tidy up

zk/Bus.md

@@ -19,8 +19,8 @@ can mean:
 ## Main buses
 
 | Bus type      | Description                                                                                                                                                                                           |
-| ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| System bus    | The primary pathway between the CPU and [memory](Memory.md). It comprises the **data bus** that transfers data from the memory to the CPU and the **address bus** which transmits requests from the CPU to memory. |
+| ------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| System bus    | The primary pathway between the CPU and memory. It comprises the **data bus** that transfers data from the memory to the CPU and the **address bus** which transmits requests from the CPU to memory. |
 | Internal bus  | Connects local devices for example the harddisk to the CPU.                                                                                                                                           |
 | External bus  | Connects peripheral devices such as disks and printers to the [motherboard](Motherboard.md)                                                                                                           |
 | Expansion bus | Allows expansion boards to access the CPU and memory.                                                                                                                                                 |

zk/CPU_architecture.md

@@ -8,10 +8,10 @@ tags:
 
 At the core of a computer sits the Central Processing Unit. This is the assembly
 of chips that execute all computation. Instructions are passed to the CPU along
-the data bus part of the [system bus](Bus.md) from the
-memory. The [kernel](The_kernel.md), also residing in memory,
-sequences and schedules the sending of data to the CPU and manages requests from
-the CPU for data in memory.
+the data bus part of the [system bus](Bus.md) from the memory. The
+[kernel](/zk/The_kernel.md), also residing in memory, sequences and schedules
+the sending of data to the CPU and manages requests from the CPU for data in
+memory.
 
 The CPU comprises three core components:
 
@@ -29,13 +29,12 @@ The CPU comprises three core components:
 ## Registers
 
 This is the part of the CPU that stores data. The memory cells that comprise it
-do not have [capacitors](Memory.md) (unlike RAM)
-so they cannot store very much data but they work faster, which is what is
-important. Because their memory capacity is so small, we measure the size of
-registers in bits rather than bytes.
+do not have capacitors (unlike RAM) so they cannot store very much data but they
+work faster, which is what is important. Because their memory capacity is so
+small, we measure the size of registers in bits rather than bytes.
 
 In terms of speed, registers sit at the top part of the overall
-[memory hierarchy](Memory.md#the-memory-hierarchy).
+[memory hierarchy](./The_memory_hierarchy.md).
 
 There are five main types of register in the CPU:
 
@@ -49,15 +48,15 @@ There are five main types of register in the CPU:
 
 ## Arithmetic Logic Unit
 
-See [Arithmetic Logic Unit](Arithmetic_Logic_Unit.md)
+See [Arithmetic Logic Unit](././Arithmetic_Logic_Unit.md))
 
 ## Control Unit
 
-The CPU's [controller](Chipset_and_controllers.md). It
-takes the instructions in binary form from RAM memory (separate from the CPU,
-but connected) and then signals to the to ALU and memory registers what it is
-supposed to do to execute the instructions. Think of it as the overseer that
-gets the ALU and registers to work together to run program instructions.
+The CPU's [controller](Chipset_and_controllers.md). It takes the instructions in
+binary form from RAM memory (separate from the CPU, but connected) and then
+signals to the to ALU and memory registers what it is supposed to do to execute
+the instructions. Think of it as the overseer that gets the ALU and registers to
+work together to run program instructions.
 
 ## The system clock
 
@@ -73,11 +72,9 @@ cycle_.
 The clock's circuitry is based on a quartz crystal system like that used in
 watches. At precisely timed intervals, the clock sends out pulses of electricity
 that cause bits to move from place to place within
-[logic gates](Logic_gates.md) or
-between logic gates and
-[registers](CPU_architecture.md#registers). This is
-covered in greater detail in the discussion of
-[clock signals in digital circuits](Clock_signals.md).
+[logic gates](/zk/Logic_gates.md) or between logic gates and
+[registers](./CPU_architecture.md). This is covered in greater detail in the
+discussion of [clock signals in digital circuits](Clock_signals.md).
 
 Simple instructions such as add can often be executed in just one clock cycle,
 whilst complex operations such as divide will require a number of smaller steps,
@@ -95,16 +92,14 @@ Hz a processor possesses.
 ## Processing cycles
 
 Each "cycle" is the execution of a process that commences once the
-[kernel](The_kernel.md) hands control to the CPU. Each cycle
-follows a sequence of events known as
-[fetch, decode, and execute](Fetch_decode_execute.md).
+[kernel](The_kernel.md) hands control to the CPU. Each cycle follows a sequence
+of events known as [fetch, decode, and execute](Fetch_decode_execute.md).
 
 ## Electromagnetism: broader scientific context
 
 Hertz was the scientist who detected
-[electromagentic waves](Electromagnetism.md).
-We use Hertz as a measure of the frequency of electromatic wave cycles in a
-signal.
+[electromagentic waves](Electromagnetism.md). We use Hertz as a measure of the
+frequency of electromatic wave cycles in a signal.
 
 ![](/img/hertz_wave_freq.gif)
 

zk/Chipset_and_controllers.md

@@ -10,8 +10,7 @@ A **controller** is simply a circuit that controls a process. The **chipset** is
 a combination of controllers placed on the same piece of silicon.
 
 The chipset manages the data flow between the different components that comprise
-the [motherboard](Motherboard.md): processor,
-[memory](Memory.md),
+the [motherboard](Motherboard.md): processor, memory,
 [harddisk](What_are_disks.md) and peripherals.
 
 Buses run in and out of the chipset into these key motherboard components. The

zk/Filesystems.md

@@ -10,9 +10,9 @@ tags:
 We cannot yet mount or interact with the partitions we have created. This is
 because we have not added a filesystem to each partition.
 
-> A filesytem is a form of [database](Basic_database_concepts.md); it
-> supplies the structure to transform a simple block device into the
-> sophisticated hierarchy of files and subdirectories that users can understand.
+> A filesytem is a form of database; it supplies the structure to transform a
+> simple block device into the sophisticated hierarchy of files and
+> subdirectories that users can understand.
 
 Linux recognises many types of filesystems. The native Linux filesystem is the
 **ext4** (Fourth Extended Filesystem). Another common filesystem is **FAT**
@@ -87,10 +87,9 @@ UUID=c53577b5-92ef-4a0a-9a19-e488bfdfa39c	/home     	ext4      	rw,relatime	0 2
 
 ```
 
-It shows my root and home filesystems and my
-[swap](Swap_space.md) file. Note that we use the UUID
-to name the partition rather than its name in `/dev/`. The order of the
-parameters is as follows:
+It shows my root and home filesystems and my [swap](Swap_space.md) file. Note
+that we use the UUID to name the partition rather than its name in `/dev/`. The
+order of the parameters is as follows:
 
 - Device name or UUID
 - The mount point

zk/Machine_code.md

@@ -11,7 +11,8 @@ created: Monday, March 11, 2024
 # Machine code
 
 No matter how a program was originally written, it eventually needs to execute
-on a [[CPU_architecture|CPU]] as a series of machine language instructions.
+on a [CPU architecture](/zk/CPU_architecture.md) as a series of machine language
+instructions.
 
 ## Example machine instruction
 
@@ -60,5 +61,5 @@ instruction:
 ## Difficulty
 
 Binary sequences are hard to understand, even if converted to the
-[[Hexadecimal_number_system]]. We have a better way of managing operations on
-the machine level: [assembly](Assembly.md)
+[hexadecimal number system](./Hexadecimal_number_system.md). We have a better
+way of managing operations on the machine level: [assembly](Assembly.md)

zk/The_kernel.md

@@ -65,8 +65,7 @@ It has the following jobs to manage:
 - Managing read-only memory
 - Allowing for the use of disk space as auxiliary memory
 
-> Modern CPUs include a
-> [memory management unit](Virtual_memory_and_the_MMU_in_Linux.md#the-memory-management-unit-mmu)
+> Modern CPUs include a [memory management unit](./Memory_Management_Unit.md)
 > which provides the kernel with **virtual** memory. In this scenario, memory
 > isn't directly accessed by the process instead it works on the assumption that
 > is has access to the entire memory of the machine and this is then translated

zk/What_are_disks.md

@@ -6,8 +6,8 @@ tags:
 
 # What are disks?
 
-A disk is a mass storage [block_device](Devices.md) which we
-can write to and read from.
+A disk is a mass storage [block_device](Devices.md) which we can write to and
+read from.
 
 ## SCSI
 
@@ -22,10 +22,9 @@ The following diagram represents the basic anatomy of a disk device.
 
 ![](/img/harddisk.png)
 
-- A disk is divided up into [partitions](Partitions.md)
-  which are subsections of the overall disk. The kernel presents each partition
-  as a [block device](Devices.md) as it would with an entire
-  disk.
+- A disk is divided up into [partitions](./Linux_disk_partitions.md) which are
+  subsections of the overall disk. The kernel presents each partition as a
+  [block device](Devices.md) as it would with an entire disk.
 - The disk dedicates a small part of its contents to a **partition table**: this
   defines the different partitions that comprise the total disk space.
 - The **filesystem** is a database of files and directories: this comprises the