[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/kernel/vm_space.cpp

@@ -1,10 +1,11 @@
 #include <string.h>
 
-#include "kernel_memory.h"
+#include <arch/memory.h>
 
 #include "assert.h"
 #include "frame_allocator.h"
 #include "log.h"
+#include "memory.h"
 #include "objects/process.h"
 #include "objects/thread.h"
 #include "objects/vm_area.h"
@@ -42,8 +43,8 @@ vm_space::vm_space() :
     m_pml4 = page_table::get_table_page();
     page_table *kpml4 = kernel_space().m_pml4;
 
-    memset(m_pml4, 0, memory::frame_size/2);
-    for (unsigned i = memory::pml4e_kernel; i < memory::table_entries; ++i)
+    memset(m_pml4, 0, mem::frame_size/2);
+    for (unsigned i = arch::kernel_root_index; i < arch::table_entries; ++i)
         m_pml4->entries[i] = kpml4->entries[i];
 }
 
@@ -81,7 +82,7 @@ void
 vm_space::remove_area(vm_area *area)
 {
     area->remove_from(this);
-    clear(*area, 0, memory::page_count(area->size()));
+    clear(*area, 0, mem::page_count(area->size()));
     area->handle_release();
 }
 
@@ -153,7 +154,7 @@ vm_space::copy_from(const vm_space &source, const vm_area &vma)
     if (!find_vma(vma, from) || !source.find_vma(vma, from))
         return;
 
-    size_t count = memory::page_count(vma.size());
+    size_t count = mem::page_count(vma.size());
     page_table::iterator dit {to, m_pml4};
     page_table::iterator sit {from, source.m_pml4};
 
@@ -169,7 +170,7 @@ vm_space::copy_from(const vm_space &source, const vm_area &vma)
 void
 vm_space::page_in(const vm_area &vma, uintptr_t offset, uintptr_t phys, size_t count)
 {
-    using memory::frame_size;
+    using mem::frame_size;
     util::scoped_lock lock {m_lock};
 
     uintptr_t base = 0;
@@ -197,7 +198,7 @@ vm_space::page_in(const vm_area &vma, uintptr_t offset, uintptr_t phys, size_t c
 void
 vm_space::clear(const vm_area &vma, uintptr_t offset, size_t count, bool free)
 {
-    using memory::frame_size;
+    using mem::frame_size;
     util::scoped_lock lock {m_lock};
 
     uintptr_t base = 0;
@@ -248,13 +249,13 @@ vm_space::active() const
 {
     uintptr_t pml4 = 0;
     __asm__ __volatile__ ( "mov %%cr3, %0" : "=r" (pml4) );
-    return memory::to_virtual<page_table>(pml4 & ~0xfffull) == m_pml4;
+    return mem::to_virtual<page_table>(pml4 & ~0xfffull) == m_pml4;
 }
 
 void
 vm_space::activate() const
 {
-    constexpr uint64_t phys_mask = ~memory::page_offset & ~0xfffull;
+    constexpr uint64_t phys_mask = ~mem::linear_offset & ~0xfffull;
     uintptr_t p = reinterpret_cast<uintptr_t>(m_pml4) & phys_mask;
     __asm__ __volatile__ ( "mov %0, %%cr3" :: "r" (p) );
 }
@@ -264,7 +265,7 @@ vm_space::initialize_tcb(TCB &tcb)
 {
     tcb.pml4 =
         reinterpret_cast<uintptr_t>(m_pml4) &
-        ~memory::page_offset;
+        ~mem::linear_offset;
 }
 
 bool
@@ -300,8 +301,8 @@ vm_space::copy(vm_space &source, vm_space &dest, const void *from, void *to, siz
     // TODO: iterate page mappings and continue copying. For now i'm blindly
     // assuming both buffers are fully contained within single pages
     memcpy(
-        memory::to_virtual<void>((*dit & ~0xfffull) | (ito & 0xffful)),
-        memory::to_virtual<void>((*sit & ~0xfffull) | (ifrom & 0xffful)),
+        mem::to_virtual<void>((*dit & ~0xfffull) | (ito & 0xffful)),
+        mem::to_virtual<void>((*sit & ~0xfffull) | (ifrom & 0xffful)),
         length);
 
     return length;