[all] Remove dependencies on non-freestanding libc

This is the first of two rather big changes to clean up includes
throughout the project. In this commit, the implicit semi-dependency on
libc that bonnibel adds to every module is removed. Previously, I was
sloppy with includes of libc headers and include directory order. Now,
the freestanding headers from libc are split out into libc_free, and an
implicit real dependency is added onto this module, unless `no_libc` is
set to `True`. The full libc needs to be explicitly specified as a
dependency to be used.

Several things needed to change in order to do this:

- Many places use `memset` or `memcpy` that cannot depend on libc. The
  kernel has basic implementations of them itself for this reason. Now
  those functions are moved into the lower-level `j6/memutils.h`, and
  libc merely references them. Other modules are now free to reference
  those functions from libj6 instead.
- The kernel's `assert.h` was renamed kassert.h (matching its `kassert`
  function) so that the new `util/assert.h` can use `__has_include` to
  detect it and make sure the `assert` macro is usable in libutil code.
- Several implementation header files under `__libj6/` also moved under
  the new libc_free.
- A new `include_phase` property has been added to modules for Bonnibel,
  which can be "normal" (default) or "late" which uses `-idirafter`
  instead of `-I` for includes.
- Since `<utility>` and `<new>` are not freestanding, implementations of
  `remove_reference`, `forward`, `move`, and `swap` were added to the
  `util` namespace to replace those from `std`, and `util/new.h` was
  added to declare `operator new` and `operator delete`.

src/kernel/apic.cpp

@@ -1,5 +1,5 @@
 #include "apic.h"
-#include "assert.h"
+#include "kassert.h"
 #include "clock.h"
 #include "interrupts.h"
 #include "io.h"

src/kernel/cpprt.cpp

@@ -1,4 +1,4 @@
-#include "assert.h"
+#include "kassert.h"
 
 using __exit_func = void (*)(void *);
 

src/kernel/cpu.cpp

@@ -1,10 +1,9 @@
-#include <new>
 #include <stdint.h>
-#include <string.h>
+#include <j6/memutils.h>
 #include <util/bitset.h>
 #include <util/no_construct.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "cpu.h"
 #include "device_manager.h"
 #include "gdt.h"

src/kernel/device_manager.cpp

@@ -1,11 +1,10 @@
-#include <new>
 #include <stddef.h>
 #include <stdint.h>
 #include <util/misc.h> // for checksum
 #include <util/pointers.h>
 #include <arch/acpi/tables.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "apic.h"
 #include "clock.h"
 #include "device_manager.h"

src/kernel/frame_allocator.cpp

@@ -1,6 +1,6 @@
 #include <bootproto/kernel.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "debugcon.h"
 #include "frame_allocator.h"
 #include "logger.h"

src/kernel/gdt.cpp

@@ -1,9 +1,7 @@
-#include <stdint.h>
-#include <string.h>
-
+#include <j6/memutils.h>
 #include <util/no_construct.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "cpu.h"
 #include "gdt.h"
 #include "logger.h"

src/kernel/heap_allocator.cpp

@@ -1,11 +1,10 @@
-#include <new>
 #include <stdint.h>
-#include <string.h>
 
+#include <j6/memutils.h>
 #include <util/pointers.h>
 #include <util/util.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "heap_allocator.h"
 #include "memory.h"
 #include "objects/vm_area.h"

src/kernel/hpet.cpp

@@ -1,4 +1,4 @@
-#include "assert.h"
+#include "kassert.h"
 #include "device_manager.h"
 #include "hpet.h"
 #include "io.h"

src/kernel/idt.cpp

@@ -1,5 +1,4 @@
-#include <string.h>
-
+#include <j6/memutils.h>
 #include <util/no_construct.h>
 
 #include "cpu.h"

src/kernel/idt.h

@@ -2,7 +2,7 @@
 /// \file idt.h
 /// Definitions relating to a CPU's IDT table
 #include <stdint.h>
-#include "assert.h"
+#include "kassert.h"
 
 class IDT
 {

src/kernel/interrupts.cpp

@@ -1,7 +1,7 @@
 #include <stdint.h>
 #include <util/format.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "cpu.h"
 #include "device_manager.h"
 #include "idt.h"

src/kernel/kassert.cpp

@@ -1,4 +1,4 @@
-#include "assert.h"
+#include "kassert.h"
 #include "idt.h"
 
 namespace panic {

src/kernel/kernel.module

@@ -10,7 +10,7 @@ kernel = module("kernel",
     ld_script = "kernel.ld",
     sources = [
         "apic.cpp",
-        "assert.cpp",
+        "kassert.cpp",
         "boot.s",
         "capabilities.cpp",
         "clock.cpp",

src/kernel/kernel_main.cpp

@@ -1,11 +1,11 @@
 #include <stddef.h>
 #include <stdint.h>
-#include <string.h>
 
+#include <j6/memutils.h>
 #include <bootproto/kernel.h>
 #include <util/vector.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "capabilities.h"
 #include "cpu.h"
 #include "debugcon.h"

src/kernel/logger.cpp

@@ -1,10 +1,8 @@
-#include <new>
-#include <string.h>
-
+#include <j6/memutils.h>
 #include <util/format.h>
 #include <util/no_construct.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "logger.h"
 #include "objects/system.h"
 #include "objects/thread.h"

src/kernel/memory.cpp

@@ -2,27 +2,4 @@
 
 namespace std {
     enum class __attribute__ ((__type_visibility("default"))) align_val_t : size_t { };
-}
-
-// Implementation of memset and memcpy because we're not
-// linking libc into the kernel
-extern "C" {
-
-void *
-memset(void *s, uint8_t v, size_t n)
-{
-    uint8_t *p = reinterpret_cast<uint8_t *>(s);
-    for (size_t i = 0; i < n; ++i) p[i] = v;
-    return s;
-}
-
-void *
-memcpy(void *dest, const void *src, size_t n)
-{
-    const uint8_t *s = reinterpret_cast<const uint8_t *>(src);
-    uint8_t *d = reinterpret_cast<uint8_t *>(dest);
-    for (size_t i = 0; i < n; ++i) d[i] = s[i];
-    return d;
-}
-
-}
+}

src/kernel/memory_bootstrap.cpp

@@ -1,11 +1,8 @@
-#include <new>
-#include <utility>
-
 #include <arch/memory.h>
 #include <bootproto/kernel.h>
 #include <util/no_construct.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "capabilities.h"
 #include "device_manager.h"
 #include "frame_allocator.h"

src/kernel/objects/kobject.cpp

@@ -1,7 +1,7 @@
 #include <j6/errors.h>
 #include <j6/types.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "logger.h"
 #include "objects/kobject.h"
 #include "objects/thread.h"

src/kernel/objects/process.cpp

@@ -1,8 +1,6 @@
-#include <new>
-
 #include <util/no_construct.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "capabilities.h"
 #include "cpu.h"
 #include "objects/process.h"

src/kernel/objects/thread.cpp

@@ -1,5 +1,6 @@
 #include <util/pointers.h>
 
+#include "kassert.h"
 #include "capabilities.h"
 #include "cpu.h"
 #include "logger.h"

src/kernel/objects/vm_area.cpp

@@ -1,5 +1,5 @@
 
-#include "assert.h"
+#include "kassert.h"
 #include "frame_allocator.h"
 #include "memory.h"
 #include "objects/vm_area.h"

src/kernel/page_table.cpp

@@ -1,7 +1,7 @@
-#include <string.h>
+#include <j6/memutils.h>
 #include <util/pointers.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "memory.h"
 #include "frame_allocator.h"
 #include "page_table.h"

src/kernel/page_tree.cpp

@@ -1,8 +1,7 @@
-#include <string.h>
-
+#include <j6/memutils.h>
 #include <arch/memory.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "frame_allocator.h"
 #include "page_tree.h"
 

src/kernel/panic.serial/main.cpp

@@ -1,4 +1,4 @@
-#include <new>
+#include <util/new.h>
 #include <util/no_construct.h>
 
 #include "cpu.h"

src/kernel/scheduler.cpp

@@ -3,7 +3,7 @@
 #include <util/spinlock.h>
 
 #include "apic.h"
-#include "assert.h"
+#include "kassert.h"
 #include "clock.h"
 #include "cpu.h"
 #include "debug.h"

src/kernel/slab_allocated.h

@@ -2,10 +2,11 @@
 /// \file slab_allocated.h
 /// A parent template class for slab-allocated objects
 
-#include <stdlib.h>
+#include <j6/memutils.h>
 #include <util/pointers.h>
 #include <util/vector.h>
 
+#include "kassert.h"
 #include "memory.h"
 
 template <typename T, size_t N>

src/kernel/syscall.cpp.cog

@@ -1,6 +1,6 @@
 // vim: ft=cpp
 #include <stddef.h>
-#include <string.h>
+#include <j6/memutils.h>
 
 
 #include "debug.h"

src/kernel/syscalls/futex.cpp

@@ -1,4 +1,5 @@
 #include <j6/errors.h>
+#include <util/basic_types.h>
 #include <util/node_map.h>
 #include <util/spinlock.h>
 
@@ -20,11 +21,11 @@ struct futex
     futex() = default;
     futex(futex &&other) :
         address {other.address},
-        queue {std::move(other.queue)} {}
+        queue {util::move(other.queue)} {}
 
     futex & operator=(futex &&other) {
         address = other.address;
-        queue = std::move(other.queue);
+        queue = util::move(other.queue);
         return *this;
     }
 };

src/kernel/syscalls/object.cpp

@@ -2,7 +2,7 @@
 #include <j6/types.h>
 #include <util/vector.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "logger.h"
 #include "objects/thread.h"
 #include "syscalls/helpers.h"

src/kernel/sysconf.cpp

@@ -1,6 +1,6 @@
-#include <string.h>
+#include <j6/memutils.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "cpu.h"
 #include "frame_allocator.h"
 #include "memory.h"

src/kernel/tss.cpp

@@ -1,7 +1,7 @@
-#include <string.h>
+#include <j6/memutils.h>
 #include <util/no_construct.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "cpu.h"
 #include "logger.h"
 #include "memory.h"

src/kernel/vm_space.cpp

@@ -1,8 +1,7 @@
-#include <string.h>
-
+#include <j6/memutils.h>
 #include <arch/memory.h>
 
-#include "assert.h"
+#include "kassert.h"
 #include "frame_allocator.h"
 #include "logger.h"
 #include "memory.h"

src/kernel/wait_queue.cpp

@@ -1,9 +1,9 @@
-#include <utility>
+#include <util/basic_types.h>
 #include "objects/thread.h"
 #include "wait_queue.h"
 
 wait_queue::wait_queue(wait_queue &&other) :
-    m_threads {std::move(other.m_threads)} {}
+    m_threads {util::move(other.m_threads)} {}
 
 wait_queue::~wait_queue() { clear(); }
 
@@ -11,7 +11,7 @@ wait_queue &
 wait_queue::operator=(wait_queue &&other)
 {
     clear();
-    m_threads = std::move(other.m_threads);
+    m_threads = util::move(other.m_threads);
     return *this;
 }