[build] Update to using pb 3

Updating the build to the new version of bonnibel. This also includes
some updates to make sure things keep working with LLVM 11.

src/kernel/module.toml

@@ -0,0 +1,56 @@
+name = "kernel"
+kind = "exe"
+output = "jsix.elf"
+targets = ["kernel"]
+deps = ["kutil", "cpu"]
+includes = ["src/kernel"]
+sources = [
+    "apic.cpp",
+    "ap_startup.s",
+    "assert.cpp",
+    "boot.s",
+    "clock.cpp",
+    "console.cpp",
+    "cpprt.cpp",
+    "cpu.cpp",
+    "debug.cpp",
+    "debug.s",
+    "device_manager.cpp",
+    "frame_allocator.cpp",
+    "gdt.cpp",
+    "gdtidt.s",
+    "hpet.cpp",
+    "idt.cpp",
+    "interrupts.cpp",
+    "interrupts.s",
+    "io.cpp",
+    "log.cpp",
+    "main.cpp",
+    "memory_bootstrap.cpp",
+    "msr.cpp",
+    "objects/channel.cpp",
+    "objects/endpoint.cpp",
+    "objects/kobject.cpp",
+    "objects/thread.cpp",
+    "objects/process.cpp",
+    "objects/system.cpp",
+    "objects/vm_area.cpp",
+    "page_table.cpp",
+    "page_tree.cpp",
+    "pci.cpp",
+    "scheduler.cpp",
+    "serial.cpp",
+    "symbol_table.cpp",
+    "syscall.cpp",
+    "syscall.s",
+    "syscalls/channel.cpp",
+    "syscalls/endpoint.cpp",
+    "syscalls/object.cpp",
+    "syscalls/process.cpp",
+    "syscalls/system.cpp",
+    "syscalls/thread.cpp",
+    "syscalls/vm_area.cpp",
+    "task.s",
+    "tss.cpp",
+    "vm_space.cpp",
+]