diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000000..c5a1abbe51
Binary files /dev/null and b/.DS_Store differ
diff --git a/cmd/notary/cert.go b/cmd/notary/cert.go
index 9ed6937724..e941dd4249 100644
--- a/cmd/notary/cert.go
+++ b/cmd/notary/cert.go
@@ -53,9 +53,9 @@ func certRemove(cmd *cobra.Command, args []string) {
 		cmd.Usage()
 		fatalf("Must specify the cert ID or the GUN of the certificates to remove")
 	}
-
 	parseConfig()
 
+	trustDir := mainViper.GetString("trustDir")
 	keysPath := filepath.Join(trustDir, notary.PrivDir)
 	fileKeyStore, err := trustmanager.NewKeyFileStore(keysPath, retriever)
 	if err != nil {
@@ -122,9 +122,9 @@ func certList(cmd *cobra.Command, args []string) {
 		cmd.Usage()
 		os.Exit(1)
 	}
-
 	parseConfig()
 
+	trustDir := mainViper.GetString("trustDir")
 	keysPath := filepath.Join(trustDir, notary.PrivDir)
 	fileKeyStore, err := trustmanager.NewKeyFileStore(keysPath, retriever)
 	if err != nil {
diff --git a/cmd/notary/integration_test.go b/cmd/notary/integration_test.go
index 0cf30fee4b..f2c0c09e27 100644
--- a/cmd/notary/integration_test.go
+++ b/cmd/notary/integration_test.go
@@ -510,6 +510,27 @@ func TestClientCertInteraction(t *testing.T) {
 	assertNumCerts(t, tempDir, 0)
 }
 
+// Tests default root key generation
+func TestDefaultRootKeyGeneration(t *testing.T) {
+	// -- setup --
+	cleanup := setUp(t)
+	defer cleanup()
+
+	tempDir, err := ioutil.TempDir("/tmp", "repo")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tempDir)
+
+	// -- tests --
+
+	// starts out with no keys
+	assertNumKeys(t, tempDir, 0, 0, true)
+
+	// generate root key with no algorithm produces a single ECDSA root key and no other keys
+	_, err = runCommand(t, tempDir, "key", "generate")
+	assert.NoError(t, err)
+	assertNumKeys(t, tempDir, 1, 0, true)
+}
+
 func TestMain(m *testing.M) {
 	if testing.Short() {
 		// skip
diff --git a/cmd/notary/keys.go b/cmd/notary/keys.go
index 985d33e427..b8e179c180 100644
--- a/cmd/notary/keys.go
+++ b/cmd/notary/keys.go
@@ -97,7 +97,7 @@ func keysList(cmd *cobra.Command, args []string) {
 
 	parseConfig()
 
-	stores := getKeyStores(cmd, trustDir, retriever, true)
+	stores := getKeyStores(cmd, mainViper.GetString("trustDir"), retriever, true)
 
 	keys := make(map[trustmanager.KeyStore]map[string]string)
 	for _, store := range stores {
@@ -137,15 +137,19 @@ func keysList(cmd *cobra.Command, args []string) {
 }
 
 func keysGenerateRootKey(cmd *cobra.Command, args []string) {
-	if len(args) < 1 {
-		cmd.Usage()
-		fatalf("Must specify an Algorithm (RSA, ECDSA)")
+	parseConfig()
+
+	// If no param is given to generate, generates an ecdsa key by default
+	algorithm := data.ECDSAKey
+
+	// If we were provided an argument lets attempt to use it as an algorithm
+	if len(args) > 0 {
+		algorithm = args[0]
 	}
 
-	algorithm := args[0]
 	allowedCiphers := map[string]bool{
-		"rsa":   true,
-		"ecdsa": true,
+		data.ECDSAKey: true,
+		data.RSAKey:   true,
 	}
 
 	if !allowedCiphers[strings.ToLower(algorithm)] {
@@ -156,7 +160,7 @@ func keysGenerateRootKey(cmd *cobra.Command, args []string) {
 
 	cs := cryptoservice.NewCryptoService(
 		"",
-		getKeyStores(cmd, trustDir, retriever, true)...,
+		getKeyStores(cmd, mainViper.GetString("trustDir"), retriever, true)...,
 	)
 
 	pubKey, err := cs.Create(data.CanonicalRootRole, algorithm)
@@ -174,13 +178,12 @@ func keysExport(cmd *cobra.Command, args []string) {
 		fatalf("Must specify output filename for export")
 	}
 
-	exportFilename := args[0]
-
 	parseConfig()
+	exportFilename := args[0]
 
 	cs := cryptoservice.NewCryptoService(
 		"",
-		getKeyStores(cmd, trustDir, retriever, true)...,
+		getKeyStores(cmd, mainViper.GetString("trustDir"), retriever, true)...,
 	)
 
 	exportFile, err := os.Create(exportFilename)
@@ -212,6 +215,8 @@ func keysExportRoot(cmd *cobra.Command, args []string) {
 		fatalf("Must specify key ID and output filename for export")
 	}
 
+	parseConfig()
+
 	keyID := args[0]
 	exportFilename := args[1]
 
@@ -223,7 +228,7 @@ func keysExportRoot(cmd *cobra.Command, args []string) {
 
 	cs := cryptoservice.NewCryptoService(
 		"",
-		getKeyStores(cmd, trustDir, retriever, true)...,
+		getKeyStores(cmd, mainViper.GetString("trustDir"), retriever, true)...,
 	)
 
 	exportFile, err := os.Create(exportFilename)
@@ -258,7 +263,7 @@ func keysImport(cmd *cobra.Command, args []string) {
 
 	cs := cryptoservice.NewCryptoService(
 		"",
-		getKeyStores(cmd, trustDir, retriever, true)...,
+		getKeyStores(cmd, mainViper.GetString("trustDir"), retriever, true)...,
 	)
 
 	zipReader, err := zip.OpenReader(importFilename)
@@ -281,15 +286,15 @@ func keysImportRoot(cmd *cobra.Command, args []string) {
 		fatalf("Must specify input filename for import")
 	}
 
-	importFilename := args[0]
-
 	parseConfig()
 
 	cs := cryptoservice.NewCryptoService(
 		"",
-		getKeyStores(cmd, trustDir, retriever, true)...,
+		getKeyStores(cmd, mainViper.GetString("trustDir"), retriever, true)...,
 	)
 
+	importFilename := args[0]
+
 	importFile, err := os.Open(importFilename)
 	if err != nil {
 		fatalf("Opening file for import: %v", err)
@@ -317,7 +322,7 @@ func keysRotate(cmd *cobra.Command, args []string) {
 	parseConfig()
 
 	gun := args[0]
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, remoteTrustServer, nil, retriever)
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, remoteTrustServer, nil, retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
diff --git a/cmd/notary/main.go b/cmd/notary/main.go
index 78791f80b0..c01fb0cae5 100644
--- a/cmd/notary/main.go
+++ b/cmd/notary/main.go
@@ -43,21 +43,17 @@ func parseConfig() {
 		logrus.SetOutput(os.Stderr)
 	}
 
-	if trustDir == "" {
-		// Get home directory for current user
-		homeDir, err := homedir.Dir()
-		if err != nil {
-			fatalf("Cannot get current user home directory: %v", err)
-		}
-		if homeDir == "" {
-			fatalf("Cannot get current user home directory")
-		}
-		trustDir = filepath.Join(homeDir, filepath.Dir(configDir))
-
-		logrus.Debugf("no trust directory provided, using default: %s", trustDir)
-	} else {
-		logrus.Debugf("trust directory provided: %s", trustDir)
+	// Get home directory for current user
+	homeDir, err := homedir.Dir()
+	if err != nil {
+		fatalf("Cannot get current user home directory: %v", err)
 	}
+	if homeDir == "" {
+		fatalf("Cannot get current user home directory")
+	}
+
+	// By default our trust directory (where keys are stored) is in ~/.notary/
+	mainViper.SetDefault("trustDir", filepath.Join(homeDir, filepath.Dir(configDir)))
 
 	// If there was a commandline configFile set, we parse that.
 	// If there wasn't we attempt to find it on the default location ~/.notary/config
@@ -66,7 +62,7 @@ func parseConfig() {
 		configFileName = strings.TrimSuffix(filepath.Base(configFile), filepath.Ext(configFile))
 		configPath = filepath.Dir(configFile)
 	} else {
-		configPath = trustDir
+		configPath = filepath.Join(homeDir, filepath.Dir(configDir))
 	}
 
 	// Setup the configuration details into viper
@@ -75,7 +71,7 @@ func parseConfig() {
 	mainViper.AddConfigPath(configPath)
 
 	// Find and read the config file
-	err := mainViper.ReadInConfig()
+	err = mainViper.ReadInConfig()
 	if err != nil {
 		logrus.Debugf("configuration file not found, using defaults")
 		// Ignore if the configuration file doesn't exist, we can use the defaults
@@ -83,6 +79,20 @@ func parseConfig() {
 			fatalf("Fatal error config file: %v", err)
 		}
 	}
+
+	// At this point we either have the default value or the one set by the config.
+	// Either way, the command-line flag has precedence and overwrives the value
+	if trustDir != "" {
+		mainViper.Set("trustDir", trustDir)
+	}
+
+	// Expands all the possible ~/ that have been given, either through -d or config
+	// If there is no error, user it, if not, attempt to use whatever the user gave us
+	expandedTrustDir, err := homedir.Expand(mainViper.GetString("trustDir"))
+	if err == nil {
+		mainViper.Set("trustDir", expandedTrustDir)
+	}
+	logrus.Debugf("using the following trust directory: %s", mainViper.GetString("trustDir"))
 }
 
 func setupCommand(notaryCmd *cobra.Command) {
@@ -97,7 +107,7 @@ func setupCommand(notaryCmd *cobra.Command) {
 
 	notaryCmd.AddCommand(versionCmd)
 
-	notaryCmd.PersistentFlags().StringVarP(&trustDir, "trustdir", "d", "", "Directory where the trust data is persisted to")
+	notaryCmd.PersistentFlags().StringVarP(&trustDir, "trustDir", "d", "", "Directory where the trust data is persisted to")
 	notaryCmd.PersistentFlags().StringVarP(&configFile, "configFile", "c", "", "Path to the configuration file to use")
 	notaryCmd.PersistentFlags().BoolVarP(&verbose, "verbose", "v", false, "Verbose output")
 	notaryCmd.PersistentFlags().StringVarP(&remoteTrustServer, "server", "s", "", "Remote trust server location")
diff --git a/cmd/notary/tuf.go b/cmd/notary/tuf.go
index 16b6ef57d7..299bb18f77 100644
--- a/cmd/notary/tuf.go
+++ b/cmd/notary/tuf.go
@@ -86,15 +86,15 @@ func tufAdd(cmd *cobra.Command, args []string) {
 		cmd.Usage()
 		fatalf("Must specify a GUN, target, and path to target data")
 	}
+	parseConfig()
 
 	gun := args[0]
 	targetName := args[1]
 	targetPath := args[2]
 
-	parseConfig()
 	// no online operations are performed by add so the transport argument
 	// should be nil
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), nil, retriever)
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), nil, retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
@@ -118,10 +118,10 @@ func tufInit(cmd *cobra.Command, args []string) {
 		fatalf("Must specify a GUN")
 	}
 
-	gun := args[0]
 	parseConfig()
+	gun := args[0]
 
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), getTransport(gun, false), retriever)
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), getTransport(gun, false), retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
@@ -154,10 +154,10 @@ func tufList(cmd *cobra.Command, args []string) {
 		cmd.Usage()
 		fatalf("Must specify a GUN")
 	}
-	gun := args[0]
 	parseConfig()
+	gun := args[0]
 
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), getTransport(gun, true), retriever)
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), getTransport(gun, true), retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
@@ -179,11 +179,12 @@ func tufLookup(cmd *cobra.Command, args []string) {
 		cmd.Usage()
 		fatalf("Must specify a GUN and target")
 	}
-	gun := args[0]
-	targetName := args[1]
 	parseConfig()
 
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), getTransport(gun, true), retriever)
+	gun := args[0]
+	targetName := args[1]
+
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), getTransport(gun, true), retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
@@ -202,10 +203,10 @@ func tufStatus(cmd *cobra.Command, args []string) {
 		fatalf("Must specify a GUN")
 	}
 
-	gun := args[0]
 	parseConfig()
+	gun := args[0]
 
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), nil, retriever)
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), nil, retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
@@ -234,12 +235,12 @@ func tufPublish(cmd *cobra.Command, args []string) {
 		fatalf("Must specify a GUN")
 	}
 
-	gun := args[0]
 	parseConfig()
+	gun := args[0]
 
 	cmd.Println("Pushing changes to", gun)
 
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), getTransport(gun, false), retriever)
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), getTransport(gun, false), retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
@@ -255,13 +256,14 @@ func tufRemove(cmd *cobra.Command, args []string) {
 		cmd.Usage()
 		fatalf("Must specify a GUN and target")
 	}
+	parseConfig()
+
 	gun := args[0]
 	targetName := args[1]
-	parseConfig()
 
 	// no online operation are performed by remove so the transport argument
 	// should be nil.
-	repo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), nil, retriever)
+	repo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), nil, retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}
@@ -278,6 +280,7 @@ func verify(cmd *cobra.Command, args []string) {
 		cmd.Usage()
 		fatalf("Must specify a GUN and target")
 	}
+
 	parseConfig()
 
 	// Reads all of the data on STDIN
@@ -288,7 +291,7 @@ func verify(cmd *cobra.Command, args []string) {
 
 	gun := args[0]
 	targetName := args[1]
-	nRepo, err := notaryclient.NewNotaryRepository(trustDir, gun, getRemoteTrustServer(), getTransport(gun, true), retriever)
+	nRepo, err := notaryclient.NewNotaryRepository(mainViper.GetString("trustDir"), gun, getRemoteTrustServer(), getTransport(gun, true), retriever)
 	if err != nil {
 		fatalf(err.Error())
 	}