[bootproto] Create new bootproto lib

This is a rather large commit that is widely focused on cleaning things
out of the 'junk drawer' that is src/include. Most notably, several
things that were put in there because they needed somewhere where both
the kernel, boot, and init could read them have been moved to a new lib,
'bootproto'.

- Moved kernel_args.h and init_args.h to bootproto as kernel.h and
  init.h, respectively.

- Moved counted.h and pointer_manipulation.h into util, renaming the
  latter to util/pointers.h.

- Created a new src/include/arch for very arch-dependent definitions,
  and moved some kernel_memory.h constants like frame size, page table
  entry count, etc to arch/amd64/memory.h. Also created arch/memory.h
  which detects platform and includes the former.

- Got rid of kernel_memory.h entirely in favor of a new, cog-based
  approach. The new definitions/memory_layout.csv lists memory regions
  in descending order from the top of memory, their sizes, and whether
  they are shared outside the kernel (ie, boot needs to know them). The
  new header bootproto/memory.h exposes the addresses of the shared
  regions, while the kernel's memory.h gains the start and size of all
  the regions. Also renamed the badly-named page-offset area the linear
  area.

- The python build scripts got a few new features: the ability to parse
  the csv mentioned above in a new memory.py module; the ability to add
  dependencies to existing source files (The list of files that I had to
  pull out of the main list just to add them with the dependency on
  memory.h was getting too large. So I put them back into the sources
  list, and added the dependency post-hoc.); and the ability to
  reference 'source_root', 'build_root', and 'module_root' variables in
  .module files.

- Some utility functions that were in the kernel's memory.h got moved to
  util/pointers.h and util/misc.h, and misc.h's byteswap was renamed
  byteswap32 to be more specific.

src/boot/loader.cpp

@@ -1,27 +1,26 @@
 #include <uefi/boot_services.h>
 #include <uefi/types.h>
 
+#include <bootproto/init.h>
+#include <elf/file.h>
+#include <elf/headers.h>
+#include <util/pointers.h>
+
 #include "allocator.h"
 #include "console.h"
-#include "elf/file.h"
-#include "elf/headers.h"
 #include "error.h"
 #include "fs.h"
-#include "init_args.h"
 #include "loader.h"
 #include "memory.h"
 #include "paging.h"
-#include "pointer_manipulation.h"
 #include "status.h"
 
-namespace init = kernel::init;
-
 namespace boot {
 namespace loader {
 
 using memory::alloc_type;
 
-buffer
+util::buffer
 load_file(
     fs::file &disk,
     const program_desc &desc)
@@ -29,7 +28,7 @@ load_file(
     status_line status(L"Loading file", desc.path);
 
     fs::file file = disk.open(desc.path);
-    buffer b = file.load();
+    util::buffer b = file.load();
 
     //console::print(L"    Loaded at: 0x%lx, %d bytes\r\n", b.data, b.size);
     return b;
@@ -37,17 +36,17 @@ load_file(
 
 
 static void
-create_module(buffer data, const program_desc &desc, bool loaded)
+create_module(util::buffer data, const program_desc &desc, bool loaded)
 {
     size_t path_len = wstrlen(desc.path);
-    init::module_program *mod = g_alloc.allocate_module<init::module_program>(path_len);
-    mod->mod_type = init::module_type::program;
+    bootproto::module_program *mod = g_alloc.allocate_module<bootproto::module_program>(path_len);
+    mod->mod_type = bootproto::module_type::program;
     mod->base_address = reinterpret_cast<uintptr_t>(data.pointer);
     mod->size = data.count;
     if (loaded)
-        mod->mod_flags = static_cast<init::module_flags>(
+        mod->mod_flags = static_cast<bootproto::module_flags>(
             static_cast<uint8_t>(mod->mod_flags) |
-            static_cast<uint8_t>(init::module_flags::no_load));
+            static_cast<uint8_t>(bootproto::module_flags::no_load));
 
     // TODO: support non-ascii path characters and do real utf-16 to utf-8
     // conversion
@@ -56,7 +55,7 @@ create_module(buffer data, const program_desc &desc, bool loaded)
     mod->filename[path_len] = 0;
 }
 
-init::program *
+bootproto::program *
 load_program(
     fs::file &disk,
     const program_desc &desc,
@@ -64,7 +63,7 @@ load_program(
 {
     status_line status(L"Loading program", desc.name);
 
-    buffer data = load_file(disk, desc);
+    util::buffer data = load_file(disk, desc);
 
     if (add_module)
         create_module(data, desc, true);
@@ -79,20 +78,20 @@ load_program(
             ++num_sections;
     }
 
-    init::program_section *sections = new init::program_section [num_sections];
+    bootproto::program_section *sections = new bootproto::program_section [num_sections];
 
     size_t next_section = 0;
     for (auto &seg : program.programs()) {
         if (seg.type != elf::segment_type::load)
             continue;
 
-        init::program_section &section = sections[next_section++];
+        bootproto::program_section &section = sections[next_section++];
 
         size_t page_count = memory::bytes_to_pages(seg.mem_size);
 
         if (seg.mem_size > seg.file_size) {
             void *pages = g_alloc.allocate_pages(page_count, alloc_type::program, true);
-            void *source = offset_ptr<void>(data.pointer, seg.offset);
+            void *source = util::offset_pointer(data.pointer, seg.offset);
             g_alloc.copy(pages, source, seg.file_size);
             section.phys_addr = reinterpret_cast<uintptr_t>(pages);
         } else {
@@ -101,10 +100,10 @@ load_program(
 
         section.virt_addr = seg.vaddr;
         section.size = seg.mem_size;
-        section.type = static_cast<init::section_flags>(seg.flags);
+        section.type = static_cast<bootproto::section_flags>(seg.flags);
     }
 
-    init::program *prog = new init::program;
+    bootproto::program *prog = new bootproto::program;
     prog->sections = { .pointer = sections, .count = num_sections };
     prog->phys_base = program.base();
     prog->entrypoint = program.entrypoint();
@@ -118,25 +117,25 @@ load_module(
 {
     status_line status(L"Loading module", desc.name);
 
-    buffer data = load_file(disk, desc);
+    util::buffer data = load_file(disk, desc);
     create_module(data, desc, false);
 }
 
 void
-verify_kernel_header(init::program &program)
+verify_kernel_header(bootproto::program &program)
 {
     status_line status(L"Verifying kernel header");
 
-    const init::header *header =
-        reinterpret_cast<const init::header *>(program.sections[0].phys_addr);
+    const bootproto::header *header =
+        reinterpret_cast<const bootproto::header *>(program.sections[0].phys_addr);
 
-    if (header->magic != init::header_magic)
+    if (header->magic != bootproto::header_magic)
         error::raise(uefi::status::load_error, L"Bad kernel magic number");
 
-    if (header->length < sizeof(init::header))
+    if (header->length < sizeof(bootproto::header))
         error::raise(uefi::status::load_error, L"Bad kernel header length");
 
-    if (header->version < init::min_header_version)
+    if (header->version < bootproto::min_header_version)
         error::raise(uefi::status::unsupported, L"Kernel header version not supported");
 
     console::print(L"    Loaded kernel vserion: %d.%d.%d %x\r\n",