.h b/pcsx2/PAD/Linux/wx_dialog/GamepadConfiguration.h
index aa4d65c0b4..bc9fa1cb1b 100644
--- a/pcsx2/PAD/Linux/wx_dialog/GamepadConfiguration.h
+++ b/pcsx2/PAD/Linux/wx_dialog/GamepadConfiguration.h
@@ -20,9 +20,9 @@
 
 #include <wx/wx.h>
 
-#include "../GamePad.h"
-#include "../keyboard.h"
-#include "../PAD.h"
+#include "PAD/Linux/GamePad.h"
+#include "PAD/Linux/keyboard.h"
+#include "PAD/Linux/PAD.h"
 
 static const s32 rumble_slider_id = wxID_HIGHEST + 200 + 1;
 static const s32 joy_slider_id = wxID_HIGHEST + 200 + 2;
diff --git a/pcsx2/PAD/Linux/wx_dialog/JoystickConfiguration.h b/pcsx2/PAD/Linux/wx_dialog/JoystickConfiguration.h
index 5d58a188c7..a396ff43c1 100644
--- a/pcsx2/PAD/Linux/wx_dialog/JoystickConfiguration.h
+++ b/pcsx2/PAD/Linux/wx_dialog/JoystickConfiguration.h
@@ -20,9 +20,9 @@
 
 #include <wx/wx.h>
 
-#include "../GamePad.h"
-#include "../keyboard.h"
-#include "../PAD.h"
+#include "PAD/Linux/GamePad.h"
+#include "PAD/Linux/keyboard.h"
+#include "PAD/Linux/PAD.h"
 
 class JoystickConfiguration : public wxDialog
 {
diff --git a/pcsx2/PAD/Linux/wx_dialog/dialog.h b/pcsx2/PAD/Linux/wx_dialog/dialog.h
index 810afb9f08..ea41f690d5 100644
--- a/pcsx2/PAD/Linux/wx_dialog/dialog.h
+++ b/pcsx2/PAD/Linux/wx_dialog/dialog.h
@@ -31,9 +31,9 @@
 #include <string>
 #include <sstream>
 
-#include "../GamePad.h"
-#include "../keyboard.h"
-#include "../PAD.h"
+#include "PAD/Linux/GamePad.h"
+#include "PAD/Linux/keyboard.h"
+#include "PAD/Linux/PAD.h"
 #include "opPanel.h"
 
 #include "GamepadConfiguration.h"
diff --git a/pcsx2/R3000A.cpp b/pcsx2/R3000A.cpp
index 248fe2f489..4c8074528a 100644
--- a/pcsx2/R3000A.cpp
+++ b/pcsx2/R3000A.cpp
@@ -19,7 +19,7 @@
 
 #include "Sio.h"
 #include "Sif.h"
-#include "../DebugTools/Breakpoints.h"
+#include "DebugTools/Breakpoints.h"
 #include "R5900OpcodeTables.h"
 
 using namespace R3000A;
diff --git a/pcsx2/R3000AInterpreter.cpp b/pcsx2/R3000AInterpreter.cpp
index 25e08cbffc..b906bd8695 100644
--- a/pcsx2/R3000AInterpreter.cpp
+++ b/pcsx2/R3000AInterpreter.cpp
@@ -19,7 +19,7 @@
 #include "App.h" // For host irx injection hack
 
 #include "R5900OpcodeTables.h"
-#include "../DebugTools/Breakpoints.h"
+#include "DebugTools/Breakpoints.h"
 
 using namespace R3000A;
 
diff --git a/pcsx2/R5900.cpp b/pcsx2/R5900.cpp
index 809c547122..6944cd6b4b 100644
--- a/pcsx2/R5900.cpp
+++ b/pcsx2/R5900.cpp
@@ -36,7 +36,7 @@
 #include "Patch.h"
 #include "GameDatabase.h"
 
-#include "../DebugTools/Breakpoints.h"
+#include "DebugTools/Breakpoints.h"
 #include "R5900OpcodeTables.h"
 
 using namespace R5900;	// for R5900 disasm tools
diff --git a/pcsx2/SPU2/Linux/Alsa.cpp b/pcsx2/SPU2/Linux/Alsa.cpp
index 47af27dae9..0d4ed4e55f 100644
--- a/pcsx2/SPU2/Linux/Alsa.cpp
+++ b/pcsx2/SPU2/Linux/Alsa.cpp
@@ -20,9 +20,9 @@
 #include "PrecompiledHeader.h"
 #include <alsa/asoundlib.h>
 
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Alsa.h"
-#include "../SndOut.h"
+#include "SPU2/SndOut.h"
 
 // Does not work, except as effectively a null plugin.
 class AlsaMod : public SndOutModule
diff --git a/pcsx2/SPU2/Linux/Config.cpp b/pcsx2/SPU2/Linux/Config.cpp
index 248f0f21ae..212ce685dd 100644
--- a/pcsx2/SPU2/Linux/Config.cpp
+++ b/pcsx2/SPU2/Linux/Config.cpp
@@ -14,14 +14,14 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 #include "Config.h"
 
 #if defined(__unix__) || defined(__APPLE__)
 #include <SDL.h>
 #include <SDL_audio.h>
-#include "../wx/wxConfig.h"
+#include "SPU2/wx/wxConfig.h"
 #endif
 
 int AutoDMAPlayRate[2] = {0, 0};
diff --git a/pcsx2/SPU2/Linux/ConfigDebug.cpp b/pcsx2/SPU2/Linux/ConfigDebug.cpp
index 345266f8e6..9438162c0d 100644
--- a/pcsx2/SPU2/Linux/ConfigDebug.cpp
+++ b/pcsx2/SPU2/Linux/ConfigDebug.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 #include "Config.h"
 #include "Utilities/Path.h"
diff --git a/pcsx2/SPU2/Linux/ConfigSoundTouch.cpp b/pcsx2/SPU2/Linux/ConfigSoundTouch.cpp
index eb6e6b07bc..7914b427c6 100644
--- a/pcsx2/SPU2/Linux/ConfigSoundTouch.cpp
+++ b/pcsx2/SPU2/Linux/ConfigSoundTouch.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 #include "Config.h"
 #include "soundtouch/SoundTouch.h"
diff --git a/pcsx2/SPU2/Linux/Dialogs.h b/pcsx2/SPU2/Linux/Dialogs.h
index 6f6992cf08..3176931116 100644
--- a/pcsx2/SPU2/Linux/Dialogs.h
+++ b/pcsx2/SPU2/Linux/Dialogs.h
@@ -16,8 +16,8 @@
 #ifndef DIALOG_H_INCLUDED
 #define DIALOG_H_INCLUDED
 
-#include "../Global.h"
-#include "../Config.h"
+#include "SPU2/Global.h"
+#include "SPU2/Config.h"
 
 namespace DebugConfig
 {
diff --git a/pcsx2/SPU2/Windows/CfgHelpers.cpp b/pcsx2/SPU2/Windows/CfgHelpers.cpp
index 29d1a508c1..cea3492f4e 100644
--- a/pcsx2/SPU2/Windows/CfgHelpers.cpp
+++ b/pcsx2/SPU2/Windows/CfgHelpers.cpp
@@ -15,7 +15,7 @@
 
 #include "PrecompiledHeader.h"
 #include "AppConfig.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 
 #include "Utilities/StringHelpers.h"
diff --git a/pcsx2/SPU2/Windows/Config.cpp b/pcsx2/SPU2/Windows/Config.cpp
index 9bd4f7ff43..bbf7a2bb07 100644
--- a/pcsx2/SPU2/Windows/Config.cpp
+++ b/pcsx2/SPU2/Windows/Config.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 #include "Config.h"
 #include <math.h>
diff --git a/pcsx2/SPU2/Windows/ConfigDebug.cpp b/pcsx2/SPU2/Windows/ConfigDebug.cpp
index 051244b14d..6c3da3e811 100644
--- a/pcsx2/SPU2/Windows/ConfigDebug.cpp
+++ b/pcsx2/SPU2/Windows/ConfigDebug.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 #include "Utilities\Path.h"
 
diff --git a/pcsx2/SPU2/Windows/ConfigSoundtouch.cpp b/pcsx2/SPU2/Windows/ConfigSoundtouch.cpp
index ed86a88f03..b76c259b4d 100644
--- a/pcsx2/SPU2/Windows/ConfigSoundtouch.cpp
+++ b/pcsx2/SPU2/Windows/ConfigSoundtouch.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 
 #include "soundtouch/SoundTouch.h"
diff --git a/pcsx2/SPU2/Windows/RealtimeDebugger.cpp b/pcsx2/SPU2/Windows/RealtimeDebugger.cpp
index 4f05090cf0..7b25e04867 100644
--- a/pcsx2/SPU2/Windows/RealtimeDebugger.cpp
+++ b/pcsx2/SPU2/Windows/RealtimeDebugger.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 
 bool debugDialogOpen = false;
diff --git a/pcsx2/SPU2/Windows/SndOut_XAudio2.cpp b/pcsx2/SPU2/Windows/SndOut_XAudio2.cpp
index 79761b94ee..2e676a30fe 100644
--- a/pcsx2/SPU2/Windows/SndOut_XAudio2.cpp
+++ b/pcsx2/SPU2/Windows/SndOut_XAudio2.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 
 #undef _WIN32_WINNT
diff --git a/pcsx2/SPU2/Windows/SndOut_waveOut.cpp b/pcsx2/SPU2/Windows/SndOut_waveOut.cpp
index 0e397141a9..e601c0f56a 100644
--- a/pcsx2/SPU2/Windows/SndOut_waveOut.cpp
+++ b/pcsx2/SPU2/Windows/SndOut_waveOut.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 
 
diff --git a/pcsx2/SPU2/Windows/UIHelpers.cpp b/pcsx2/SPU2/Windows/UIHelpers.cpp
index 5a69407944..22c1a6c8e6 100644
--- a/pcsx2/SPU2/Windows/UIHelpers.cpp
+++ b/pcsx2/SPU2/Windows/UIHelpers.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "Dialogs.h"
 
 int SendDialogMsg(HWND hwnd, int dlgId, UINT code, WPARAM wParam, LPARAM lParam)
diff --git a/pcsx2/SPU2/Windows/dsp.cpp b/pcsx2/SPU2/Windows/dsp.cpp
index 0fcd6c0926..c7c72c1891 100644
--- a/pcsx2/SPU2/Windows/dsp.cpp
+++ b/pcsx2/SPU2/Windows/dsp.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Global.h"
+#include "SPU2/Global.h"
 
 #define _WIN32_WINNT 0x0600
 #include <windows.h>
diff --git a/pcsx2/SPU2/wx/wxConfig.cpp b/pcsx2/SPU2/wx/wxConfig.cpp
index e24b95c82d..ff72d6c24a 100644
--- a/pcsx2/SPU2/wx/wxConfig.cpp
+++ b/pcsx2/SPU2/wx/wxConfig.cpp
@@ -14,11 +14,11 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../Config.h"
+#include "SPU2/Config.h"
 #if defined(__linux__) || defined(__APPLE__)
-#include "../Linux/Config.h"
+#include "SPU2/Linux/Config.h"
 #endif
-#include "../Global.h"
+#include "SPU2/Global.h"
 #include "wxConfig.h"
 
 MixerTab::MixerTab(wxWindow* parent)
diff --git a/pcsx2/System/SysCoreThread.cpp b/pcsx2/System/SysCoreThread.cpp
index c137b5c023..5a912a2a67 100644
--- a/pcsx2/System/SysCoreThread.cpp
+++ b/pcsx2/System/SysCoreThread.cpp
@@ -37,8 +37,8 @@
 #include "PAD/Linux/PAD.h"
 #endif
 
-#include "../DebugTools/MIPSAnalyst.h"
-#include "../DebugTools/SymbolMap.h"
+#include "DebugTools/MIPSAnalyst.h"
+#include "DebugTools/SymbolMap.h"
 
 #include "Utilities/PageFaultSource.h"
 #include "Utilities/Threading.h"
diff --git a/pcsx2/USB/Win32/Config_usb.cpp b/pcsx2/USB/Win32/Config_usb.cpp
index 80bf4fb8fd..94d88451fc 100644
--- a/pcsx2/USB/Win32/Config_usb.cpp
+++ b/pcsx2/USB/Win32/Config_usb.cpp
@@ -15,14 +15,14 @@
 
 #include "PrecompiledHeader.h"
 #include "AppCoreThread.h"
-#include "../USB.h"
+#include "USB/USB.h"
 #include "resource_usb.h"
 #include "Config_usb.h"
-#include "../deviceproxy.h"
-#include "../usb-pad/padproxy.h"
-#include "../usb-mic/audiodeviceproxy.h"
-#include "../configuration.h"
-#include "../shared/inifile_usb.h"
+#include "USB/deviceproxy.h"
+#include "USB/usb-pad/padproxy.h"
+#include "USB/usb-mic/audiodeviceproxy.h"
+#include "USB/configuration.h"
+#include "USB/shared/inifile_usb.h"
 
 HINSTANCE hInstUSB;
 
diff --git a/pcsx2/USB/linux/config-gtk.cpp b/pcsx2/USB/linux/config-gtk.cpp
index 7e4acbffe4..3700621844 100644
--- a/pcsx2/USB/linux/config-gtk.cpp
+++ b/pcsx2/USB/linux/config-gtk.cpp
@@ -21,15 +21,15 @@
 #include <vector>
 #include <string>
 #include "AppCoreThread.h"
-#include "../gtk.h"
+#include "USB/gtk.h"
 
-#include "../configuration.h"
-#include "../deviceproxy.h"
-#include "../usb-pad/padproxy.h"
-#include "../usb-mic/audiodeviceproxy.h"
+#include "USB/configuration.h"
+#include "USB/deviceproxy.h"
+#include "USB/usb-pad/padproxy.h"
+#include "USB/usb-mic/audiodeviceproxy.h"
 
 #include "config.h"
-#include "../USB.h"
+#include "USB/USB.h"
 
 struct SettingsCB
 {
diff --git a/pcsx2/USB/linux/config.cpp b/pcsx2/USB/linux/config.cpp
index 468414053d..bafd2e65c2 100644
--- a/pcsx2/USB/linux/config.cpp
+++ b/pcsx2/USB/linux/config.cpp
@@ -15,10 +15,10 @@
 
 #include "config.h"
 
-#include "../configuration.h"
-#include "../deviceproxy.h"
-#include "../usb-pad/padproxy.h"
-#include "../usb-mic/audiodeviceproxy.h"
+#include "USB/configuration.h"
+#include "USB/deviceproxy.h"
+#include "USB/usb-pad/padproxy.h"
+#include "USB/usb-mic/audiodeviceproxy.h"
 #include "Utilities/Console.h"
 
 void SysMessage_stderr(const char* fmt, ...)
diff --git a/pcsx2/USB/qemu-usb/core.cpp b/pcsx2/USB/qemu-usb/core.cpp
index c149487438..c9acd9b62c 100644
--- a/pcsx2/USB/qemu-usb/core.cpp
+++ b/pcsx2/USB/qemu-usb/core.cpp
@@ -25,7 +25,7 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../platcompat.h"
+#include "USB/platcompat.h"
 #include "vl.h"
 #include "iov.h"
 //#include "trace.h"
diff --git a/pcsx2/USB/qemu-usb/desc.h b/pcsx2/USB/qemu-usb/desc.h
index a17675dc4f..1df5e974b2 100644
--- a/pcsx2/USB/qemu-usb/desc.h
+++ b/pcsx2/USB/qemu-usb/desc.h
@@ -17,7 +17,7 @@
 
 #include <wchar.h>
 #include <vector>
-#include "../platcompat.h"
+#include "USB/platcompat.h"
 
 /* binary representation */
 PACK(
diff --git a/pcsx2/USB/qemu-usb/iov.h b/pcsx2/USB/qemu-usb/iov.h
index acb3f5b8e1..6798b7eff8 100644
--- a/pcsx2/USB/qemu-usb/iov.h
+++ b/pcsx2/USB/qemu-usb/iov.h
@@ -11,7 +11,7 @@
  * the COPYING file in the top-level directory.
  */
 
-#include "../platcompat.h"
+#include "USB/platcompat.h"
 
 #ifndef IOV_H
 #define IOV_H
diff --git a/pcsx2/USB/shared/rawinput_usb.cpp b/pcsx2/USB/shared/rawinput_usb.cpp
index 6f11c2ab4e..cd589c8eb6 100644
--- a/pcsx2/USB/shared/rawinput_usb.cpp
+++ b/pcsx2/USB/shared/rawinput_usb.cpp
@@ -19,7 +19,7 @@
 #include <vector>
 #include <algorithm>
 #include <mutex>
-#include "../platcompat.h"
+#include "USB/platcompat.h"
 #include "PAD/Windows/WndProcEater.h"
 
 extern HINSTANCE hInst;
diff --git a/pcsx2/USB/usb-eyetoy/cam-linux.cpp b/pcsx2/USB/usb-eyetoy/cam-linux.cpp
index 584f633fcc..ea0b066d3d 100644
--- a/pcsx2/USB/usb-eyetoy/cam-linux.cpp
+++ b/pcsx2/USB/usb-eyetoy/cam-linux.cpp
@@ -17,7 +17,7 @@
 #include "usb-eyetoy-webcam.h"
 #include "jpgd/jpgd.h"
 #include "jo_mpeg.h"
-#include "../gtk.h"
+#include "USB/gtk.h"
 #include "Utilities/Console.h"
 
 #include <stdio.h>
diff --git a/pcsx2/USB/usb-eyetoy/cam-windows.cpp b/pcsx2/USB/usb-eyetoy/cam-windows.cpp
index 4c0bfb136e..1984931619 100644
--- a/pcsx2/USB/usb-eyetoy/cam-windows.cpp
+++ b/pcsx2/USB/usb-eyetoy/cam-windows.cpp
@@ -19,8 +19,8 @@
 #include "usb-eyetoy-webcam.h"
 #include "jo_mpeg.h"
 
-#include "../Win32/Config_usb.h"
-#include "../Win32/resource_usb.h"
+#include "USB/Win32/Config_usb.h"
+#include "USB/Win32/resource_usb.h"
 
 namespace usb_eyetoy
 {
diff --git a/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.cpp b/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.cpp
index fb87916939..ad9da21346 100644
--- a/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.cpp
+++ b/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.cpp
@@ -17,8 +17,8 @@
 #include "videodeviceproxy.h"
 #include "usb-eyetoy-webcam.h"
 #include "ov519.h"
-#include "../qemu-usb/desc.h"
-#include "../shared/inifile_usb.h"
+#include "USB/qemu-usb/desc.h"
+#include "USB/shared/inifile_usb.h"
 
 namespace usb_eyetoy
 {
diff --git a/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.h b/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.h
index 2c3bed2be1..bd060c0ea9 100644
--- a/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.h
+++ b/pcsx2/USB/usb-eyetoy/usb-eyetoy-webcam.h
@@ -16,9 +16,9 @@
 #ifndef USBEYETOYWEBCAM_H
 #define USBEYETOYWEBCAM_H
 
-#include "../qemu-usb/vl.h"
-#include "../configuration.h"
-#include "../deviceproxy.h"
+#include "USB/qemu-usb/vl.h"
+#include "USB/configuration.h"
+#include "USB/deviceproxy.h"
 #include "videodeviceproxy.h"
 #include <mutex>
 
diff --git a/pcsx2/USB/usb-eyetoy/videodev.h b/pcsx2/USB/usb-eyetoy/videodev.h
index 5458651517..2db5850a01 100644
--- a/pcsx2/USB/usb-eyetoy/videodev.h
+++ b/pcsx2/USB/usb-eyetoy/videodev.h
@@ -15,8 +15,8 @@
 
 #ifndef VIDEODEV_H
 #define VIDEODEV_H
-#include "../qemu-usb/vl.h"
-#include "../configuration.h"
+#include "USB/qemu-usb/vl.h"
+#include "USB/configuration.h"
 
 namespace usb_eyetoy
 {
diff --git a/pcsx2/USB/usb-eyetoy/videodeviceproxy.h b/pcsx2/USB/usb-eyetoy/videodeviceproxy.h
index 65d07136aa..379b2e6828 100644
--- a/pcsx2/USB/usb-eyetoy/videodeviceproxy.h
+++ b/pcsx2/USB/usb-eyetoy/videodeviceproxy.h
@@ -21,8 +21,8 @@
 #include <algorithm>
 #include <iterator>
 #include "videodev.h"
-#include "../helpers.h"
-#include "../deviceproxy.h"
+#include "USB/helpers.h"
+#include "USB/deviceproxy.h"
 
 namespace usb_eyetoy
 {
diff --git a/pcsx2/USB/usb-hid/evdev/evdev-gtk.cpp b/pcsx2/USB/usb-hid/evdev/evdev-gtk.cpp
index 3d3968d2b5..4bca91cb01 100644
--- a/pcsx2/USB/usb-hid/evdev/evdev-gtk.cpp
+++ b/pcsx2/USB/usb-hid/evdev/evdev-gtk.cpp
@@ -13,10 +13,10 @@
  *  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../usb-hid.h"
+#include "USB/usb-hid/usb-hid.h"
 #include "evdev.h"
 #include <linux/input.h>
-#include "../../gtk.h"
+#include "USB/gtk.h"
 #include <cstdio>
 #include <sstream>
 
diff --git a/pcsx2/USB/usb-hid/evdev/evdev.cpp b/pcsx2/USB/usb-hid/evdev/evdev.cpp
index 2117fe0aff..d6aaaccb39 100644
--- a/pcsx2/USB/usb-hid/evdev/evdev.cpp
+++ b/pcsx2/USB/usb-hid/evdev/evdev.cpp
@@ -16,8 +16,8 @@
 #include "evdev.h"
 #include <cassert>
 #include <sstream>
-#include "../hidproxy.h"
-#include "../../qemu-usb/input-keymap-linux-to-qcode.h"
+#include "USB/usb-hid/hidproxy.h"
+#include "USB/qemu-usb/input-keymap-linux-to-qcode.h"
 
 #ifdef USING_X11
 #include <X11/Xlib.h>
diff --git a/pcsx2/USB/usb-hid/evdev/evdev.h b/pcsx2/USB/usb-hid/evdev/evdev.h
index 206e407513..bad0e15420 100644
--- a/pcsx2/USB/usb-hid/evdev/evdev.h
+++ b/pcsx2/USB/usb-hid/evdev/evdev.h
@@ -14,8 +14,8 @@
  */
 
 #pragma once
-#include "../usb-hid.h"
-#include "../../linux/util.h"
+#include "USB/usb-hid/usb-hid.h"
+#include "USB/linux/util.h"
 #include "Utilities/Console.h"
 #include <linux/input.h>
 #include <unistd.h>
diff --git a/pcsx2/USB/usb-hid/hidproxy.h b/pcsx2/USB/usb-hid/hidproxy.h
index 86895fa0c9..08ae7673b5 100644
--- a/pcsx2/USB/usb-hid/hidproxy.h
+++ b/pcsx2/USB/usb-hid/hidproxy.h
@@ -21,8 +21,8 @@
 #include <algorithm>
 #include <iterator>
 #include "usb-hid.h"
-#include "../helpers.h"
-#include "../deviceproxy.h"
+#include "USB/helpers.h"
+#include "USB/deviceproxy.h"
 
 namespace usb_hid
 {
diff --git a/pcsx2/USB/usb-hid/raw/rawinput.cpp b/pcsx2/USB/usb-hid/raw/rawinput.cpp
index d636f86977..26c7d398cc 100644
--- a/pcsx2/USB/usb-hid/raw/rawinput.cpp
+++ b/pcsx2/USB/usb-hid/raw/rawinput.cpp
@@ -15,9 +15,9 @@
 
 #include "PrecompiledHeader.h"
 #include "rawinput.h"
-#include "../../Win32/Config_usb.h"
-#include "../../qemu-usb/input-keymap.h"
-#include "../../qemu-usb/input-keymap-win32-to-qcode.h"
+#include "USB/Win32/Config_usb.h"
+#include "USB/qemu-usb/input-keymap.h"
+#include "USB/qemu-usb/input-keymap-win32-to-qcode.h"
 
 namespace usb_hid
 {
diff --git a/pcsx2/USB/usb-hid/raw/rawinput.h b/pcsx2/USB/usb-hid/raw/rawinput.h
index 8fa7dccd02..5d3199d9a0 100644
--- a/pcsx2/USB/usb-hid/raw/rawinput.h
+++ b/pcsx2/USB/usb-hid/raw/rawinput.h
@@ -13,9 +13,9 @@
  *  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../../shared/rawinput_usb.h"
-#include "../hidproxy.h"
-#include "../usb-hid.h"
+#include "USB/shared/rawinput_usb.h"
+#include "USB/usb-hid/hidproxy.h"
+#include "USB/usb-hid/usb-hid.h"
 
 namespace usb_hid
 {
diff --git a/pcsx2/USB/usb-hid/usb-buzzer.cpp b/pcsx2/USB/usb-hid/usb-buzzer.cpp
index 130612a0c9..0adf2139cc 100644
--- a/pcsx2/USB/usb-hid/usb-buzzer.cpp
+++ b/pcsx2/USB/usb-hid/usb-buzzer.cpp
@@ -25,7 +25,7 @@
 #include <windows.h>
 #include <setupapi.h>
 extern "C" {
-#include "../ddk/hidsdi.h"
+#include "USB/ddk/hidsdi.h"
 }
 
 #pragma comment(lib, "setupapi.lib")
diff --git a/pcsx2/USB/usb-hid/usb-hid.cpp b/pcsx2/USB/usb-hid/usb-hid.cpp
index 0ed89e7925..c0d818db62 100644
--- a/pcsx2/USB/usb-hid/usb-hid.cpp
+++ b/pcsx2/USB/usb-hid/usb-hid.cpp
@@ -24,11 +24,11 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../deviceproxy.h"
+#include "USB/deviceproxy.h"
 #include "hidproxy.h"
-#include "../qemu-usb/desc.h"
+#include "USB/qemu-usb/desc.h"
 #include "usb-hid.h"
-#include "../shared/inifile_usb.h"
+#include "USB/shared/inifile_usb.h"
 
 #define CONTAINER_OF(p, type, field) ((type*)((char*)p - ((ptrdiff_t) & ((type*)0)->field)))
 
diff --git a/pcsx2/USB/usb-hid/usb-hid.h b/pcsx2/USB/usb-hid/usb-hid.h
index c3b2450252..467c590431 100644
--- a/pcsx2/USB/usb-hid/usb-hid.h
+++ b/pcsx2/USB/usb-hid/usb-hid.h
@@ -14,8 +14,8 @@
  */
 
 #pragma once
-#include "../configuration.h"
-#include "../qemu-usb/hid.h"
+#include "USB/configuration.h"
+#include "USB/qemu-usb/hid.h"
 #include <list>
 #include <string>
 
diff --git a/pcsx2/USB/usb-mic/audiodev-pulse.cpp b/pcsx2/USB/usb-mic/audiodev-pulse.cpp
index 8a90437ac2..9149298e45 100644
--- a/pcsx2/USB/usb-mic/audiodev-pulse.cpp
+++ b/pcsx2/USB/usb-mic/audiodev-pulse.cpp
@@ -13,10 +13,10 @@
  *  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../gtk.h"
+#include "USB/gtk.h"
 #include "audiodev-pulse.h"
 #ifdef DYNLINK_PULSE
-#include "../dynlink/pulse.h"
+#include "USB/dynlink/pulse.h"
 #endif
 
 GtkWidget* new_combobox(const char* label, GtkWidget* vbox); // src/linux/config-gtk.cpp
diff --git a/pcsx2/USB/usb-mic/audiodev-pulse.h b/pcsx2/USB/usb-mic/audiodev-pulse.h
index c01fbefacc..b77796ee81 100644
--- a/pcsx2/USB/usb-mic/audiodev-pulse.h
+++ b/pcsx2/USB/usb-mic/audiodev-pulse.h
@@ -16,7 +16,7 @@
 #include <cstdint>
 #include <cstring>
 #include <pulse/pulseaudio.h>
-#include "../shared/ringbuffer.h"
+#include "USB/shared/ringbuffer.h"
 #include "audiodeviceproxy.h"
 #include <samplerate.h>
 //#include <typeinfo>
diff --git a/pcsx2/USB/usb-mic/audiodev-wasapi.cpp b/pcsx2/USB/usb-mic/audiodev-wasapi.cpp
index 12fdd1f82c..87bf1713a8 100644
--- a/pcsx2/USB/usb-mic/audiodev-wasapi.cpp
+++ b/pcsx2/USB/usb-mic/audiodev-wasapi.cpp
@@ -22,8 +22,8 @@
 #include <functiondiscoverykeys_devpkey.h>
 #include <process.h>
 #include "audiodev-wasapi.h"
-#include "../Win32/Config_usb.h"
-#include "../Win32/resource_usb.h"
+#include "USB/Win32/Config_usb.h"
+#include "USB/Win32/resource_usb.h"
 
 #define SafeRelease(x) \
 	if (x)             \
diff --git a/pcsx2/USB/usb-mic/audiodev-wasapi.h b/pcsx2/USB/usb-mic/audiodev-wasapi.h
index 8af3cacee0..58b3927186 100644
--- a/pcsx2/USB/usb-mic/audiodev-wasapi.h
+++ b/pcsx2/USB/usb-mic/audiodev-wasapi.h
@@ -16,8 +16,8 @@
 // Used OBS as example
 
 #include "audiodeviceproxy.h"
-#include "../libsamplerate/samplerate.h"
-#include "../shared/ringbuffer.h"
+#include "USB/libsamplerate/samplerate.h"
+#include "USB/shared/ringbuffer.h"
 
 #include <mmdeviceapi.h>
 #include <audioclient.h>
diff --git a/pcsx2/USB/usb-mic/audiodeviceproxy.h b/pcsx2/USB/usb-mic/audiodeviceproxy.h
index 8c45d9ebd5..3998048da9 100644
--- a/pcsx2/USB/usb-mic/audiodeviceproxy.h
+++ b/pcsx2/USB/usb-mic/audiodeviceproxy.h
@@ -21,9 +21,9 @@
 #include <list>
 #include <algorithm>
 #include <iterator>
-#include "../helpers.h"
-#include "../configuration.h"
-#include "../deviceproxy.h"
+#include "USB/helpers.h"
+#include "USB/configuration.h"
+#include "USB/deviceproxy.h"
 #include "audiodev.h"
 
 namespace usb_mic
diff --git a/pcsx2/USB/usb-mic/usb-headset.cpp b/pcsx2/USB/usb-mic/usb-headset.cpp
index b663189078..c8d776c546 100644
--- a/pcsx2/USB/usb-mic/usb-headset.cpp
+++ b/pcsx2/USB/usb-mic/usb-headset.cpp
@@ -25,9 +25,9 @@
 // Most stuff is based on Qemu 1.7 USB soundcard passthrough code.
 
 #include "PrecompiledHeader.h"
-#include "../qemu-usb/vl.h"
-#include "../qemu-usb/desc.h"
-#include "../shared/inifile_usb.h"
+#include "USB/qemu-usb/vl.h"
+#include "USB/qemu-usb/desc.h"
+#include "USB/shared/inifile_usb.h"
 #include <assert.h>
 
 #include "audio.h"
diff --git a/pcsx2/USB/usb-mic/usb-headset.h b/pcsx2/USB/usb-mic/usb-headset.h
index f6cdda8c45..c088ba407f 100644
--- a/pcsx2/USB/usb-mic/usb-headset.h
+++ b/pcsx2/USB/usb-mic/usb-headset.h
@@ -13,7 +13,7 @@
  *  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../deviceproxy.h"
+#include "USB/deviceproxy.h"
 #include "audiodeviceproxy.h"
 
 namespace usb_mic
diff --git a/pcsx2/USB/usb-mic/usb-mic-logitech.cpp b/pcsx2/USB/usb-mic/usb-mic-logitech.cpp
index c662f19e3e..1b8eff2b6f 100644
--- a/pcsx2/USB/usb-mic/usb-mic-logitech.cpp
+++ b/pcsx2/USB/usb-mic/usb-mic-logitech.cpp
@@ -16,8 +16,8 @@
 #include "PrecompiledHeader.h"
 #include "usb-mic-singstar.h"
 #include "audio.h"
-#include "../qemu-usb/desc.h"
-#include "../shared/inifile_usb.h"
+#include "USB/qemu-usb/desc.h"
+#include "USB/shared/inifile_usb.h"
 
 namespace usb_mic
 {
diff --git a/pcsx2/USB/usb-mic/usb-mic-singstar.cpp b/pcsx2/USB/usb-mic/usb-mic-singstar.cpp
index 4d1cd868e2..5660375713 100644
--- a/pcsx2/USB/usb-mic/usb-mic-singstar.cpp
+++ b/pcsx2/USB/usb-mic/usb-mic-singstar.cpp
@@ -25,10 +25,10 @@
 // Most stuff is based on Qemu 1.7 USB soundcard passthrough code.
 
 #include "PrecompiledHeader.h"
-#include "../qemu-usb/vl.h"
-#include "../qemu-usb/desc.h"
+#include "USB/qemu-usb/vl.h"
+#include "USB/qemu-usb/desc.h"
 #include "usb-mic-singstar.h"
-#include "../shared/inifile_usb.h"
+#include "USB/shared/inifile_usb.h"
 #include <assert.h>
 
 static FILE* file = NULL;
diff --git a/pcsx2/USB/usb-mic/usb-mic-singstar.h b/pcsx2/USB/usb-mic/usb-mic-singstar.h
index 92d2348f52..c1d77c8f7d 100644
--- a/pcsx2/USB/usb-mic/usb-mic-singstar.h
+++ b/pcsx2/USB/usb-mic/usb-mic-singstar.h
@@ -15,7 +15,7 @@
 
 #ifndef USBMICSINGSTAR_H
 #define USBMICSINGSTAR_H
-#include "../deviceproxy.h"
+#include "USB/deviceproxy.h"
 #include "audiodeviceproxy.h"
 
 struct USBDevice;
diff --git a/pcsx2/USB/usb-msd/usb-msd-gtk.cpp b/pcsx2/USB/usb-msd/usb-msd-gtk.cpp
index 7e4be25bee..401f716ce1 100644
--- a/pcsx2/USB/usb-msd/usb-msd-gtk.cpp
+++ b/pcsx2/USB/usb-msd/usb-msd-gtk.cpp
@@ -14,9 +14,9 @@
  */
 
 #include "usb-msd.h"
-#include "../linux/ini.h"
-#include "../configuration.h"
-#include "../gtk.h"
+#include "USB/linux/ini.h"
+#include "USB/configuration.h"
+#include "USB/gtk.h"
 #include "Utilities/Console.h"
 
 namespace usb_msd
diff --git a/pcsx2/USB/usb-msd/usb-msd-win32.cpp b/pcsx2/USB/usb-msd/usb-msd-win32.cpp
index de21e958ea..bef935b8c2 100644
--- a/pcsx2/USB/usb-msd/usb-msd-win32.cpp
+++ b/pcsx2/USB/usb-msd/usb-msd-win32.cpp
@@ -16,8 +16,8 @@
 #include "PrecompiledHeader.h"
 #include <commdlg.h>
 #include "usb-msd.h"
-#include "../Win32/Config_usb.h"
-#include "../Win32/resource_usb.h"
+#include "USB/Win32/Config_usb.h"
+#include "USB/Win32/resource_usb.h"
 
 namespace usb_msd
 {
diff --git a/pcsx2/USB/usb-msd/usb-msd.cpp b/pcsx2/USB/usb-msd/usb-msd.cpp
index 07f99db4d0..f3aad4cc53 100644
--- a/pcsx2/USB/usb-msd/usb-msd.cpp
+++ b/pcsx2/USB/usb-msd/usb-msd.cpp
@@ -11,8 +11,8 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "../qemu-usb/vl.h"
-#include "../qemu-usb/desc.h"
+#include "USB/qemu-usb/vl.h"
+#include "USB/qemu-usb/desc.h"
 #include "usb-msd.h"
 
 #define le32_to_cpu(x) (x)
diff --git a/pcsx2/USB/usb-msd/usb-msd.h b/pcsx2/USB/usb-msd/usb-msd.h
index 7c760f8f09..b31fd7414a 100644
--- a/pcsx2/USB/usb-msd/usb-msd.h
+++ b/pcsx2/USB/usb-msd/usb-msd.h
@@ -15,7 +15,7 @@
 
 #ifndef USBMSD_H
 #define USBMSD_H
-#include "../deviceproxy.h"
+#include "USB/deviceproxy.h"
 
 namespace usb_msd
 {
diff --git a/pcsx2/USB/usb-pad/bitjuggling.cpp b/pcsx2/USB/usb-pad/bitjuggling.cpp
index 4762235d8e..3267e41d3c 100644
--- a/pcsx2/USB/usb-pad/bitjuggling.cpp
+++ b/pcsx2/USB/usb-pad/bitjuggling.cpp
@@ -13,7 +13,7 @@
  *  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../qemu-usb/vl.h"
+#include "USB/qemu-usb/vl.h"
 
 #include <limits.h>
 #include <string.h>
diff --git a/pcsx2/USB/usb-pad/dx/dinput-config.cpp b/pcsx2/USB/usb-pad/dx/dinput-config.cpp
index 36adc14060..eff1e45ba6 100644
--- a/pcsx2/USB/usb-pad/dx/dinput-config.cpp
+++ b/pcsx2/USB/usb-pad/dx/dinput-config.cpp
@@ -28,7 +28,7 @@
 #include "versionproxy.h"
 
 #include "usb-pad-dx.h"
-#include "../../shared/inifile_usb.h"
+#include "USB/shared/inifile_usb.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/dx/dx.h b/pcsx2/USB/usb-pad/dx/dx.h
index 57ff3c0f11..84bb27491f 100644
--- a/pcsx2/USB/usb-pad/dx/dx.h
+++ b/pcsx2/USB/usb-pad/dx/dx.h
@@ -30,9 +30,9 @@
 #include <map>
 #include <sstream>
 
-#include "../usb-pad.h"
-#include "../../configuration.h"
-#include "../../usb-pad/lg/lg_ff.h"
+#include "USB/usb-pad/usb-pad.h"
+#include "USB/configuration.h"
+#include "USB/usb-pad/lg/lg_ff.h"
 
 #define DINPUT_AXES_COUNT 32
 
diff --git a/pcsx2/USB/usb-pad/dx/usb-pad-dx.h b/pcsx2/USB/usb-pad/dx/usb-pad-dx.h
index 7aa6e3a969..ecf1821134 100644
--- a/pcsx2/USB/usb-pad/dx/usb-pad-dx.h
+++ b/pcsx2/USB/usb-pad/dx/usb-pad-dx.h
@@ -13,8 +13,8 @@
  *  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../padproxy.h"
-#include "../../Win32/Config_usb.h"
+#include "USB/usb-pad/padproxy.h"
+#include "USB/Win32/Config_usb.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/evdev/evdev-ff.cpp b/pcsx2/USB/usb-pad/evdev/evdev-ff.cpp
index 06186a8b03..4f05366545 100644
--- a/pcsx2/USB/usb-pad/evdev/evdev-ff.cpp
+++ b/pcsx2/USB/usb-pad/evdev/evdev-ff.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "evdev-ff.h"
-#include "../../usb-pad/lg/lg_ff.h"
+#include "USB/usb-pad/lg/lg_ff.h"
 #include <unistd.h>
 #include <cerrno>
 #include <cstring>
diff --git a/pcsx2/USB/usb-pad/evdev/evdev-ff.h b/pcsx2/USB/usb-pad/evdev/evdev-ff.h
index eb87af4058..082cf988d9 100644
--- a/pcsx2/USB/usb-pad/evdev/evdev-ff.h
+++ b/pcsx2/USB/usb-pad/evdev/evdev-ff.h
@@ -17,7 +17,7 @@
 #define EVDEV_FF_H
 
 #include <linux/input.h>
-#include "../usb-pad.h"
+#include "USB/usb-pad/usb-pad.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/evdev/evdev-gtk.cpp b/pcsx2/USB/usb-pad/evdev/evdev-gtk.cpp
index 548f4aaae1..28a5e965df 100644
--- a/pcsx2/USB/usb-pad/evdev/evdev-gtk.cpp
+++ b/pcsx2/USB/usb-pad/evdev/evdev-gtk.cpp
@@ -19,7 +19,7 @@
 #include <thread>
 #include <stdio.h>
 #include <sstream>
-#include "../../gtk.h"
+#include "USB/gtk.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/evdev/evdev.cpp b/pcsx2/USB/usb-pad/evdev/evdev.cpp
index 2b46f7b5ee..766764a7a7 100644
--- a/pcsx2/USB/usb-pad/evdev/evdev.cpp
+++ b/pcsx2/USB/usb-pad/evdev/evdev.cpp
@@ -17,7 +17,7 @@
 #include <cassert>
 #include <sstream>
 #include <linux/hidraw.h>
-#include "../../linux/util.h"
+#include "USB/linux/util.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/evdev/evdev.h b/pcsx2/USB/usb-pad/evdev/evdev.h
index 5ab7e95f34..efd54da4b3 100644
--- a/pcsx2/USB/usb-pad/evdev/evdev.h
+++ b/pcsx2/USB/usb-pad/evdev/evdev.h
@@ -16,8 +16,8 @@
 #pragma once
 #include "evdev-ff.h"
 #include "shared.h"
-#include "../../linux/util.h"
-#include "../../readerwriterqueue/readerwriterqueue.h"
+#include "USB/linux/util.h"
+#include "USB/readerwriterqueue/readerwriterqueue.h"
 #include "Utilities/Console.h"
 //#include <dirent.h> //gtk.h pulls in?
 #include <thread>
diff --git a/pcsx2/USB/usb-pad/evdev/shared-gtk.cpp b/pcsx2/USB/usb-pad/evdev/shared-gtk.cpp
index 45c22349a2..d6e2d88a46 100644
--- a/pcsx2/USB/usb-pad/evdev/shared-gtk.cpp
+++ b/pcsx2/USB/usb-pad/evdev/shared-gtk.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "shared.h"
-#include "../../icon_buzz_24.h"
+#include "USB/icon_buzz_24.h"
 
 #include <chrono>
 #include <thread>
diff --git a/pcsx2/USB/usb-pad/evdev/shared.h b/pcsx2/USB/usb-pad/evdev/shared.h
index 090cd6f76a..5b3919447a 100644
--- a/pcsx2/USB/usb-pad/evdev/shared.h
+++ b/pcsx2/USB/usb-pad/evdev/shared.h
@@ -16,9 +16,9 @@
 #pragma once
 #include <linux/joystick.h>
 #include <unistd.h>
-#include "../../gtk.h"
-#include "../padproxy.h"
-#include "../../configuration.h"
+#include "USB/gtk.h"
+#include "USB/usb-pad/padproxy.h"
+#include "USB/configuration.h"
 
 #define N_HIDRAW_FF_PT "hidraw_ff_pt"
 #define N_GAIN_ENABLED "gain_enabled"
diff --git a/pcsx2/USB/usb-pad/joydev/joydev-gtk.cpp b/pcsx2/USB/usb-pad/joydev/joydev-gtk.cpp
index de2bdd9187..ede5c01b29 100644
--- a/pcsx2/USB/usb-pad/joydev/joydev-gtk.cpp
+++ b/pcsx2/USB/usb-pad/joydev/joydev-gtk.cpp
@@ -19,7 +19,7 @@
 #include <thread>
 #include <stdio.h>
 #include <sstream>
-#include "../../gtk.h"
+#include "USB/gtk.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/joydev/joydev.cpp b/pcsx2/USB/usb-pad/joydev/joydev.cpp
index 3e3a9adc01..c9a9dfe59d 100644
--- a/pcsx2/USB/usb-pad/joydev/joydev.cpp
+++ b/pcsx2/USB/usb-pad/joydev/joydev.cpp
@@ -14,7 +14,7 @@
  */
 
 #include "joydev.h"
-#include "../../linux/util.h"
+#include "USB/linux/util.h"
 #include "Utilities/Console.h"
 #include <cassert>
 #include <sstream>
diff --git a/pcsx2/USB/usb-pad/joydev/joydev.h b/pcsx2/USB/usb-pad/joydev/joydev.h
index 064791508b..acd64efa88 100644
--- a/pcsx2/USB/usb-pad/joydev/joydev.h
+++ b/pcsx2/USB/usb-pad/joydev/joydev.h
@@ -14,9 +14,9 @@
  */
 
 #pragma once
-#include "../../linux/util.h"
-#include "../evdev/evdev-ff.h"
-#include "../evdev/shared.h"
+#include "USB/linux/util.h"
+#include "USB/usb-pad/evdev/evdev-ff.h"
+#include "USB/usb-pad/evdev/shared.h"
 #include "Utilities/Console.h"
 
 namespace usb_pad
diff --git a/pcsx2/USB/usb-pad/padproxy.h b/pcsx2/USB/usb-pad/padproxy.h
index a28a22ec77..8e825e32d4 100644
--- a/pcsx2/USB/usb-pad/padproxy.h
+++ b/pcsx2/USB/usb-pad/padproxy.h
@@ -22,8 +22,8 @@
 #include <algorithm>
 #include <iterator>
 #include "usb-pad.h"
-#include "../helpers.h"
-#include "../deviceproxy.h"
+#include "USB/helpers.h"
+#include "USB/deviceproxy.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/raw/raw-config.cpp b/pcsx2/USB/usb-pad/raw/raw-config.cpp
index b8b33b3151..b124d07286 100644
--- a/pcsx2/USB/usb-pad/raw/raw-config.cpp
+++ b/pcsx2/USB/usb-pad/raw/raw-config.cpp
@@ -26,7 +26,7 @@
 
 #include <algorithm>
 #include <map>
-#include "../../configuration.h"
+#include "USB/configuration.h"
 #include "usb-pad-raw.h"
 #include "raw-config-res.h"
 #include <strsafe.h>
diff --git a/pcsx2/USB/usb-pad/raw/usb-pad-raw.cpp b/pcsx2/USB/usb-pad/raw/usb-pad-raw.cpp
index c34ba17b6e..032ffe5a57 100644
--- a/pcsx2/USB/usb-pad/raw/usb-pad-raw.cpp
+++ b/pcsx2/USB/usb-pad/raw/usb-pad-raw.cpp
@@ -14,8 +14,8 @@
  */
 
 #include "PrecompiledHeader.h"
-#include "../../USB.h"
-#include "../../Win32/Config_usb.h"
+#include "USB/USB.h"
+#include "USB/Win32/Config_usb.h"
 #include "usb-pad-raw.h"
 
 namespace usb_pad
diff --git a/pcsx2/USB/usb-pad/raw/usb-pad-raw.h b/pcsx2/USB/usb-pad/raw/usb-pad-raw.h
index 728b314eb7..e931dc113c 100644
--- a/pcsx2/USB/usb-pad/raw/usb-pad-raw.h
+++ b/pcsx2/USB/usb-pad/raw/usb-pad-raw.h
@@ -18,10 +18,10 @@
 #include <thread>
 #include <array>
 #include <atomic>
-#include "../padproxy.h"
-#include "../usb-pad.h"
-#include "../../shared/rawinput_usb.h"
-#include "../../readerwriterqueue/readerwriterqueue.h"
+#include "USB/usb-pad/padproxy.h"
+#include "USB/usb-pad/usb-pad.h"
+#include "USB/shared/rawinput_usb.h"
+#include "USB/readerwriterqueue/readerwriterqueue.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/usb-pad.cpp b/pcsx2/USB/usb-pad/usb-pad.cpp
index 6ab017b68c..a75c3922cc 100644
--- a/pcsx2/USB/usb-pad/usb-pad.cpp
+++ b/pcsx2/USB/usb-pad/usb-pad.cpp
@@ -16,8 +16,8 @@
 #include "PrecompiledHeader.h"
 #include "padproxy.h"
 #include "usb-pad.h"
-#include "../qemu-usb/desc.h"
-#include "../shared/inifile_usb.h"
+#include "USB/qemu-usb/desc.h"
+#include "USB/shared/inifile_usb.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/usb-pad.h b/pcsx2/USB/usb-pad/usb-pad.h
index d4e0d43373..74f73bf9b2 100644
--- a/pcsx2/USB/usb-pad/usb-pad.h
+++ b/pcsx2/USB/usb-pad/usb-pad.h
@@ -16,9 +16,9 @@
 #ifndef USBPAD_H
 #define USBPAD_H
 
-#include "../qemu-usb/vl.h"
-#include "../configuration.h"
-#include "../deviceproxy.h"
+#include "USB/qemu-usb/vl.h"
+#include "USB/configuration.h"
+#include "USB/deviceproxy.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/USB/usb-pad/usb-seamic.cpp b/pcsx2/USB/usb-pad/usb-seamic.cpp
index 4b1b5bfc1a..d7f4b172cc 100644
--- a/pcsx2/USB/usb-pad/usb-seamic.cpp
+++ b/pcsx2/USB/usb-pad/usb-seamic.cpp
@@ -16,9 +16,9 @@
 #include "PrecompiledHeader.h"
 #include "padproxy.h"
 #include "usb-pad.h"
-#include "../qemu-usb/desc.h"
-#include "../usb-mic/usb-mic-singstar.h"
-#include "../shared/inifile_usb.h"
+#include "USB/qemu-usb/desc.h"
+#include "USB/usb-mic/usb-mic-singstar.h"
+#include "USB/shared/inifile_usb.h"
 
 namespace usb_pad
 {
diff --git a/pcsx2/gui/Debugger/DisassemblyDialog.h b/pcsx2/gui/Debugger/DisassemblyDialog.h
index f0f6270e4b..24ab8c7b80 100644
--- a/pcsx2/gui/Debugger/DisassemblyDialog.h
+++ b/pcsx2/gui/Debugger/DisassemblyDialog.h
@@ -23,7 +23,7 @@
 #include "CtrlMemView.h"
 #include "DebugEvents.h"
 #include "DebuggerLists.h"
-#include "../MSWstuff.h"
+#include "gui/MSWstuff.h"
 
 class DebuggerHelpDialog: public wxDialog
 {
diff --git a/pcsx2/gui/DriveList.cpp b/pcsx2/gui/DriveList.cpp
index da7dd50787..b8aa3935db 100644
--- a/pcsx2/gui/DriveList.cpp
+++ b/pcsx2/gui/DriveList.cpp
@@ -16,7 +16,7 @@
 #include "PrecompiledHeader.h"
 #include "DriveList.h"
 #include "MainFrame.h"
-#include "../CDVD/CDVDdiscReader.h"
+#include "CDVD/CDVDdiscReader.h"
 
 DriveList::DriveList()
 {
diff --git a/pcsx2/gui/Panels/MemoryCardListPanel.cpp b/pcsx2/gui/Panels/MemoryCardListPanel.cpp
index 7876af8f5c..0c99e9dcd6 100644
--- a/pcsx2/gui/Panels/MemoryCardListPanel.cpp
+++ b/pcsx2/gui/Panels/MemoryCardListPanel.cpp
@@ -23,7 +23,7 @@
 
 #include "Dialogs/ConfigurationDialog.h"
 #include "Utilities/IniInterface.h"
-#include "../../Sio.h"
+#include "Sio.h"
 
 #include <wx/filepicker.h>
 #include <wx/ffile.h>
diff --git a/pcsx2/x86/iR3000A.cpp b/pcsx2/x86/iR3000A.cpp
index 04fe1fd875..74dfe09cbb 100644
--- a/pcsx2/x86/iR3000A.cpp
+++ b/pcsx2/x86/iR3000A.cpp
@@ -38,7 +38,7 @@
 #include "AppConfig.h"
 
 #include "Utilities/Perf.h"
-#include "../DebugTools/Breakpoints.h"
+#include "DebugTools/Breakpoints.h"
 
 using namespace x86Emitter;
 
diff --git a/pcsx2/x86/ix86-32/iR5900-32.cpp b/pcsx2/x86/ix86-32/iR5900-32.cpp
index 3da5442b89..67cbca0564 100644
--- a/pcsx2/x86/ix86-32/iR5900-32.cpp
+++ b/pcsx2/x86/ix86-32/iR5900-32.cpp
@@ -32,7 +32,7 @@
 #include "CDVD/CDVD.h"
 #include "Elfheader.h"
 
-#include "../DebugTools/Breakpoints.h"
+#include "DebugTools/Breakpoints.h"
 #include "Patch.h"
 
 #if !PCSX2_SEH