diff --git a/cmd/captplanet/main.go b/cmd/captplanet/main.go
index abbd23dec..945732117 100644
--- a/cmd/captplanet/main.go
+++ b/cmd/captplanet/main.go
@@ -4,11 +4,9 @@
 package main
 
 import (
-	"flag"
 	"path/filepath"
 
 	"github.com/spf13/cobra"
-	"github.com/spf13/pflag"
 	monkit "gopkg.in/spacemonkeygo/monkit.v2"
 	"storj.io/storj/pkg/process"
 )
@@ -25,7 +23,10 @@ var (
 )
 
 func main() {
-	pflag.CommandLine.AddGoFlagSet(flag.CommandLine)
-	process.ExecuteWithConfig(rootCmd,
-		filepath.Join(defaultConfDir, "config.yaml"))
+	// process.Exec will load this for this command.
+	runCmd.Flags().String("config",
+		filepath.Join(defaultConfDir, "config.yaml"), "path to configuration")
+	setupCmd.Flags().String("config",
+		filepath.Join(defaultConfDir, "setup.yaml"), "path to configuration")
+	process.Exec(rootCmd)
 }
diff --git a/cmd/captplanet/run.go b/cmd/captplanet/run.go
index d304d2f9f..63270586a 100644
--- a/cmd/captplanet/run.go
+++ b/cmd/captplanet/run.go
@@ -5,8 +5,6 @@ package main
 
 import (
 	"fmt"
-	"net"
-	"path/filepath"
 
 	"github.com/spf13/cobra"
 
@@ -20,122 +18,76 @@ import (
 	"storj.io/storj/pkg/provider"
 )
 
+const (
+	farmerCount = 40
+)
+
+type HeavyClient struct {
+	Identity  provider.IdentityConfig
+	Kademlia  kademlia.Config
+	PointerDB pointerdb.Config
+	Overlay   overlay.Config
+}
+
+type Farmer struct {
+	Identity provider.IdentityConfig
+	Kademlia kademlia.Config
+	Storage  psservice.Config
+}
+
 var (
 	runCmd = &cobra.Command{
 		Use:   "run",
 		Short: "Run all providers",
 		RunE:  cmdRun,
 	}
-	runCfg Config
+
+	runCfg struct {
+		HeavyClient HeavyClient
+		Farmers     [farmerCount]Farmer
+		Gateway     miniogw.Config
+	}
 )
 
 func init() {
 	rootCmd.AddCommand(runCmd)
-	cfgstruct.Bind(runCmd.Flags(), &runCfg,
-		cfgstruct.ConfDir(defaultConfDir),
-	)
+	cfgstruct.Bind(runCmd.Flags(), &runCfg, cfgstruct.ConfDir(defaultConfDir))
 }
 
 func cmdRun(cmd *cobra.Command, args []string) (err error) {
 	ctx := process.Ctx(cmd)
 	defer mon.Task()(&ctx)(&err)
 
-	startingPort := runCfg.StartingPort
-
-	errch := make(chan error, runCfg.FarmerCount+2)
-
-	// define heavy client config programmatically
-	type HeavyClient struct {
-		Identity  provider.IdentityConfig
-		Kademlia  kademlia.Config
-		PointerDB pointerdb.Config
-		Overlay   overlay.Config
-	}
-
-	hc := HeavyClient{
-		Identity: provider.IdentityConfig{
-			CertPath: filepath.Join(runCfg.BasePath, "hc", "ident.leaf.cert"),
-			KeyPath:  filepath.Join(runCfg.BasePath, "hc", "ident.leaf.key"),
-			Address:  joinHostPort(runCfg.ListenHost, startingPort+1),
-		},
-		Kademlia: kademlia.Config{
-			TODOListenAddr: joinHostPort(runCfg.ListenHost, startingPort+2),
-			BootstrapAddr:  joinHostPort(runCfg.ListenHost, startingPort+4),
-		},
-		PointerDB: pointerdb.Config{
-			DatabaseURL: "bolt://" + filepath.Join(
-				runCfg.BasePath, "hc", "pointerdb.db"),
-		},
-		Overlay: overlay.Config{
-			DatabaseURL: "bolt://" + filepath.Join(
-				runCfg.BasePath, "hc", "overlay.db"),
-		},
-	}
+	errch := make(chan error, len(runCfg.Farmers)+2)
 
 	// start heavy client
 	go func() {
-		_, _ = fmt.Printf("starting heavy client on %s\n", hc.Identity.Address)
-		errch <- hc.Identity.Run(ctx, hc.Kademlia, hc.PointerDB, hc.Overlay)
+		_, _ = fmt.Printf("starting heavy client on %s\n",
+			runCfg.HeavyClient.Identity.Address)
+		errch <- runCfg.HeavyClient.Identity.Run(ctx,
+			runCfg.HeavyClient.Kademlia,
+			runCfg.HeavyClient.PointerDB,
+			runCfg.HeavyClient.Overlay)
 	}()
 
-	// define and start a bunch of farmers programmatically
-	type Farmer struct {
-		Identity provider.IdentityConfig
-		Kademlia kademlia.Config
-		Storage  psservice.Config
-	}
-
-	for i := 0; i < runCfg.FarmerCount; i++ {
-		basepath := filepath.Join(runCfg.BasePath, fmt.Sprintf("f%d", i))
-		farmer := Farmer{
-			Identity: provider.IdentityConfig{
-				CertPath: filepath.Join(basepath, "ident.leaf.cert"),
-				KeyPath:  filepath.Join(basepath, "ident.leaf.key"),
-				Address:  joinHostPort(runCfg.ListenHost, startingPort+i*2+3),
-			},
-			Kademlia: kademlia.Config{
-				TODOListenAddr: joinHostPort(runCfg.ListenHost, startingPort+i*2+4),
-				BootstrapAddr:  joinHostPort(runCfg.ListenHost, startingPort+1),
-			},
-			Storage: psservice.Config{
-				Path: filepath.Join(basepath, "data"),
-			},
-		}
+	// start the farmers
+	for i := 0; i < len(runCfg.Farmers); i++ {
 		go func(i int) {
-			_, _ = fmt.Printf("starting farmer %d grpc on %s, kad on %s\n",
-				i, farmer.Identity.Address, farmer.Kademlia.TODOListenAddr)
-			errch <- farmer.Identity.Run(ctx, farmer.Kademlia, farmer.Storage)
+			_, _ = fmt.Printf("starting farmer %d grpc on %s, kad on %s\n", i,
+				runCfg.Farmers[i].Identity.Address,
+				runCfg.Farmers[i].Kademlia.TODOListenAddr)
+			errch <- runCfg.Farmers[i].Identity.Run(ctx,
+				runCfg.Farmers[i].Kademlia,
+				runCfg.Farmers[i].Storage)
 		}(i)
 	}
 
-	// start s3 gateway
-	gw := miniogw.Config{
-		IdentityConfig: provider.IdentityConfig{
-			CertPath: filepath.Join(runCfg.BasePath, "gw", "ident.leaf.cert"),
-			KeyPath:  filepath.Join(runCfg.BasePath, "gw", "ident.leaf.key"),
-			Address:  joinHostPort(runCfg.ListenHost, startingPort),
-		},
-		MinioConfig: runCfg.MinioConfig,
-		ClientConfig: miniogw.ClientConfig{
-			OverlayAddr: joinHostPort(
-				runCfg.ListenHost, startingPort+1),
-			PointerDBAddr: joinHostPort(
-				runCfg.ListenHost, startingPort+1),
-		},
-		RSConfig: runCfg.RSConfig,
-	}
-	gw.MinioConfig.MinioDir = filepath.Join(runCfg.BasePath, "gw", "minio")
-
 	// start s3 gateway
 	go func() {
 		_, _ = fmt.Printf("starting minio gateway on %s\n",
-			gw.IdentityConfig.Address)
-		errch <- gw.Run(ctx)
+			runCfg.Gateway.IdentityConfig.Address)
+		errch <- runCfg.Gateway.Run(ctx)
 	}()
 
 	return <-errch
 }
-
-func joinHostPort(host string, port int) string {
-	return net.JoinHostPort(host, fmt.Sprint(port))
-}
diff --git a/cmd/captplanet/setup.go b/cmd/captplanet/setup.go
index 1a462b03d..67f7bb8a6 100644
--- a/cmd/captplanet/setup.go
+++ b/cmd/captplanet/setup.go
@@ -5,25 +5,22 @@ package main
 
 import (
 	"fmt"
+	"net"
 	"os"
 	"path/filepath"
 
 	"github.com/spf13/cobra"
 
 	"storj.io/storj/pkg/cfgstruct"
-	"storj.io/storj/pkg/miniogw"
 	"storj.io/storj/pkg/peertls"
 	"storj.io/storj/pkg/process"
 )
 
 // Config defines broad Captain Planet configuration
 type Config struct {
-	FarmerCount  int    `help:"number of farmers to run" default:"20"`
 	BasePath     string `help:"base path for captain planet storage" default:"$CONFDIR"`
 	ListenHost   string `help:"the host for providers to listen on" default:"127.0.0.1"`
 	StartingPort int    `help:"all providers will listen on ports consecutively starting with this one" default:"7777"`
-	miniogw.RSConfig
-	miniogw.MinioConfig
 }
 
 var (
@@ -54,7 +51,7 @@ func cmdSetup(cmd *cobra.Command, args []string) (err error) {
 		return err
 	}
 
-	for i := 0; i < setupCfg.FarmerCount; i++ {
+	for i := 0; i < len(runCfg.Farmers); i++ {
 		farmerPath := filepath.Join(setupCfg.BasePath, fmt.Sprintf("f%d", i))
 		err = os.MkdirAll(farmerPath, 0700)
 		if err != nil {
@@ -78,5 +75,58 @@ func cmdSetup(cmd *cobra.Command, args []string) (err error) {
 		return err
 	}
 
-	return process.SaveConfig(cmd)
+	startingPort := setupCfg.StartingPort
+
+	overrides := map[string]interface{}{
+		"heavy-client.identity.cert-path": filepath.Join(
+			setupCfg.BasePath, "hc", "ident.leaf.cert"),
+		"heavy-client.identity.key-path": filepath.Join(
+			setupCfg.BasePath, "hc", "ident.leaf.key"),
+		"heavy-client.identity.address": joinHostPort(
+			setupCfg.ListenHost, startingPort+1),
+		"heavy-client.kademlia.todo-listen-addr": joinHostPort(
+			setupCfg.ListenHost, startingPort+2),
+		"heavy-client.kademlia.bootstrap-addr": joinHostPort(
+			setupCfg.ListenHost, startingPort+4),
+		"heavy-client.pointer-db.database-url": "bolt://" + filepath.Join(
+			setupCfg.BasePath, "hc", "pointerdb.db"),
+		"heavy-client.overlay.database-url": "bolt://" + filepath.Join(
+			setupCfg.BasePath, "hc", "overlay.db"),
+		"gateway.cert-path": filepath.Join(
+			setupCfg.BasePath, "gw", "ident.leaf.cert"),
+		"gateway.key-path": filepath.Join(
+			setupCfg.BasePath, "gw", "ident.leaf.key"),
+		"gateway.address": joinHostPort(
+			setupCfg.ListenHost, startingPort),
+		"gateway.overlay-addr": joinHostPort(
+			setupCfg.ListenHost, startingPort+1),
+		"gateway.pointer-db-addr": joinHostPort(
+			setupCfg.ListenHost, startingPort+1),
+		"gateway.minio-dir": filepath.Join(
+			setupCfg.BasePath, "gw", "minio"),
+		"pointer-db.auth.api-key": "abc123",
+	}
+
+	for i := 0; i < len(runCfg.Farmers); i++ {
+		basepath := filepath.Join(setupCfg.BasePath, fmt.Sprintf("f%d", i))
+		farmer := fmt.Sprintf("farmers.%02d.", i)
+		overrides[farmer+"identity.cert-path"] = filepath.Join(
+			basepath, "ident.leaf.cert")
+		overrides[farmer+"identity.key-path"] = filepath.Join(
+			basepath, "ident.leaf.key")
+		overrides[farmer+"identity.address"] = joinHostPort(
+			setupCfg.ListenHost, startingPort+i*2+3)
+		overrides[farmer+"kademlia.todo-listen-addr"] = joinHostPort(
+			setupCfg.ListenHost, startingPort+i*2+4)
+		overrides[farmer+"kademlia.bootstrap-addr"] = joinHostPort(
+			setupCfg.ListenHost, startingPort+1)
+		overrides[farmer+"storage.path"] = filepath.Join(basepath, "data")
+	}
+
+	return process.SaveConfig(runCmd.Flags(),
+		filepath.Join(setupCfg.BasePath, "config.yaml"), overrides)
+}
+
+func joinHostPort(host string, port int) string {
+	return net.JoinHostPort(host, fmt.Sprint(port))
 }
diff --git a/cmd/gw/main.go b/cmd/gw/main.go
index 3d25a86ae..1a57c1224 100644
--- a/cmd/gw/main.go
+++ b/cmd/gw/main.go
@@ -4,10 +4,8 @@
 package main
 
 import (
-	"fmt"
 	"os"
 	"path/filepath"
-	"strings"
 
 	"github.com/spf13/cobra"
 
@@ -22,67 +20,54 @@ var (
 		Use:   "gw",
 		Short: "Gateway",
 	}
+	runCmd = &cobra.Command{
+		Use:   "run",
+		Short: "Run the gateway",
+		RunE:  cmdRun,
+	}
+	setupCmd = &cobra.Command{
+		Use:   "setup",
+		Short: "Create config files",
+		RunE:  cmdSetup,
+	}
 
-	cfg miniogw.Config
+	runCfg   miniogw.Config
+	setupCfg struct {
+		BasePath string `default:"$CONFDIR" help:"base path for setup"`
+	}
 
 	defaultConfDir = "$HOME/.storj/gw"
 )
 
 func init() {
-	rootCmd.AddCommand(&cobra.Command{
-		Use:   "run",
-		Short: "Run the gateway",
-		RunE:  cmdRun,
-	})
-	rootCmd.AddCommand(&cobra.Command{
-		Use:   "setup",
-		Short: "Create config files",
-		RunE:  cmdSetup,
-	})
-	cfgstruct.Bind(rootCmd.PersistentFlags(), &cfg,
-		cfgstruct.ConfDir(defaultConfDir))
+	rootCmd.AddCommand(runCmd)
+	rootCmd.AddCommand(setupCmd)
+	cfgstruct.Bind(runCmd.Flags(), &runCfg, cfgstruct.ConfDir(defaultConfDir))
+	cfgstruct.Bind(setupCmd.Flags(), &setupCfg, cfgstruct.ConfDir(defaultConfDir))
 }
 
 func cmdRun(cmd *cobra.Command, args []string) (err error) {
-	return cfg.Run(process.Ctx(cmd))
+	return runCfg.Run(process.Ctx(cmd))
 }
 
 func cmdSetup(cmd *cobra.Command, args []string) (err error) {
-	ctx := process.Ctx(cmd)
-
-	// TODO: clean this up somehow?
-	if !strings.HasSuffix(cfg.IdentityConfig.CertPath, ".leaf.cert") {
-		return fmt.Errorf("certificate path should end with .leaf.cert")
-	}
-	certpath := strings.TrimSuffix(cfg.IdentityConfig.CertPath, ".leaf.cert")
-	if !strings.HasSuffix(cfg.IdentityConfig.KeyPath, ".leaf.key") {
-		return fmt.Errorf("key path should end with .leaf.key")
-	}
-	keypath := strings.TrimSuffix(cfg.IdentityConfig.KeyPath, ".leaf.key")
-
-	err = os.MkdirAll(filepath.Dir(certpath), 0700)
-	if err != nil {
-		return err
-	}
-	err = os.MkdirAll(filepath.Dir(keypath), 0700)
+	err = os.MkdirAll(setupCfg.BasePath, 0700)
 	if err != nil {
 		return err
 	}
 
-	_, err = peertls.NewTLSFileOptions(certpath, keypath, true, false)
+	identityPath := filepath.Join(setupCfg.BasePath, "identity")
+	_, err = peertls.NewTLSFileOptions(identityPath, identityPath, true, false)
 	if err != nil {
 		return err
 	}
 
-	err = os.MkdirAll(filepath.Dir(process.CfgPath(ctx)), 0700)
-	if err != nil {
-		return err
-	}
-
-	return process.SaveConfigAs(cmd, process.CfgPath(ctx))
+	return process.SaveConfig(runCmd.Flags(),
+		filepath.Join(setupCfg.BasePath, "config.yaml"), nil)
 }
 
 func main() {
-	process.ExecuteWithConfig(rootCmd,
-		filepath.Join(defaultConfDir, "config.yaml"))
+	runCmd.Flags().String("config",
+		filepath.Join(defaultConfDir, "config.yaml"), "path to configuration")
+	process.Exec(rootCmd)
 }
diff --git a/cmd/hc/main.go b/cmd/hc/main.go
index 385f4f0ea..3bf3c504b 100644
--- a/cmd/hc/main.go
+++ b/cmd/hc/main.go
@@ -4,10 +4,8 @@
 package main
 
 import (
-	"fmt"
 	"os"
 	"path/filepath"
-	"strings"
 
 	"github.com/spf13/cobra"
 
@@ -20,80 +18,65 @@ import (
 	"storj.io/storj/pkg/provider"
 )
 
-const (
-	defaultConfFolder = "$HOME/.storj/hc"
-)
-
 var (
 	rootCmd = &cobra.Command{
 		Use:   "hc",
 		Short: "Heavy client",
 	}
+	runCmd = &cobra.Command{
+		Use:   "run",
+		Short: "Run the heavy client",
+		RunE:  cmdRun,
+	}
+	setupCmd = &cobra.Command{
+		Use:   "setup",
+		Short: "Create config files",
+		RunE:  cmdSetup,
+	}
 
-	cfg struct {
+	runCfg struct {
 		Identity  provider.IdentityConfig
 		Kademlia  kademlia.Config
 		PointerDB pointerdb.Config
 		Overlay   overlay.Config
 	}
+	setupCfg struct {
+		BasePath string `default:"$CONFDIR" help:"base path for setup"`
+	}
+
+	defaultConfDir = "$HOME/.storj/hc"
 )
 
 func init() {
-	rootCmd.AddCommand(&cobra.Command{
-		Use:   "run",
-		Short: "Run the heavy client",
-		RunE:  cmdRun,
-	})
-	rootCmd.AddCommand(&cobra.Command{
-		Use:   "setup",
-		Short: "Create config files",
-		RunE:  cmdSetup,
-	})
-	cfgstruct.Bind(rootCmd.PersistentFlags(), &cfg,
-		cfgstruct.ConfDir(defaultConfFolder))
+	rootCmd.AddCommand(runCmd)
+	rootCmd.AddCommand(setupCmd)
+	cfgstruct.Bind(runCmd.Flags(), &runCfg, cfgstruct.ConfDir(defaultConfDir))
+	cfgstruct.Bind(setupCmd.Flags(), &setupCfg, cfgstruct.ConfDir(defaultConfDir))
 }
 
 func cmdRun(cmd *cobra.Command, args []string) (err error) {
-	return cfg.Identity.Run(process.Ctx(cmd),
-		cfg.Kademlia, cfg.PointerDB, cfg.Overlay)
+	return runCfg.Identity.Run(process.Ctx(cmd),
+		runCfg.Kademlia, runCfg.PointerDB, runCfg.Overlay)
 }
 
 func cmdSetup(cmd *cobra.Command, args []string) (err error) {
-	ctx := process.Ctx(cmd)
-
-	// TODO: clean this up somehow?
-	if !strings.HasSuffix(cfg.Identity.CertPath, ".leaf.cert") {
-		return fmt.Errorf("certificate path should end with .leaf.cert")
-	}
-	certpath := strings.TrimSuffix(cfg.Identity.CertPath, ".leaf.cert")
-	if !strings.HasSuffix(cfg.Identity.KeyPath, ".leaf.key") {
-		return fmt.Errorf("key path should end with .leaf.key")
-	}
-	keypath := strings.TrimSuffix(cfg.Identity.KeyPath, ".leaf.key")
-
-	err = os.MkdirAll(filepath.Dir(certpath), 0700)
-	if err != nil {
-		return err
-	}
-	err = os.MkdirAll(filepath.Dir(keypath), 0700)
+	err = os.MkdirAll(setupCfg.BasePath, 0700)
 	if err != nil {
 		return err
 	}
 
-	_, err = peertls.NewTLSFileOptions(certpath, keypath, true, false)
+	identityPath := filepath.Join(setupCfg.BasePath, "identity")
+	_, err = peertls.NewTLSFileOptions(identityPath, identityPath, true, false)
 	if err != nil {
 		return err
 	}
 
-	err = os.MkdirAll(filepath.Dir(process.CfgPath(ctx)), 0700)
-	if err != nil {
-		return err
-	}
-
-	return process.SaveConfigAs(cmd, process.CfgPath(ctx))
+	return process.SaveConfig(runCmd.Flags(),
+		filepath.Join(setupCfg.BasePath, "config.yaml"), nil)
 }
 
 func main() {
-	process.ExecuteWithConfig(rootCmd,
-		filepath.Join(defaultConfFolder, "config.yaml"))
+	runCmd.Flags().String("config",
+		filepath.Join(defaultConfDir, "config.yaml"), "path to configuration")
+	process.Exec(rootCmd)
 }
diff --git a/pkg/process/exec_conf.go b/pkg/process/exec_conf.go
index 062ac2cfd..90a0edc2a 100644
--- a/pkg/process/exec_conf.go
+++ b/pkg/process/exec_conf.go
@@ -8,7 +8,6 @@ import (
 	"flag"
 	"log"
 	"os"
-	"strings"
 	"sync"
 
 	"github.com/spf13/cobra"
@@ -23,9 +22,15 @@ import (
 
 // ExecuteWithConfig runs a Cobra command with the provided default config
 func ExecuteWithConfig(cmd *cobra.Command, defaultConfig string) {
-	cfgFile := flag.String("config", os.ExpandEnv(defaultConfig), "config file")
+	flag.String("config", os.ExpandEnv(defaultConfig), "config file")
+	Exec(cmd)
+}
+
+// Exec runs a Cobra command. If a "config" flag is defined it will be parsed
+// and loaded using viper.
+func Exec(cmd *cobra.Command) {
 	pflag.CommandLine.AddGoFlagSet(flag.CommandLine)
-	cleanup(cmd, cfgFile)
+	cleanup(cmd)
 	_ = cmd.Execute()
 }
 
@@ -36,6 +41,39 @@ var (
 	contexts   = map[*cobra.Command]context.Context{}
 )
 
+// SaveConfig will save all flags with default values to outfilewith specific
+// values specified in 'overrides' overridden.
+func SaveConfig(flagset *pflag.FlagSet, outfile string,
+	overrides map[string]interface{}) error {
+
+	vip := viper.New()
+	err := vip.BindPFlags(pflag.CommandLine)
+	if err != nil {
+		return err
+	}
+	flagset.VisitAll(func(f *pflag.Flag) {
+		// stop processing if we hit an error on a BindPFlag call
+		if err != nil {
+			return
+		}
+		if f.Name == "config" {
+			return
+		}
+		err = vip.BindPFlag(f.Name, f)
+	})
+	if err != nil {
+		return err
+	}
+
+	if overrides != nil {
+		for key, val := range overrides {
+			vip.Set(key, val)
+		}
+	}
+
+	return vip.WriteConfigAs(os.ExpandEnv(outfile))
+}
+
 // Ctx returns the appropriate context.Context for ExecuteWithConfig commands
 func Ctx(cmd *cobra.Command) context.Context {
 	contextMtx.Lock()
@@ -47,44 +85,9 @@ func Ctx(cmd *cobra.Command) context.Context {
 	return ctx
 }
 
-type ctxKey int
-
-const (
-	ctxKeyVip ctxKey = iota
-	ctxKeyCfg
-)
-
-// SaveConfig outputs the configuration to the configured (or default) config
-// file given to ExecuteWithConfig
-func SaveConfig(cmd *cobra.Command) error {
-	ctx := Ctx(cmd)
-	return getViper(ctx).WriteConfigAs(CfgPath(ctx))
-}
-
-// SaveConfigAs outputs the configuration to the provided path assuming the
-// command was executed with ExecuteWithConfig
-func SaveConfigAs(cmd *cobra.Command, path string) error {
-	return getViper(Ctx(cmd)).WriteConfigAs(path)
-}
-
-func getViper(ctx context.Context) *viper.Viper {
-	if v, ok := ctx.Value(ctxKeyVip).(*viper.Viper); ok {
-		return v
-	}
-	return nil
-}
-
-// CfgPath returns the configuration path used with ExecuteWithConfig
-func CfgPath(ctx context.Context) string {
-	if v, ok := ctx.Value(ctxKeyCfg).(string); ok {
-		return v
-	}
-	return ""
-}
-
-func cleanup(cmd *cobra.Command, cfgFile *string) {
+func cleanup(cmd *cobra.Command) {
 	for _, ccmd := range cmd.Commands() {
-		cleanup(ccmd, cfgFile)
+		cleanup(ccmd)
 	}
 	if cmd.Run != nil {
 		panic("Please use cobra's RunE instead of Run")
@@ -104,16 +107,22 @@ func cleanup(cmd *cobra.Command, cfgFile *string) {
 		}
 		vip.SetEnvPrefix("storj")
 		vip.AutomaticEnv()
-		if *cfgFile != "" && fileExists(*cfgFile) {
-			vip.SetConfigFile(*cfgFile)
-			err = vip.ReadInConfig()
-			if err != nil {
-				return err
+
+		cfgFlag := cmd.Flags().Lookup("config")
+		if cfgFlag != nil && cfgFlag.Value.String() != "" {
+			path := os.ExpandEnv(cfgFlag.Value.String())
+			if cfgFlag.Changed || fileExists(path) {
+				vip.SetConfigFile(path)
+				err = vip.ReadInConfig()
+				if err != nil {
+					return err
+				}
 			}
 		}
 
 		// go back and propagate changed config values to appropriate flags
 		var brokenKeys []string
+		var brokenVals []string
 		for _, key := range vip.AllKeys() {
 			if cmd.Flags().Lookup(key) == nil {
 				// flag couldn't be found
@@ -122,14 +131,11 @@ func cleanup(cmd *cobra.Command, cfgFile *string) {
 				err := cmd.Flags().Set(key, vip.GetString(key))
 				if err != nil {
 					// flag couldn't be set
-					brokenKeys = append(brokenKeys, key)
+					brokenVals = append(brokenVals, key)
 				}
 			}
 		}
 
-		ctx = context.WithValue(ctx, ctxKeyVip, vip)
-		ctx = context.WithValue(ctx, ctxKeyCfg, *cfgFile)
-
 		logger, err := utils.NewLogger(*logDisposition)
 		if err != nil {
 			return err
@@ -139,12 +145,11 @@ func cleanup(cmd *cobra.Command, cfgFile *string) {
 		defer zap.RedirectStdLog(logger)()
 
 		// okay now that logging is working, inform about the broken keys
-		// these keys are almost certainly broken because they have capital
-		// letters
-		if len(brokenKeys) > 0 {
-			logger.Sugar().Infof("TODO: these flags are not configurable via "+
-				"config file, probably due to having uppercase letters: %s",
-				strings.Join(brokenKeys, ", "))
+		for _, key := range brokenKeys {
+			logger.Sugar().Infof("Invalid configuration file key: %s", key)
+		}
+		for _, key := range brokenVals {
+			logger.Sugar().Infof("Invalid configuration file value for key: %s", key)
 		}
 
 		err = initMetrics(ctx, monkit.Default,