diff --git a/cmd/upgrade.go b/cmd/upgrade.go
new file mode 100644
index 000000000..b03d81f78
--- /dev/null
+++ b/cmd/upgrade.go
@@ -0,0 +1,40 @@
+package cmd
+
+import (
+	"os"
+
+	"github.com/chanzuckerberg/fogg/config"
+	"github.com/chanzuckerberg/fogg/errs"
+	"github.com/spf13/afero"
+	"github.com/spf13/cobra"
+)
+
+func init() {
+	upgrade.Flags().StringP("config", "c", "fogg.json", "Use this to override the fogg config file.")
+	rootCmd.AddCommand(upgrade)
+}
+
+var upgrade = &cobra.Command{
+	Use:   "upgrade",
+	Short: "Upgrades a fogg config",
+	Long: `This command will upgrade a fogg config.
+	Note that this might be a lossy transformation.`,
+	RunE: func(cmd *cobra.Command, args []string) error {
+		// Set up fs
+		pwd, err := os.Getwd()
+		if err != nil {
+			return errs.WrapUser(err, "can't get pwd")
+		}
+		fs := afero.NewBasePathFs(afero.NewOsFs(), pwd)
+
+		// handle flags
+		configFile, err := cmd.Flags().GetString("config")
+		if err != nil {
+			return errs.WrapInternal(err, "couldn't parse config flag")
+		}
+
+		// check that we are at root of initialized git repo
+		openGitOrExit(fs)
+		return config.Upgrade(fs, configFile)
+	},
+}
diff --git a/cmd/util.go b/cmd/util.go
index 2419cf0f0..4bd7c7842 100644
--- a/cmd/util.go
+++ b/cmd/util.go
@@ -8,7 +8,7 @@ import (
 	"strings"
 
 	"github.com/chanzuckerberg/fogg/config"
-	"github.com/chanzuckerberg/fogg/config/v2"
+	v2 "github.com/chanzuckerberg/fogg/config/v2"
 	"github.com/chanzuckerberg/fogg/errs"
 	"github.com/kr/pretty"
 	"github.com/sirupsen/logrus"
diff --git a/config/config.go b/config/config.go
index 1d3f9c498..4ec049173 100644
--- a/config/config.go
+++ b/config/config.go
@@ -5,8 +5,8 @@ import (
 	"io"
 	"io/ioutil"
 
-	"github.com/chanzuckerberg/fogg/config/v1"
-	"github.com/chanzuckerberg/fogg/config/v2"
+	v1 "github.com/chanzuckerberg/fogg/config/v1"
+	v2 "github.com/chanzuckerberg/fogg/config/v2"
 	"github.com/chanzuckerberg/fogg/errs"
 	"github.com/chanzuckerberg/fogg/util"
 	"github.com/sirupsen/logrus"
@@ -35,25 +35,33 @@ func InitConfig(project, region, bucket, table, awsProfile, owner, awsProviderVe
 	}
 }
 
-func FindAndReadConfig(fs afero.Fs, configFile string) (*v2.Config, error) {
+// FindConfig loads a config and its version into memory
+func FindConfig(fs afero.Fs, configFile string) ([]byte, int, error) {
 	f, err := fs.Open(configFile)
 	if err != nil {
-		return nil, errs.WrapUser(err, "unable to open config file")
+		return nil, 0, errs.WrapUser(err, "unable to open config file")
 	}
 	reader := io.ReadCloser(f)
 	defer reader.Close()
 
 	b, e := ioutil.ReadAll(reader)
 	if e != nil {
-		return nil, errs.WrapUser(e, "unable to read config")
+		return nil, 0, errs.WrapUser(e, "unable to read config")
 	}
 
 	v, err := detectVersion(b)
 	if err != nil {
-		return nil, err
+		return nil, 0, err
 	}
 	logrus.Debugf("config file version: %#v\n", v)
+	return b, v, nil
+}
 
+func FindAndReadConfig(fs afero.Fs, configFile string) (*v2.Config, error) {
+	b, v, err := FindConfig(fs, configFile)
+	if err != nil {
+		return nil, err
+	}
 	switch v {
 	case 1:
 		c, err := v1.ReadConfig(b)
@@ -71,13 +79,13 @@ func FindAndReadConfig(fs afero.Fs, configFile string) (*v2.Config, error) {
 	default:
 		return nil, errs.NewUser("could not figure out config file version")
 	}
-
 }
 
 type ver struct {
 	Version int `json:"version"`
 }
 
+// detectVersion will detect the version of a config
 func detectVersion(b []byte) (int, error) {
 	v := &ver{}
 	err := json.Unmarshal(b, v)
@@ -135,40 +143,37 @@ func UpgradeConfigVersion(c1 *v1.Config) (*v2.Config, error) {
 	}
 
 	for acctName, acct := range c1.Accounts {
-		c2.Accounts[acctName] = v2.Account{
-			Common: v2.Common{
-				Backend: &v2.Backend{
-					Bucket:      acct.InfraBucket,
-					DynamoTable: acct.InfraDynamoTable,
-					Profile:     acct.AWSProfileBackend,
-					Region:      acct.AWSRegionBackend,
-				},
-				ExtraVars: acct.ExtraVars,
-				Providers: &v2.Providers{
-					AWS: &v2.AWSProvider{
-						AccountID:         acct.AccountID,
-						AdditionalRegions: acct.AWSRegions,
-						Profile:           acct.AWSProfileProvider,
-						Region:            acct.AWSRegionProvider,
-						Version:           acct.AWSProviderVersion,
-					},
+		common := v2.Common{
+			ExtraVars: acct.ExtraVars,
+			Providers: &v2.Providers{
+				AWS: &v2.AWSProvider{
+					AccountID:         acct.AccountID,
+					AdditionalRegions: acct.AWSRegions,
+					Profile:           acct.AWSProfileProvider,
+					Region:            acct.AWSRegionProvider,
+					Version:           acct.AWSProviderVersion,
 				},
-				Owner:            acct.Owner,
-				Project:          acct.Project,
-				TerraformVersion: acct.TerraformVersion,
 			},
+			Owner:            acct.Owner,
+			Project:          acct.Project,
+			TerraformVersion: acct.TerraformVersion,
+		}
+		if acct.InfraBucket != nil || acct.InfraDynamoTable != nil || acct.AWSProfileBackend != nil || acct.AWSRegionBackend != nil {
+			common.Backend = &v2.Backend{
+				Bucket:      acct.InfraBucket,
+				DynamoTable: acct.InfraDynamoTable,
+				Profile:     acct.AWSProfileBackend,
+				Region:      acct.AWSRegionBackend,
+			}
+		}
+		c2.Accounts[acctName] = v2.Account{
+			Common: common,
 		}
 	}
 
 	for envName, env := range c1.Envs {
 		env2 := v2.Env{
 			Common: v2.Common{
-				Backend: &v2.Backend{
-					Bucket:      env.InfraBucket,
-					DynamoTable: env.InfraDynamoTable,
-					Profile:     env.AWSProfileBackend,
-					Region:      env.AWSRegionBackend,
-				},
 				ExtraVars: env.ExtraVars,
 				Providers: &v2.Providers{
 					AWS: &v2.AWSProvider{
@@ -184,6 +189,16 @@ func UpgradeConfigVersion(c1 *v1.Config) (*v2.Config, error) {
 				TerraformVersion: env.TerraformVersion,
 			},
 		}
+
+		if env.InfraBucket != nil || env.InfraDynamoTable != nil || env.AWSProfileBackend != nil || env.AWSRegionBackend != nil {
+			env2.Common.Backend = &v2.Backend{
+				Bucket:      env.InfraBucket,
+				DynamoTable: env.InfraDynamoTable,
+				Profile:     env.AWSProfileBackend,
+				Region:      env.AWSRegionBackend,
+			}
+		}
+
 		env2.Components = map[string]v2.Component{}
 
 		for componentName, component := range env.Components {
@@ -209,7 +224,6 @@ func UpgradeConfigVersion(c1 *v1.Config) (*v2.Config, error) {
 			}
 
 			if component.AccountID != nil || component.AWSRegions != nil || component.AWSProfileProvider != nil || component.AWSRegionProvider != nil || component.TerraformVersion != nil {
-
 				c2.Providers = &v2.Providers{
 					AWS: &v2.AWSProvider{
 						AccountID:         component.AccountID,
diff --git a/config/config_test.go b/config/config_test.go
index 2ada7ea08..157a1e771 100644
--- a/config/config_test.go
+++ b/config/config_test.go
@@ -4,8 +4,8 @@ import (
 	"os"
 	"testing"
 
-	"github.com/chanzuckerberg/fogg/config/v1"
-	"github.com/chanzuckerberg/fogg/config/v2"
+	v1 "github.com/chanzuckerberg/fogg/config/v1"
+	v2 "github.com/chanzuckerberg/fogg/config/v2"
 	"github.com/chanzuckerberg/fogg/plugins"
 	"github.com/chanzuckerberg/fogg/util"
 	"github.com/go-test/deep"
@@ -227,7 +227,7 @@ func TestUpgradeConfigVersion(t *testing.T) {
 				"plugin": &plugins.CustomPlugin{
 					URL:    "https://example.com/plugin.tgz",
 					Format: plugins.TypePluginFormatTar,
-					TarConfig: plugins.TarConfig{
+					TarConfig: &plugins.TarConfig{
 						StripComponents: 7,
 					},
 				},
@@ -236,7 +236,7 @@ func TestUpgradeConfigVersion(t *testing.T) {
 				"provider": &plugins.CustomPlugin{
 					URL:    "https://example.com/provider.tgz",
 					Format: plugins.TypePluginFormatTar,
-					TarConfig: plugins.TarConfig{
+					TarConfig: &plugins.TarConfig{
 						StripComponents: 7,
 					},
 				},
diff --git a/config/upgrade.go b/config/upgrade.go
new file mode 100644
index 000000000..3531c6675
--- /dev/null
+++ b/config/upgrade.go
@@ -0,0 +1,42 @@
+package config
+
+import (
+	"encoding/json"
+
+	v1 "github.com/chanzuckerberg/fogg/config/v1"
+	"github.com/chanzuckerberg/fogg/errs"
+	"github.com/sirupsen/logrus"
+	"github.com/spf13/afero"
+)
+
+// Upgrade applies in-place upgrades to a configFile
+func Upgrade(fs afero.Fs, configFile string) error {
+	bytes, version, err := FindConfig(fs, configFile)
+	if err != nil {
+		return err
+	}
+	switch version {
+	case 1:
+		c1, err := v1.ReadConfig(bytes)
+		if err != nil {
+			return err
+		}
+		c2, err := UpgradeConfigVersion(c1)
+		if err != nil {
+			return err
+		}
+
+		marshalled, err := json.MarshalIndent(c2, "", "  ")
+		if err != nil {
+			return errs.WrapInternal(err, "Could not serialize config to json.")
+		}
+		err = afero.WriteFile(fs, configFile, marshalled, 0644)
+		return errs.WrapInternal(err, "Could not write config to disk")
+	case 2:
+		logrus.Infof("config already v%d, nothing to do", version)
+		return nil
+
+	default:
+		return errs.NewUserf("config version %d unrecognized", version)
+	}
+}
diff --git a/config/upgrade_test.go b/config/upgrade_test.go
new file mode 100644
index 000000000..4c25e246d
--- /dev/null
+++ b/config/upgrade_test.go
@@ -0,0 +1,57 @@
+package config
+
+import (
+	"testing"
+
+	"github.com/chanzuckerberg/fogg/util"
+	"github.com/spf13/afero"
+	"github.com/stretchr/testify/require"
+)
+
+func TestUpgradeV2(t *testing.T) {
+	r := require.New(t)
+	confPath := "config"
+	conf := []byte(`{"version": 1}`)
+	fs, _, err := util.TestFs()
+	r.Nil(err)
+	err = afero.WriteFile(fs, confPath, conf, 0644)
+	r.Nil(err)
+	err = Upgrade(fs, confPath)
+	r.Nil(err)
+}
+
+func TestUpgradeUnknownVersion(t *testing.T) {
+	r := require.New(t)
+	confPath := "config"
+	conf := []byte(`{"version": 100}`)
+	fs, _, err := util.TestFs()
+	r.Nil(err)
+	err = afero.WriteFile(fs, confPath, conf, 0644)
+	r.Nil(err)
+	err = Upgrade(fs, confPath)
+	r.Error(err, "config version 100 unrecognized")
+}
+
+func TestUpgradeV1(t *testing.T) {
+	r := require.New(t)
+	confPath := "config"
+	fs, _, err := util.TestFs()
+	r.Nil(err)
+
+	v1, err := util.TestFile("v1_full")
+	r.NoError(err)
+
+	err = afero.WriteFile(fs, confPath, v1, 0644)
+	r.NoError(err)
+
+	_, v, err := FindConfig(fs, confPath)
+	r.NoError(err)
+	r.Equal(1, v)
+
+	err = Upgrade(fs, confPath)
+	r.NoError(err)
+
+	_, v, err = FindConfig(fs, confPath)
+	r.NoError(err)
+	r.Equal(2, v) // now upgraded
+}
diff --git a/config/v1/config.go b/config/v1/config.go
index 59a8e41d2..bb5999908 100644
--- a/config/v1/config.go
+++ b/config/v1/config.go
@@ -122,11 +122,11 @@ type Plugins struct {
 
 // Module is a module
 type Module struct {
-	TerraformVersion *string `json:"terraform_version"`
+	TerraformVersion *string `json:"terraform_version,omitempty"`
 }
 
 type TravisCI struct {
-	Enabled        bool   `json:"enabled"`
+	Enabled        bool   `json:"enabled,omitempty"`
 	AWSIAMRoleName string `json:"aws_iam_role_name"`
 	TestBuckets    int    `json:"test_buckets"`
 }
@@ -134,11 +134,11 @@ type TravisCI struct {
 type Config struct {
 	Accounts map[string]Account `json:"accounts"`
 	Defaults Defaults           `json:"defaults"`
-	Docker   bool               `json:"docker"`
+	Docker   bool               `json:"docker,omitempty"`
 	Envs     map[string]Env     `json:"envs"`
 	Modules  map[string]Module  `json:"modules"`
-	Plugins  Plugins            `json:"plugins"`
-	TravisCI *TravisCI          `json:"travis_ci"`
+	Plugins  Plugins            `json:"plugins,omitempty"`
+	TravisCI *TravisCI          `json:"travis_ci,omitempty"`
 }
 
 func ReadConfig(b []byte) (*Config, error) {
diff --git a/config/v2/config.go b/config/v2/config.go
index 19a50b883..a8074a5e0 100644
--- a/config/v2/config.go
+++ b/config/v2/config.go
@@ -56,7 +56,7 @@ type Tools struct {
 type Env struct {
 	Common
 
-	Components map[string]Component `json:"components"`
+	Components map[string]Component `json:"components,omitempty"`
 }
 
 type Component struct {
@@ -64,13 +64,13 @@ type Component struct {
 
 	EKS          *v1.EKSConfig     `json:"eks,omitempty"`
 	Kind         *v1.ComponentKind `json:"kind,omitempty"`
-	ModuleSource *string           `json:"module_source"`
+	ModuleSource *string           `json:"module_source,omitempty"`
 }
 
 type Providers struct {
-	AWS       *AWSProvider       `json:"aws"`
-	Snowflake *SnowflakeProvider `json:"snowflake"`
-	Bless     *BlessProvider     `json:"bless"`
+	AWS       *AWSProvider       `json:"aws,omitempty"`
+	Snowflake *SnowflakeProvider `json:"snowflake,omitempty"`
+	Bless     *BlessProvider     `json:"bless,omitempty"`
 }
 
 // BlessProvider allows for terraform-provider-bless configuration
diff --git a/plugins/custom_plugin.go b/plugins/custom_plugin.go
index 9c6187445..b9578d1d0 100644
--- a/plugins/custom_plugin.go
+++ b/plugins/custom_plugin.go
@@ -37,13 +37,20 @@ const (
 type CustomPlugin struct {
 	URL       string           `json:"url" validate:"required"`
 	Format    TypePluginFormat `json:"format" validate:"required"`
-	TarConfig TarConfig        `json:"tar_config,omitempty"`
-	TargetDir string
+	TarConfig *TarConfig       `json:"tar_config,omitempty"`
+	TargetDir string           `json:"target_dir,omitempty"`
 }
 
 // TarConfig configures the tar unpacking
 type TarConfig struct {
-	StripComponents int `json:"strip_components"`
+	StripComponents int `json:"strip_components,omitempty"`
+}
+
+func (tc *TarConfig) getStripComponents() int {
+	if tc == nil {
+		return 0
+	}
+	return tc.StripComponents
 }
 
 // Install installs the custom plugin
@@ -202,11 +209,11 @@ func (cp *CustomPlugin) processTar(fs afero.Fs, path string, targetDir string) e
 			filepath.Clean(header.Name),
 			string(os.PathSeparator))
 		// remove components if we can, otherwise skip this
-		if len(splitTarget) <= cp.TarConfig.StripComponents {
+		if len(splitTarget) <= cp.TarConfig.getStripComponents() {
 			continue
 		}
 		target := filepath.Join(targetDir,
-			filepath.Join(splitTarget[cp.TarConfig.StripComponents:]...))
+			filepath.Join(splitTarget[cp.TarConfig.getStripComponents():]...))
 
 		switch header.Typeflag {
 		case tar.TypeDir: // if its a dir and it doesn't exist create it
diff --git a/plugins/custom_plugin_test.go b/plugins/custom_plugin_test.go
index 687c53273..15908a805 100644
--- a/plugins/custom_plugin_test.go
+++ b/plugins/custom_plugin_test.go
@@ -88,7 +88,7 @@ func TestCustomPluginTarStripComponents(t *testing.T) {
 	customPlugin := &plugins.CustomPlugin{
 		URL:    ts.URL,
 		Format: plugins.TypePluginFormatTar,
-		TarConfig: plugins.TarConfig{
+		TarConfig: &plugins.TarConfig{
 			StripComponents: 1,
 		},
 	}