diff --git a/yggdrasil.go b/yggdrasil.go
index 87f7627d..385878a5 100644
--- a/yggdrasil.go
+++ b/yggdrasil.go
@@ -31,10 +31,20 @@ type node struct {
 	core Core
 }
 
+// Generates default configuration. This is used when outputting the -genconf
+// parameter and also when using -autoconf. The isAutoconf flag is used to
+// determine whether the operating system should select a free port by itself
+// (which guarantees that there will not be a conflict with any other services)
+// or whether to generate a random port number. The only side effect of setting
+// isAutoconf is that the TCP and UDP ports will likely end up with different
+// port numbers.
 func generateConfig(isAutoconf bool) *nodeConfig {
+	// Create a new core.
 	core := Core{}
+	// Generate encryption keys.
 	bpub, bpriv := core.NewEncryptionKeys()
 	spub, spriv := core.NewSigningKeys()
+	// Create a node configuration and populate it.
 	cfg := nodeConfig{}
 	if isAutoconf {
 		cfg.Listen = "[::]:0"
@@ -57,6 +67,8 @@ func generateConfig(isAutoconf bool) *nodeConfig {
 	return &cfg
 }
 
+// Generates a new configuration and returns it in HJSON format. This is used
+// with -genconf.
 func doGenconf() string {
 	cfg := generateConfig(false)
 	bs, err := hjson.Marshal(cfg)
@@ -66,37 +78,51 @@ func doGenconf() string {
 	return string(bs)
 }
 
-var pprof = flag.Bool("pprof", false, "Run pprof, see http://localhost:6060/debug/pprof/")
-var genconf = flag.Bool("genconf", false, "print a new config to stdout")
-var useconf = flag.Bool("useconf", false, "read config from stdin")
-var useconffile = flag.String("useconffile", "", "read config from specified file path")
-var normaliseconf = flag.Bool("normaliseconf", false, "use in combination with either -useconf or -useconffile, outputs your configuration normalised")
-var autoconf = flag.Bool("autoconf", false, "automatic mode (dynamic IP, peer with IPv6 neighbors)")
-
+// The main function is responsible for configuring and starting Yggdrasil.
 func main() {
+	// Configure the command line parameters.
+	pprof := flag.Bool("pprof", false, "Run pprof, see http://localhost:6060/debug/pprof/")
+	genconf := flag.Bool("genconf", false, "print a new config to stdout")
+	useconf := flag.Bool("useconf", false, "read config from stdin")
+	useconffile := flag.String("useconffile", "", "read config from specified file path")
+	normaliseconf := flag.Bool("normaliseconf", false, "use in combination with either -useconf or -useconffile, outputs your configuration normalised")
+	autoconf := flag.Bool("autoconf", false, "automatic mode (dynamic IP, peer with IPv6 neighbors)")
 	flag.Parse()
+
 	var cfg *nodeConfig
 	switch {
 	case *autoconf:
+		// Use an autoconf-generated config, this will give us random keys and
+		// port numbers, and will use an automatically selected TUN/TAP interface.
 		cfg = generateConfig(true)
 	case *useconffile != "" || *useconf:
+		// Use a configuration file. If -useconf, the configuration will be read
+		// from stdin. If -useconffile, the configuration will be read from the
+		// filesystem.
 		var config []byte
 		var err error
 		if *useconffile != "" {
+			// Read the file from the filesystem
 			config, err = ioutil.ReadFile(*useconffile)
 		} else {
+			// Read the file from stdin.
 			config, err = ioutil.ReadAll(os.Stdin)
 		}
 		if err != nil {
 			panic(err)
 		}
+		// Generate a new configuration - this gives us a set of sane defaults -
+		// then parse the configuration we loaded above on top of it. The effect
+		// of this is that any configuration item that is missing from the provided
+		// configuration will use a sane default.
 		cfg = generateConfig(false)
 		var dat map[string]interface{}
 		if err := hjson.Unmarshal(config, &dat); err != nil {
 			panic(err)
 		}
 		// For now we will do a little bit to help the user adjust their
-		// configuration to match the new configuration format
+		// configuration to match the new configuration format, as some of the key
+		// names have changed recently.
 		changes := map[string]string{
 			"Multicast":      "",
 			"LinkLocal":      "MulticastInterfaces",
@@ -106,6 +132,7 @@ func main() {
 			"SigPriv":        "SigningPrivateKey",
 			"AllowedBoxPubs": "AllowedEncryptionPublicKeys",
 		}
+		// Loop over the mappings aove and see if we have anything to fix.
 		for from, to := range changes {
 			if _, ok := dat[from]; ok {
 				if to == "" {
@@ -116,15 +143,24 @@ func main() {
 					if !*normaliseconf {
 						log.Println("Warning: Deprecated config option", from, "- please rename to", to)
 					}
+					// If the configuration file doesn't already contain a line with the
+					// new name then set it to the old value. This makes sure that we
+					// don't overwrite something that was put there intentionally.
 					if _, ok := dat[to]; !ok {
 						dat[to] = dat[from]
 					}
 				}
 			}
 		}
+		// Overlay our newly mapped configuration onto the autoconf node config that
+		// we generated above.
 		if err = mapstructure.Decode(dat, &cfg); err != nil {
 			panic(err)
 		}
+		// If the -normaliseconf option was specified then remarshal the above
+		// configuration and print it back to stdout. This lets the user update
+		// their configuration file with newly mapped names (like above) or to
+		// convert from plain JSON to commented HJSON.
 		if *normaliseconf {
 			bs, err := hjson.Marshal(cfg)
 			if err != nil {
@@ -134,23 +170,35 @@ func main() {
 			return
 		}
 	case *genconf:
+		// Generate a new configuration and print it to stdout.
 		fmt.Println(doGenconf())
 	default:
+		// No flags were provided, therefore print the list of flags to stdout.
 		flag.PrintDefaults()
 	}
+	// Have we got a working configuration? If we don't then it probably means
+	// that neither -autoconf, -useconf or -useconffile were set above. Stop
+	// if we don't.
 	if cfg == nil {
 		return
 	}
+	// Create a new logger that logs output to stdout.
 	logger := log.New(os.Stdout, "", log.Flags())
+	// If the -pprof flag was provided then start the pprof service on port 6060.
 	if *pprof {
 		runtime.SetBlockProfileRate(1)
 		go func() { log.Println(http.ListenAndServe("localhost:6060", nil)) }()
 	}
-	// Setup
+	// Setup the Yggdrasil node itself. The node{} type includes a Core, so we
+	// don't need to create this manually.
 	n := node{}
+	// Check to see if any allowed encryption keys were provided in the config.
+	// If they were then set them now.
 	for _, pBoxStr := range cfg.AllowedEncryptionPublicKeys {
 		n.core.AddAllowedEncryptionPublicKey(pBoxStr)
 	}
+	// Check to see if any multicast interface expressions were provided in the
+	// config. If they were then set them now.
 	for _, ll := range cfg.MulticastInterfaces {
 		ifceExpr, err := regexp.Compile(ll)
 		if err != nil {
@@ -158,10 +206,17 @@ func main() {
 		}
 		n.core.AddMulticastInterfaceExpr(ifceExpr)
 	}
+	// Now that we have a working configuration, and we have provided any allowed
+	// encryption keys or multicast interface expressions, we can now actually
+	// start Yggdrasil. This will start the router, switch, DHT node, TCP and UDP
+	// sockets, TUN/TAP adapter and multicast discovery port.
 	if err := n.core.Start(cfg, logger); err != nil {
 		logger.Println("An error occured during startup")
 		panic(err)
 	}
+	// If any static peers were provided in the configuration above then we should
+	// configure them. The loop ensures that disconnected peers will eventually
+	// be reconnected with.
 	go func() {
 		if len(cfg.Peers) == 0 {
 			return
@@ -174,22 +229,27 @@ func main() {
 			time.Sleep(time.Minute)
 		}
 	}()
+	// The Stop function ensures that the TUN/TAP adapter is correctly shut down
+	// before the program exits.
 	defer func() {
 		n.core.Stop()
 	}()
+	// Make some nice output that tells us what our IPv6 address and subnet are.
+	// This is just logged to stdout for the user.
 	address := (*n.core.GetAddress())[:]
 	subnet := (*n.core.GetSubnet())[:]
 	subnet = append(subnet, 0, 0, 0, 0, 0, 0, 0, 0)
 	logger.Printf("Your IPv6 address is %s", net.IP(address).String())
 	logger.Printf("Your IPv6 subnet is %s/64", net.IP(subnet).String())
-	// Catch interrupt to exit gracefully
+	// Catch interrupts from the operating system to exit gracefully.
 	c := make(chan os.Signal, 1)
 	signal.Notify(c, os.Interrupt, syscall.SIGTERM)
-	// Create a function to capture the service being stopped on Windows
+	// Create a function to capture the service being stopped on Windows.
 	winTerminate := func() {
 		c <- os.Interrupt
 	}
 	minwinsvc.SetOnExit(winTerminate)
-	// Wait for the terminate/interrupt signal
+	// Wait for the terminate/interrupt signal. Once a signal is received, the
+	// deferred Stop function above will run which will shut down TUN/TAP.
 	<-c
 }