[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/main.cpp

@@ -2,10 +2,9 @@
 #include <stdint.h>
 #include <string.h>
 
+#include <bootproto/kernel.h>
 #include <j6/signals.h>
 #include <util/vector.h>
-#include <kernel_args.h>
-#include <kernel_memory.h>
 
 #include "apic.h"
 #include "assert.h"
@@ -19,6 +18,7 @@
 #include "interrupts.h"
 #include "io.h"
 #include "log.h"
+#include "memory.h"
 #include "msr.h"
 #include "objects/channel.h"
 #include "objects/event.h"
@@ -36,7 +36,7 @@
 #endif
 
 extern "C" {
-    void kernel_main(kernel::init::args *args);
+    void kernel_main(bootproto::args *args);
     void (*__ctors)(void);
     void (*__ctors_end)(void);
     void long_ap_startup(cpu_data *cpu);
@@ -45,15 +45,13 @@ extern "C" {
     void init_ap_trampoline(void*, cpu_data *, void (*)());
 }
 
-using namespace kernel;
-
 volatile size_t ap_startup_count;
 static bool scheduler_ready = false;
 
 /// Bootstrap the memory managers.
-void memory_initialize_pre_ctors(init::args &kargs);
-void memory_initialize_post_ctors(init::args &kargs);
-void load_init_server(init::program &program, uintptr_t modules_address);
+void memory_initialize_pre_ctors(bootproto::args &kargs);
+void memory_initialize_post_ctors(bootproto::args &kargs);
+void load_init_server(bootproto::program &program, uintptr_t modules_address);
 
 unsigned start_aps(lapic &apic, const util::vector<uint8_t> &ids, void *kpml4);
 
@@ -80,11 +78,11 @@ run_constructors()
 }
 
 void
-kernel_main(init::args *args)
+kernel_main(bootproto::args *args)
 {
     if (args->panic) {
         IDT::set_nmi_handler(args->panic->entrypoint);
-        panic::symbol_table = args->symbol_table | memory::page_offset;
+        panic::symbol_table = args->symbol_table | mem::linear_offset;
     }
 
     init_console();
@@ -108,7 +106,7 @@ kernel_main(init::args *args)
     cpu->rsp0 = idle_stack_end;
     cpu_early_init(cpu);
 
-    kassert(args->magic == init::args_magic,
+    kassert(args->magic == bootproto::args_magic,
             "Bad kernel args magic number");
 
     log::debug(logs::boot, "jsix init args are at: %016lx", args);
@@ -193,8 +191,8 @@ kernel_main(init::args *args)
 unsigned
 start_aps(lapic &apic, const util::vector<uint8_t> &ids, void *kpml4)
 {
-    using memory::frame_size;
-    using memory::kernel_stack_pages;
+    using mem::frame_size;
+    using mem::kernel_stack_pages;
 
     extern size_t ap_startup_code_size;
     extern process &g_kernel_process;