kernel(general): Refactor AHCI driver and clean up project structure

- Reworked AHCI command setup: fixed command slot indexing and clarified memory setup
- Updated AHCI disk initialization to use reference for ATAPI flag
- Cleaned up verbose logging in scheduler and IRQ handler for a quieter kernel log
- Updated boot image target from fat32.img to neos.img
- Renamed and moved documentation files from `doc/` to `docs/` for consistency
- Renamed `make_docs.sh` to `osx_docs.sh` to reflect platform-specific intent
- Minor formatting improvements in DiskImage struct
- Revised ReadMe: clarified mount instructions and removed outdated screenshots

Signed-off-by: Amlal El Mahrouss <amlal.elmahrouss@icloud.com>

21 files changed, 21 insertions, 27 deletions

diff --git a/ReadMe.md b/ReadMe.md
index 45e9ba17..bef76a5c 100644
--- a/ReadMe.md
+++ b/ReadMe.md
@@ -10,13 +10,10 @@
 - [GIT](https://git-scm.com/)
 - [BTB](https://github.com/ne-gh/btb)
 
-## Builders's Notice:
+## Notice for Contributors:
 
-You must mount the contents to the fat32.img prior running! Otherwise the emulator won't find a valid ESP.
-
-## Contributors's Notice:
-
-Always use `run_format.sh` before commiting and pushing your code!
+- You must mount the contents to the neos.img prior running! Otherwise the emulator won't find a valid ESP.
+- Always use `run_format.sh` before commiting and pushing your code!
 
 ## Quick Install:
 
@@ -29,10 +26,4 @@ cd kernel
 ./debug_ata.sh # Generic ATA PIO target
 ```
 
-## Screenshots:
-
-![FS](doc/filesystem.png)
-
-![APIC](doc/apic.png)
-
 ###### Copyright (C) 2024-2025 Amlal EL Mahrouss, All rights reserved.
diff --git a/dev/Boot/amd64-desktop.make b/dev/Boot/amd64-desktop.make
index c1564b77..bf61b24e 100644
--- a/dev/Boot/amd64-desktop.make
+++ b/dev/Boot/amd64-desktop.make
@@ -28,7 +28,7 @@ BIOS=OVMF.fd
 IMG=epm-master-1.img
 IMG_2=epm-master-2.img
 
-BOOT=./src/fat32.img
+BOOT=./src/neos.img
 
 DISK_DRV  =
 
diff --git a/dev/Kernel/HALKit/AMD64/HalCoreInterruptHandlerAMD64.cc b/dev/Kernel/HALKit/AMD64/HalCoreInterruptHandlerAMD64.cc
index bc4bd330..05326ecb 100644
--- a/dev/Kernel/HALKit/AMD64/HalCoreInterruptHandlerAMD64.cc
+++ b/dev/Kernel/HALKit/AMD64/HalCoreInterruptHandlerAMD64.cc
@@ -74,7 +74,6 @@ EXTERN_C void idt_handle_scheduler(NeOS::UIntPtr rsp)
 	try_count_before_brute = 100000UL;
 	kIsScheduling		   = YES;
 
-	kout << "Kernel: Timer IRQ (Scheduler Notification).\r";
 	NeOS::UserProcessHelper::StartScheduling();
 
 	kIsScheduling = NO;
diff --git a/dev/Kernel/HALKit/AMD64/Storage/AHCI+Generic.cc b/dev/Kernel/HALKit/AMD64/Storage/AHCI+Generic.cc
index 27a57a93..a17f3843 100644
--- a/dev/Kernel/HALKit/AMD64/Storage/AHCI+Generic.cc
+++ b/dev/Kernel/HALKit/AMD64/Storage/AHCI+Generic.cc
@@ -115,6 +115,8 @@ STATIC Void drv_std_input_output(UInt64 lba, UInt8* buffer, SizeT sector_sz, Siz
 
 	volatile HbaCmdHeader* command_header = ((HbaCmdHeader*)(((UInt64)kSATAHba->Ports[kSATAIndex].Clb)));
 
+	command_header += slot;
+
 	MUST_PASS(command_header);
 
 	command_header->Cfl	  = sizeof(FisRegH2D) / sizeof(UInt32);
@@ -122,6 +124,7 @@ STATIC Void drv_std_input_output(UInt64 lba, UInt8* buffer, SizeT sector_sz, Siz
 	command_header->Prdtl = (UInt16)((size_buffer - 1) >> 4) + 1;
 
 	HbaCmdTbl* command_table = (HbaCmdTbl*)((VoidPtr)((UInt64)command_header->Ctba));
+
 	rt_set_memory(command_table, 0, sizeof(HbaCmdTbl) + (command_header->Prdtl - 1) * sizeof(HbaPrdtEntry));
 
 	MUST_PASS(command_table);
@@ -166,7 +169,9 @@ STATIC Void drv_std_input_output(UInt64 lba, UInt8* buffer, SizeT sector_sz, Siz
 	h2d_fis->CountHigh = (size_buffer >> 8) & 0xFF;
 
 	while (kSATAHba->Ports[kSATAIndex].Tfd & (kSATASRBsy | kSATASRDrq))
+	{
 		;
+	}
 
 	kSATAHba->Ports[kSATAIndex].Ci = (1 << slot);
 
@@ -232,8 +237,9 @@ STATIC Void ahci_enable_and_probe()
 
 /// @brief Initializes an AHCI disk.
 /// @param pi the amount of ports that have been detected.
+/// @param atapi reference value, tells whether we should detect ATAPI instead of SATA.
 /// @return if the disk was successfully initialized or not.
-STATIC Bool drv_std_init_ahci(UInt16& pi, BOOL atapi)
+STATIC Bool drv_std_init_ahci(UInt16& pi, BOOL& atapi)
 {
 	PCI::Iterator iterator(Types::PciDeviceKind::MassStorageController);
 
@@ -390,7 +396,8 @@ Void drv_std_read(UInt64 lba, Char* buffer, SizeT sector_sz, SizeT size_buffer)
 
 Bool drv_std_init(UInt16& pi)
 {
-	return drv_std_init_ahci(pi, NO);
+	BOOL atapi = NO;
+	return drv_std_init_ahci(pi, atapi);
 }
 
 Bool drv_std_detected(Void)
diff --git a/dev/Kernel/src/UserProcessScheduler.cc b/dev/Kernel/src/UserProcessScheduler.cc
index 95885ee5..1087ac6b 100644
--- a/dev/Kernel/src/UserProcessScheduler.cc
+++ b/dev/Kernel/src/UserProcessScheduler.cc
@@ -436,9 +436,6 @@ namespace NeOS
 			kout << "UserProcessScheduler::Run(): This team doesn't have any process!\r";
 			return 0UL;
 		}
-
-		kout << "UserProcessScheduler::Run(): This team has a process capacity of: " << hex_number(mTeam.mProcessList.Capacity()) << kendl;
-
 		for (; process_index < mTeam.AsArray().Capacity(); ++process_index)
 		{
 			auto& process = mTeam.AsArray()[process_index];
diff --git a/doc/AHCI_DESIGN.drawio b/docs/AHCI_DESIGN.drawio
index 73029de7..73029de7 100644
--- a/doc/AHCI_DESIGN.drawio
+++ b/docs/AHCI_DESIGN.drawio
diff --git a/doc/DDK.pdf b/docs/DDK.pdf
index 7029e0cc..7029e0cc 100644
--- a/doc/DDK.pdf
+++ b/docs/DDK.pdf
diff --git a/doc/EPM.pdf b/docs/EPM.pdf
index d9eeebc9..d9eeebc9 100644
--- a/doc/EPM.pdf
+++ b/docs/EPM.pdf
diff --git a/doc/GUI_DESIGN.drawio b/docs/GUI_DESIGN.drawio
index 3ada69be..3ada69be 100644
--- a/doc/GUI_DESIGN.drawio
+++ b/docs/GUI_DESIGN.drawio
diff --git a/doc/MBCI.drawio b/docs/MBCI.drawio
index 9a8f4283..9a8f4283 100644
--- a/doc/MBCI.drawio
+++ b/docs/MBCI.drawio
diff --git a/doc/MFlash.pdf b/docs/MFlash.pdf
index 2e6d7d42..2e6d7d42 100644
--- a/doc/MFlash.pdf
+++ b/docs/MFlash.pdf
diff --git a/doc/NeFS.pdf b/docs/NeFS.pdf
index 1b804346..1b804346 100644
--- a/doc/NeFS.pdf
+++ b/docs/NeFS.pdf
diff --git a/doc/OS_DESIGN.drawio b/docs/OS_DESIGN.drawio
index d704b481..d704b481 100644
--- a/doc/OS_DESIGN.drawio
+++ b/docs/OS_DESIGN.drawio
diff --git a/doc/ROUND_ROBIN.drawio b/docs/ROUND_ROBIN.drawio
index 46c6304b..46c6304b 100644
--- a/doc/ROUND_ROBIN.drawio
+++ b/docs/ROUND_ROBIN.drawio
diff --git a/doc/SCHED_DESIGN.drawio b/docs/SCHED_DESIGN.drawio
index ab75d000..ab75d000 100644
--- a/doc/SCHED_DESIGN.drawio
+++ b/docs/SCHED_DESIGN.drawio
diff --git a/doc/TIMER_DESIGN.drawio b/docs/TIMER_DESIGN.drawio
index ca081fd3..ca081fd3 100644
--- a/doc/TIMER_DESIGN.drawio
+++ b/docs/TIMER_DESIGN.drawio
diff --git a/doc/ZXD.drawio b/docs/ZXD.drawio
index 7452d3f9..7452d3f9 100644
--- a/doc/ZXD.drawio
+++ b/docs/ZXD.drawio
diff --git a/doc/apic.png b/docs/apic.png
index 33954dce..33954dce 100644
--- a/doc/apic.png
+++ b/docs/apic.png
diff --git a/doc/filesystem.png b/docs/filesystem.png
index 9e3599a9..9e3599a9 100644
--- a/doc/filesystem.png
+++ b/docs/filesystem.png
diff --git a/make_docs.sh b/osx_docs.sh
index 2d9a0a22..2d9a0a22 100755
--- a/make_docs.sh
+++ b/osx_docs.sh
diff --git a/public/frameworks/DiskImage.fwrk/headers/DiskImage.h b/public/frameworks/DiskImage.fwrk/headers/DiskImage.h
index 704776a4..fb05154d 100644
--- a/public/frameworks/DiskImage.fwrk/headers/DiskImage.h
+++ b/public/frameworks/DiskImage.fwrk/headers/DiskImage.h
@@ -14,19 +14,19 @@
 #define kDISectorSz			 (512)
 #define kDIMinDiskSz		 (1024 * 1024 * 1024)
 #define kDIDefaultOutputName "disk.eimg"
-#define kDIDefaultDiskName "Disk"
-#define kDISuccessStatus (0)
-#define kDIFailureStatus (1)
+#define kDIDefaultDiskName	 "Disk"
+#define kDISuccessStatus	 (0)
+#define kDIFailureStatus	 (1)
 
 struct DI_DISK_IMAGE;
 
 struct DI_DISK_IMAGE
 {
-	Char	  disk_name[512] = kDIDefaultDiskName;
-	SInt32		  sector_sz		 = kDISectorSz;
-	SInt32 block_cnt		 = 0;
-	SizeT	  disk_sz		 = kDIMinDiskSz;
-	Char	  out_name[256]	 = kDIDefaultOutputName;
+	Char   disk_name[512] = kDIDefaultDiskName;
+	SInt32 sector_sz	  = kDISectorSz;
+	SInt32 block_cnt	  = 0;
+	SizeT  disk_sz		  = kDIMinDiskSz;
+	Char   out_name[256]  = kDIDefaultOutputName;
 };
 
 /// @brief Format with an EPM partition.