include: one folder per subsystem, and includes that name it

Sixty-five headers sat side by side in include/, so `#include "irq.h"`
said nothing about where irq.h was or what it belonged to, and errno.h,
stat.h and fcntl.h at the top shadowed the system's for any host tool
built with -I./include. They are in folders now -- arch/ core/ fs/
dev/ gfx/ net/ uapi/ (and ldls/ for the Linux driver layer) -- and
every include names the folder, as Linux's do: "core/proc.h".

Done mechanically and checked the hard way: the kernel built from this
tree disassembles identically to the one built from the tree before
it. The full image boots, and userland is the same set of programs.
Paths in docs and comments follow; docs/guides/layout.md has a table
of what is where, and tools/fix-includes.py rewrites old-style
includes from the folders in the tree, for code written before this.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01S1giNvrHTrPMPw7V6x1kQ4

kernel/drivers/storage/ahci/ahci.c

@@ -21,18 +21,18 @@
 // few milliseconds, so the cost is that, spent spinning, and it is yielded
 // once a wait goes long.
 
-#include "types.h"
-#include "defs.h"
-#include "param.h"
-#include "x86.h"
-#include "spinlock.h"
-#include "sleeplock.h"
-#include "fs.h"
-#include "file.h"
-#include "proc.h"
-#include "pci.h"
-#include "dma.h"
-#include "blkdev.h"
+#include "core/types.h"
+#include "core/defs.h"
+#include "core/param.h"
+#include "arch/x86.h"
+#include "core/spinlock.h"
+#include "core/sleeplock.h"
+#include "fs/fs.h"
+#include "fs/file.h"
+#include "core/proc.h"
+#include "dev/pci.h"
+#include "core/dma.h"
+#include "fs/blkdev.h"
 
 // --- HBA registers (section 3.1) ---------------------------------------------
 
@@ -345,7 +345,7 @@ port_init(volatile uint8 *hba, int port, uint32 cap)
     return;
   }
   // Without S64A the HBA cannot see above 4 GB. The DMA arena is below it
-  // (see include/dma.h), so this holds, and says so if that ever changes.
+  // (see include/core/dma.h), so this holds, and says so if that ever changes.
   if (!(cap & CAP_S64A) && dma_phys(p->xfer) + BSIZE > 0xFFFFFFFFULL) {
     cprintf("ahci: DMA memory above 4 GB and the HBA is 32-bit\n");
     return;