diff --git a/cli/board/attach.go b/cli/board/attach.go
index 76b611d1183..7a097cc77be 100644
--- a/cli/board/attach.go
+++ b/cli/board/attach.go
@@ -53,7 +53,11 @@ var attachFlags struct {
 }
 
 func runAttachCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	instance, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Attach board error: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
 
 	var path *paths.Path
 	if len(args) > 1 {
@@ -62,13 +66,12 @@ func runAttachCommand(cmd *cobra.Command, args []string) {
 		path = initSketchPath(path)
 	}
 
-	_, err := board.Attach(context.Background(), &rpc.BoardAttachReq{
+	if _, err = board.Attach(context.Background(), &rpc.BoardAttachReq{
 		Instance:      instance,
 		BoardUri:      args[0],
 		SketchPath:    path.String(),
 		SearchTimeout: attachFlags.searchTimeout,
-	}, output.TaskProgress())
-	if err != nil {
+	}, output.TaskProgress()); err != nil {
 		feedback.Errorf("Attach board error: %v", err)
 		os.Exit(errorcodes.ErrGeneric)
 	}
diff --git a/cli/board/details.go b/cli/board/details.go
index f34e9b7a6db..18696a68eab 100644
--- a/cli/board/details.go
+++ b/cli/board/details.go
@@ -41,8 +41,14 @@ var detailsCommand = &cobra.Command{
 }
 
 func runDetailsCommand(cmd *cobra.Command, args []string) {
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error getting board details: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
 	res, err := board.Details(context.Background(), &rpc.BoardDetailsReq{
-		Instance: instance.CreateInstance(),
+		Instance: inst,
 		Fqbn:     args[0],
 	})
 
diff --git a/cli/board/list.go b/cli/board/list.go
index a8f73929cf8..4c38cee869a 100644
--- a/cli/board/list.go
+++ b/cli/board/list.go
@@ -61,7 +61,13 @@ func runListCommand(cmd *cobra.Command, args []string) {
 		time.Sleep(timeout)
 	}
 
-	ports, err := board.List(instance.CreateInstance().GetId())
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error detecting boards: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
+	ports, err := board.List(inst.GetId())
 	if err != nil {
 		feedback.Errorf("Error detecting boards: %v", err)
 		os.Exit(errorcodes.ErrNetwork)
diff --git a/cli/board/listall.go b/cli/board/listall.go
index 47472a69cc6..4b1b4886413 100644
--- a/cli/board/listall.go
+++ b/cli/board/listall.go
@@ -46,10 +46,14 @@ var listAllCommand = &cobra.Command{
 
 // runListAllCommand list all installed boards
 func runListAllCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error listing boards: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
 
 	list, err := board.ListAll(context.Background(), &rpc.BoardListAllReq{
-		Instance:   instance,
+		Instance:   inst,
 		SearchArgs: args,
 	})
 	if err != nil {
diff --git a/cli/compile/compile.go b/cli/compile/compile.go
index 311545db64b..84514062e60 100644
--- a/cli/compile/compile.go
+++ b/cli/compile/compile.go
@@ -86,7 +86,11 @@ func NewCommand() *cobra.Command {
 }
 
 func run(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error during build: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
 
 	var path *paths.Path
 	if len(args) > 0 {
@@ -95,8 +99,8 @@ func run(cmd *cobra.Command, args []string) {
 
 	sketchPath := initSketchPath(path)
 
-	_, err := compile.Compile(context.Background(), &rpc.CompileReq{
-		Instance:        instance,
+	_, err = compile.Compile(context.Background(), &rpc.CompileReq{
+		Instance:        inst,
 		Fqbn:            fqbn,
 		SketchPath:      sketchPath.String(),
 		ShowProperties:  showProperties,
@@ -118,7 +122,7 @@ func run(cmd *cobra.Command, args []string) {
 
 	if uploadAfterCompile {
 		_, err := upload.Upload(context.Background(), &rpc.UploadReq{
-			Instance:   instance,
+			Instance:   inst,
 			Fqbn:       fqbn,
 			SketchPath: sketchPath.String(),
 			Port:       port,
diff --git a/cli/core/download.go b/cli/core/download.go
index 22d00875689..becb6df1bca 100644
--- a/cli/core/download.go
+++ b/cli/core/download.go
@@ -47,7 +47,12 @@ func initDownloadCommand() *cobra.Command {
 }
 
 func runDownloadCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error downloading: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
 	logrus.Info("Executing `arduino core download`")
 
 	platformsRefs, err := globals.ParseReferenceArgs(args, true)
@@ -58,7 +63,7 @@ func runDownloadCommand(cmd *cobra.Command, args []string) {
 
 	for i, platformRef := range platformsRefs {
 		platformDownloadreq := &rpc.PlatformDownloadReq{
-			Instance:        instance,
+			Instance:        inst,
 			PlatformPackage: platformRef.PackageName,
 			Architecture:    platformRef.Architecture,
 			Version:         platformRef.Version,
diff --git a/cli/core/install.go b/cli/core/install.go
index cc0135a0fa3..985c445b180 100644
--- a/cli/core/install.go
+++ b/cli/core/install.go
@@ -48,7 +48,12 @@ func initInstallCommand() *cobra.Command {
 }
 
 func runInstallCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error installing: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
 	logrus.Info("Executing `arduino core install`")
 
 	platformsRefs, err := globals.ParseReferenceArgs(args, true)
@@ -59,7 +64,7 @@ func runInstallCommand(cmd *cobra.Command, args []string) {
 
 	for _, platformRef := range platformsRefs {
 		plattformInstallReq := &rpc.PlatformInstallReq{
-			Instance:        instance,
+			Instance:        inst,
 			PlatformPackage: platformRef.PackageName,
 			Architecture:    platformRef.Architecture,
 			Version:         platformRef.Version,
diff --git a/cli/core/list.go b/cli/core/list.go
index c85fa4b290c..117d200a787 100644
--- a/cli/core/list.go
+++ b/cli/core/list.go
@@ -49,10 +49,15 @@ var listFlags struct {
 }
 
 func runListCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error listing platforms: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
 	logrus.Info("Executing `arduino core list`")
 
-	platforms, err := core.GetPlatforms(instance.Id, listFlags.updatableOnly)
+	platforms, err := core.GetPlatforms(inst.Id, listFlags.updatableOnly)
 	if err != nil {
 		feedback.Errorf("Error listing platforms: %v", err)
 		os.Exit(errorcodes.ErrGeneric)
diff --git a/cli/core/search.go b/cli/core/search.go
index f31a7eddb1f..8711a5ac00e 100644
--- a/cli/core/search.go
+++ b/cli/core/search.go
@@ -51,11 +51,16 @@ func initSearchCommand() *cobra.Command {
 }
 
 func runSearchCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error saerching for platforms: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
 	logrus.Info("Executing `arduino core search`")
 
 	arguments := strings.ToLower(strings.Join(args, " "))
-	resp, err := core.PlatformSearch(instance.GetId(), arguments, allVersions)
+	resp, err := core.PlatformSearch(inst.GetId(), arguments, allVersions)
 	if err != nil {
 		feedback.Errorf("Error saerching for platforms: %v", err)
 		os.Exit(errorcodes.ErrGeneric)
diff --git a/cli/core/uninstall.go b/cli/core/uninstall.go
index 05fcaf60a9e..dcfaa638b62 100644
--- a/cli/core/uninstall.go
+++ b/cli/core/uninstall.go
@@ -44,7 +44,12 @@ func initUninstallCommand() *cobra.Command {
 }
 
 func runUninstallCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error uninstalling: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
 	logrus.Info("Executing `arduino core uninstall`")
 
 	platformsRefs, err := globals.ParseReferenceArgs(args, true)
@@ -61,7 +66,7 @@ func runUninstallCommand(cmd *cobra.Command, args []string) {
 	}
 	for _, platformRef := range platformsRefs {
 		_, err := core.PlatformUninstall(context.Background(), &rpc.PlatformUninstallReq{
-			Instance:        instance,
+			Instance:        inst,
 			PlatformPackage: platformRef.PackageName,
 			Architecture:    platformRef.Architecture,
 		}, output.NewTaskProgressCB())
diff --git a/cli/core/update_index.go b/cli/core/update_index.go
index cd0f4c80444..11bef2bef4f 100644
--- a/cli/core/update_index.go
+++ b/cli/core/update_index.go
@@ -44,7 +44,7 @@ func initUpdateIndexCommand() *cobra.Command {
 }
 
 func runUpdateIndexCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 	logrus.Info("Executing `arduino core update-index`")
 
 	_, err := commands.UpdateIndex(context.Background(), &rpc.UpdateIndexReq{
diff --git a/cli/core/upgrade.go b/cli/core/upgrade.go
index 5bee93f1441..ef7e9fa804f 100644
--- a/cli/core/upgrade.go
+++ b/cli/core/upgrade.go
@@ -48,12 +48,17 @@ func initUpgradeCommand() *cobra.Command {
 }
 
 func runUpgradeCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	inst, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error upgrading: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
+
 	logrus.Info("Executing `arduino core upgrade`")
 
 	// if no platform was passed, upgrade allthethings
 	if len(args) == 0 {
-		targets, err := core.GetPlatforms(instance.Id, true)
+		targets, err := core.GetPlatforms(inst.Id, true)
 		if err != nil {
 			feedback.Errorf("Error retrieving core list: %v", err)
 			os.Exit(errorcodes.ErrGeneric)
@@ -85,7 +90,7 @@ func runUpgradeCommand(cmd *cobra.Command, args []string) {
 		}
 
 		r := &rpc.PlatformUpgradeReq{
-			Instance:        instance,
+			Instance:        inst,
 			PlatformPackage: platformRef.PackageName,
 			Architecture:    platformRef.Architecture,
 		}
diff --git a/cli/instance/instance.go b/cli/instance/instance.go
index 422d8bd1e24..37923b1638f 100644
--- a/cli/instance/instance.go
+++ b/cli/instance/instance.go
@@ -1,77 +1,100 @@
+// This file is part of arduino-cli.
+//
+// Copyright 2019 ARDUINO SA (http://www.arduino.cc/)
+//
+// This software is released under the GNU General Public License version 3,
+// which covers the main part of arduino-cli.
+// The terms of this license can be found at:
+// https://www.gnu.org/licenses/gpl-3.0.en.html
+//
+// You can be released from the requirements of the above licenses by purchasing
+// a commercial license. Buying such a license is mandatory if you want to
+// modify or otherwise use the software for commercial activities involving the
+// Arduino software without disclosing the source code of your own applications.
+// To purchase a commercial license, send an email to license@arduino.cc.
+
 package instance
 
 import (
 	"context"
-	"os"
 
-	"github.com/arduino/arduino-cli/cli/errorcodes"
-	"github.com/arduino/arduino-cli/cli/feedback"
 	"github.com/arduino/arduino-cli/cli/globals"
 	"github.com/arduino/arduino-cli/cli/output"
 	"github.com/arduino/arduino-cli/commands"
 	rpc "github.com/arduino/arduino-cli/rpc/commands"
+	"github.com/pkg/errors"
 	"github.com/sirupsen/logrus"
-	"github.com/spf13/viper"
 )
 
-// CreateInstaceIgnorePlatformIndexErrors creates and return an instance of the
+// CreateInstanceIgnorePlatformIndexErrors creates and return an instance of the
 // Arduino Core Engine, but won't stop on platforms index loading errors.
-func CreateInstaceIgnorePlatformIndexErrors() *rpc.Instance {
-	return initInstance().GetInstance()
+func CreateInstanceIgnorePlatformIndexErrors() *rpc.Instance {
+	i, _ := getInitResponse()
+	return i.GetInstance()
 }
 
 // CreateInstance creates and return an instance of the Arduino Core engine
-func CreateInstance() *rpc.Instance {
-	resp := initInstance()
-	if resp.GetPlatformsIndexErrors() != nil {
-		for _, err := range resp.GetPlatformsIndexErrors() {
-			feedback.Errorf("Error loading index: %v", err)
-		}
-		feedback.Errorf("Launch '%s core update-index' to fix or download indexes.", os.Args[0])
-		os.Exit(errorcodes.ErrGeneric)
+func CreateInstance() (*rpc.Instance, error) {
+	resp, err := getInitResponse()
+	if err != nil {
+		return nil, err
 	}
-	return resp.GetInstance()
+
+	return resp.GetInstance(), checkPlatformErrors(resp)
 }
 
-func initInstance() *rpc.InitResp {
-	logrus.Info("Initializing package manager")
-	req := packageManagerInitReq()
+func getInitResponse() (*rpc.InitResp, error) {
+	// invoke Init()
+	resp, err := commands.Init(context.Background(), &rpc.InitReq{},
+		output.ProgressBar(), output.TaskProgress(), globals.NewHTTPClientHeader())
 
-	resp, err := commands.Init(context.Background(), req, output.ProgressBar(), output.TaskProgress(), globals.NewHTTPClientHeader())
+	// Init() failed
 	if err != nil {
-		feedback.Errorf("Error initializing package manager: %v", err)
-		os.Exit(errorcodes.ErrGeneric)
+		return nil, errors.Wrap(err, "creating instance")
 	}
+
+	// Init() succeeded but there were errors loading library indexes,
+	// let's rescan and try again
 	if resp.GetLibrariesIndexError() != "" {
-		commands.UpdateLibrariesIndex(context.Background(),
+		logrus.Warnf("There were errors loading the library index, trying again...")
+
+		// update all indexes
+		err := commands.UpdateLibrariesIndex(context.Background(),
 			&rpc.UpdateLibrariesIndexReq{Instance: resp.GetInstance()}, output.ProgressBar())
-		rescResp, err := commands.Rescan(resp.GetInstance().GetId())
-		if rescResp.GetLibrariesIndexError() != "" {
-			feedback.Errorf("Error loading library index: %v", rescResp.GetLibrariesIndexError())
-			os.Exit(errorcodes.ErrGeneric)
+		if err != nil {
+			return nil, errors.Wrap(err, "updating the library index")
 		}
+
+		// rescan libraries
+		rescanResp, err := commands.Rescan(resp.GetInstance().GetId())
 		if err != nil {
-			feedback.Errorf("Error loading library index: %v", err)
-			os.Exit(errorcodes.ErrGeneric)
+			return nil, errors.Wrap(err, "during rescan")
 		}
-		resp.LibrariesIndexError = rescResp.LibrariesIndexError
-		resp.PlatformsIndexErrors = rescResp.PlatformsIndexErrors
-	}
-	return resp
-}
 
-func packageManagerInitReq() *rpc.InitReq {
-	urls := []string{globals.DefaultIndexURL}
+		// errors persist
+		if rescanResp.GetLibrariesIndexError() != "" {
+			return nil, errors.New("still errors after rescan: " + rescanResp.GetLibrariesIndexError())
+		}
 
-	for _, URL := range viper.GetStringSlice("board_manager.additional_urls") {
-		urls = append(urls, URL)
+		// succeeded, copy over PlatformsIndexErrors in case errors occurred
+		// during rescan
+		resp.LibrariesIndexError = ""
+		resp.PlatformsIndexErrors = rescanResp.PlatformsIndexErrors
 	}
 
-	conf := &rpc.Configuration{}
-	conf.DataDir = viper.GetString("directories.Data")
-	conf.DownloadsDir = viper.GetString("directories.Downloads")
-	conf.BoardManagerAdditionalUrls = urls
-	conf.SketchbookDir = viper.GetString("directories.User")
+	return resp, nil
+}
+
+func checkPlatformErrors(resp *rpc.InitResp) error {
+	// Init() and/or rescan succeeded, but there were errors loading platform indexes
+	if resp.GetPlatformsIndexErrors() != nil {
+		// log each error
+		for _, err := range resp.GetPlatformsIndexErrors() {
+			logrus.Errorf("Error loading platform index: %v", err)
+		}
+		// return
+		return errors.New("There were errors loading platform indexes")
+	}
 
-	return &rpc.InitReq{Configuration: conf}
+	return nil
 }
diff --git a/cli/lib/check_deps.go b/cli/lib/check_deps.go
index c0570f36ee3..7e9bf9575c2 100644
--- a/cli/lib/check_deps.go
+++ b/cli/lib/check_deps.go
@@ -53,7 +53,7 @@ func runDepsCommand(cmd *cobra.Command, args []string) {
 		os.Exit(errorcodes.ErrBadArgument)
 	}
 
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 	deps, err := lib.LibraryResolveDependencies(context.Background(), &rpc.LibraryResolveDependenciesReq{
 		Instance: instance,
 		Name:     libRef.Name,
diff --git a/cli/lib/download.go b/cli/lib/download.go
index 56cf64ff17a..3e2fb7b8fc6 100644
--- a/cli/lib/download.go
+++ b/cli/lib/download.go
@@ -46,7 +46,7 @@ func initDownloadCommand() *cobra.Command {
 }
 
 func runDownloadCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 	refs, err := globals.ParseLibraryReferenceArgs(args)
 	if err != nil {
 		feedback.Errorf("Invalid argument passed: %v", err)
diff --git a/cli/lib/install.go b/cli/lib/install.go
index 044ee4425ab..3f41db71cf9 100644
--- a/cli/lib/install.go
+++ b/cli/lib/install.go
@@ -51,7 +51,7 @@ var installFlags struct {
 }
 
 func runInstallCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 	libRefs, err := globals.ParseLibraryReferenceArgs(args)
 	if err != nil {
 		feedback.Errorf("Arguments error: %v", err)
diff --git a/cli/lib/list.go b/cli/lib/list.go
index 0454d2cd15a..c701ecd6fcf 100644
--- a/cli/lib/list.go
+++ b/cli/lib/list.go
@@ -51,7 +51,7 @@ var listFlags struct {
 }
 
 func runListCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 	logrus.Info("Listing")
 
 	res, err := lib.LibraryList(context.Background(), &rpc.LibraryListReq{
diff --git a/cli/lib/search.go b/cli/lib/search.go
index 5c47df9019d..b3e472b8c64 100644
--- a/cli/lib/search.go
+++ b/cli/lib/search.go
@@ -52,7 +52,7 @@ var searchFlags struct {
 }
 
 func runSearchCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 	logrus.Info("Executing `arduino lib search`")
 	searchResp, err := lib.LibrarySearch(context.Background(), &rpc.LibrarySearchReq{
 		Instance: instance,
diff --git a/cli/lib/uninstall.go b/cli/lib/uninstall.go
index cabe9743870..b2f90571277 100644
--- a/cli/lib/uninstall.go
+++ b/cli/lib/uninstall.go
@@ -47,7 +47,7 @@ func initUninstallCommand() *cobra.Command {
 func runUninstallCommand(cmd *cobra.Command, args []string) {
 	logrus.Info("Executing `arduino lib uninstall`")
 
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 	refs, err := globals.ParseLibraryReferenceArgs(args)
 	if err != nil {
 		feedback.Errorf("Invalid argument passed: %v", err)
diff --git a/cli/lib/update_index.go b/cli/lib/update_index.go
index 9301a14db1e..317094e5cd8 100644
--- a/cli/lib/update_index.go
+++ b/cli/lib/update_index.go
@@ -38,7 +38,7 @@ func initUpdateIndexCommand() *cobra.Command {
 		Example: "  " + os.Args[0] + " lib update-index",
 		Args:    cobra.NoArgs,
 		Run: func(cmd *cobra.Command, args []string) {
-			instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+			instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 			err := commands.UpdateLibrariesIndex(context.Background(), &rpc.UpdateLibrariesIndexReq{
 				Instance: instance,
 			}, output.ProgressBar())
diff --git a/cli/lib/upgrade.go b/cli/lib/upgrade.go
index 06ef2a73abe..743d546b305 100644
--- a/cli/lib/upgrade.go
+++ b/cli/lib/upgrade.go
@@ -47,7 +47,7 @@ func initUpgradeCommand() *cobra.Command {
 }
 
 func runUpgradeCommand(cmd *cobra.Command, args []string) {
-	instance := instance.CreateInstaceIgnorePlatformIndexErrors()
+	instance := instance.CreateInstanceIgnorePlatformIndexErrors()
 
 	if len(args) == 0 {
 		err := lib.LibraryUpgradeAll(instance.Id, output.ProgressBar(), output.TaskProgress(), globals.NewHTTPClientHeader())
diff --git a/cli/upload/upload.go b/cli/upload/upload.go
index f2609111355..9e536deba82 100644
--- a/cli/upload/upload.go
+++ b/cli/upload/upload.go
@@ -63,7 +63,11 @@ func NewCommand() *cobra.Command {
 }
 
 func run(command *cobra.Command, args []string) {
-	instance := instance.CreateInstance()
+	instance, err := instance.CreateInstance()
+	if err != nil {
+		feedback.Errorf("Error during Upload: %v", err)
+		os.Exit(errorcodes.ErrGeneric)
+	}
 
 	var path *paths.Path
 	if len(args) > 0 {
@@ -71,7 +75,7 @@ func run(command *cobra.Command, args []string) {
 	}
 	sketchPath := initSketchPath(path)
 
-	_, err := upload.Upload(context.Background(), &rpc.UploadReq{
+	if _, err := upload.Upload(context.Background(), &rpc.UploadReq{
 		Instance:   instance,
 		Fqbn:       fqbn,
 		SketchPath: sketchPath.String(),
@@ -79,9 +83,7 @@ func run(command *cobra.Command, args []string) {
 		Verbose:    verbose,
 		Verify:     verify,
 		ImportFile: importFile,
-	}, os.Stdout, os.Stderr)
-
-	if err != nil {
+	}, os.Stdout, os.Stderr); err != nil {
 		feedback.Errorf("Error during Upload: %v", err)
 		os.Exit(errorcodes.ErrGeneric)
 	}
diff --git a/commands/instances.go b/commands/instances.go
index 1ffb035f145..90c4d085beb 100644
--- a/commands/instances.go
+++ b/commands/instances.go
@@ -59,6 +59,13 @@ type InstanceContainer interface {
 	GetInstance() *rpc.Instance
 }
 
+type createInstanceResult struct {
+	Pm                  *packagemanager.PackageManager
+	Lm                  *librariesmanager.LibrariesManager
+	PlatformIndexErrors []string
+	LibrariesIndexError string
+}
+
 // GetInstance returns a CoreInstance for the given ID, or nil if ID
 // doesn't exist
 func GetInstance(id int32) *CoreInstance {
@@ -125,20 +132,19 @@ func (instance *CoreInstance) checkForBuiltinTools(downloadCB DownloadProgressCB
 }
 
 // Init FIXMEDOC
-func Init(ctx context.Context, req *rpc.InitReq, downloadCB DownloadProgressCB, taskCB TaskProgressCB, downloaderHeaders http.Header) (*rpc.InitResp, error) {
-	inConfig := req.GetConfiguration()
-	if inConfig == nil {
-		return nil, fmt.Errorf("invalid request")
-	}
+func Init(ctx context.Context, req *rpc.InitReq, downloadCB DownloadProgressCB, taskCB TaskProgressCB,
+	downloaderHeaders http.Header) (*rpc.InitResp, error) {
 
-	pm, lm, reqPltIndex, reqLibIndex, err := createInstance(ctx, req.GetLibraryManagerOnly())
+	res, err := createInstance(ctx, req.GetLibraryManagerOnly())
 	if err != nil {
 		return nil, fmt.Errorf("cannot initialize package manager: %s", err)
 	}
+
 	instance := &CoreInstance{
-		PackageManager: pm,
-		lm:             lm,
-		getLibOnly:     req.GetLibraryManagerOnly()}
+		PackageManager: res.Pm,
+		lm:             res.Lm,
+		getLibOnly:     req.GetLibraryManagerOnly(),
+	}
 	handle := instancesCount
 	instancesCount++
 	instances[handle] = instance
@@ -150,8 +156,8 @@ func Init(ctx context.Context, req *rpc.InitReq, downloadCB DownloadProgressCB,
 
 	return &rpc.InitResp{
 		Instance:             &rpc.Instance{Id: handle},
-		PlatformsIndexErrors: reqPltIndex,
-		LibrariesIndexError:  reqLibIndex,
+		PlatformsIndexErrors: res.PlatformIndexErrors,
+		LibrariesIndexError:  res.LibrariesIndexError,
 	}, nil
 }
 
@@ -252,88 +258,103 @@ func Rescan(instanceID int32) (*rpc.RescanResp, error) {
 		return nil, fmt.Errorf("invalid handle")
 	}
 
-	pm, lm, reqPltIndex, reqLibIndex, err := createInstance(context.Background(), coreInstance.getLibOnly)
+	res, err := createInstance(context.Background(), coreInstance.getLibOnly)
 	if err != nil {
 		return nil, fmt.Errorf("rescanning filesystem: %s", err)
 	}
-	coreInstance.PackageManager = pm
-	coreInstance.lm = lm
+	coreInstance.PackageManager = res.Pm
+	coreInstance.lm = res.Lm
 
 	return &rpc.RescanResp{
-		PlatformsIndexErrors: reqPltIndex,
-		LibrariesIndexError:  reqLibIndex,
+		PlatformsIndexErrors: res.PlatformIndexErrors,
+		LibrariesIndexError:  res.LibrariesIndexError,
 	}, nil
 }
 
-func createInstance(ctx context.Context, getLibOnly bool) (
-	*packagemanager.PackageManager, *librariesmanager.LibrariesManager, []string, string, error) {
-	var pm *packagemanager.PackageManager
-	platformIndexErrors := []string{}
-	dataDir := paths.New(viper.GetString("directories.Data"))
+func createInstance(ctx context.Context, getLibOnly bool) (*createInstanceResult, error) {
+	res := &createInstanceResult{}
+
+	// setup downloads directory
 	downloadsDir := paths.New(viper.GetString("directories.Downloads"))
+	if downloadsDir.NotExist() {
+		err := downloadsDir.MkdirAll()
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	// setup data directory
+	dataDir := paths.New(viper.GetString("directories.Data"))
+	packagesDir := configuration.PackagesDir()
+	if packagesDir.NotExist() {
+		err := packagesDir.MkdirAll()
+		if err != nil {
+			return nil, err
+		}
+	}
+
 	if !getLibOnly {
-		pm = packagemanager.NewPackageManager(
-			dataDir,
-			configuration.PackagesDir(),
-			downloadsDir,
-			dataDir.Join("tmp"))
+		res.Pm = packagemanager.NewPackageManager(dataDir, configuration.PackagesDir(),
+			downloadsDir, dataDir.Join("tmp"))
 
 		urls := []string{globals.DefaultIndexURL}
 		urls = append(urls, viper.GetStringSlice("board_manager.additional_urls")...)
 		for _, u := range urls {
 			URL, err := url.Parse(u)
 			if err != nil {
-				logrus.Warnf("unable to parse additional URL: %s", u)
+				logrus.Warnf("Unable to parse index URL: %s, skip...", u)
 				continue
 			}
-			if err := pm.LoadPackageIndex(URL); err != nil {
-				platformIndexErrors = append(platformIndexErrors, err.Error())
+
+			if err := res.Pm.LoadPackageIndex(URL); err != nil {
+				res.PlatformIndexErrors = append(res.PlatformIndexErrors, err.Error())
 			}
 		}
 
-		if err := pm.LoadHardware(); err != nil {
-			return nil, nil, nil, "", fmt.Errorf("loading hardware packages: %s", err)
+		if err := res.Pm.LoadHardware(); err != nil {
+			return res, fmt.Errorf("error loading hardware packages: %s", err)
 		}
 	}
-	if len(platformIndexErrors) == 0 {
-		platformIndexErrors = nil
+
+	if len(res.PlatformIndexErrors) == 0 {
+		res.PlatformIndexErrors = nil
 	}
 
 	// Initialize library manager
 	// --------------------------
-	lm := librariesmanager.NewLibraryManager(dataDir, downloadsDir)
+	res.Lm = librariesmanager.NewLibraryManager(dataDir, downloadsDir)
 
 	// Add IDE builtin libraries dir
 	if bundledLibsDir := configuration.IDEBundledLibrariesDir(); bundledLibsDir != nil {
-		lm.AddLibrariesDir(bundledLibsDir, libraries.IDEBuiltIn)
+		res.Lm.AddLibrariesDir(bundledLibsDir, libraries.IDEBuiltIn)
 	}
 
 	// Add user libraries dir
 	libDir := configuration.LibrariesDir()
-	lm.AddLibrariesDir(libDir, libraries.User)
+	res.Lm.AddLibrariesDir(libDir, libraries.User)
 
 	// Add libraries dirs from installed platforms
-	if pm != nil {
-		for _, targetPackage := range pm.Packages {
+	if res.Pm != nil {
+		for _, targetPackage := range res.Pm.Packages {
 			for _, platform := range targetPackage.Platforms {
-				if platformRelease := pm.GetInstalledPlatformRelease(platform); platformRelease != nil {
-					lm.AddPlatformReleaseLibrariesDir(platformRelease, libraries.PlatformBuiltIn)
+				if platformRelease := res.Pm.GetInstalledPlatformRelease(platform); platformRelease != nil {
+					res.Lm.AddPlatformReleaseLibrariesDir(platformRelease, libraries.PlatformBuiltIn)
 				}
 			}
 		}
 	}
 
 	// Load index and auto-update it if needed
-	librariesIndexError := ""
-	if err := lm.LoadIndex(); err != nil {
-		librariesIndexError = err.Error()
+	if err := res.Lm.LoadIndex(); err != nil {
+		res.LibrariesIndexError = err.Error()
 	}
 
 	// Scan for libraries
-	if err := lm.RescanLibraries(); err != nil {
-		return nil, nil, nil, "", fmt.Errorf("libraries rescan: %s", err)
+	if err := res.Lm.RescanLibraries(); err != nil {
+		return res, fmt.Errorf("libraries rescan: %s", err)
 	}
-	return pm, lm, platformIndexErrors, librariesIndexError, nil
+
+	return res, nil
 }
 
 // Download FIXMEDOC
diff --git a/rpc/commands/commands.proto b/rpc/commands/commands.proto
index 628c6626ef5..6dec9bec866 100644
--- a/rpc/commands/commands.proto
+++ b/rpc/commands/commands.proto
@@ -93,27 +93,17 @@ service ArduinoCore {
   rpc LibraryList(LibraryListReq) returns (LibraryListResp);
 }
 
-// Configuration contains information to instantiate an Arduino Platform Service
+// DEPRECATED
+// Configuration is deprecated, use the Settings Service instead
 message Configuration {
-  // dataDir represents the current root of the arduino tree (defaulted to
-  // `$HOME/.arduino15` on linux).
   string dataDir = 1;
-
-  // sketchbookDir represents the current root of the sketchbooks tree
-  // (defaulted to `$HOME/Arduino`).
   string sketchbookDir = 2;
-
-  // ArduinoIDEDirectory is the directory of the Arduino IDE if the CLI runs
-  // together with it.
   string downloadsDir = 3;
-
-  // BoardManagerAdditionalUrls contains the additional URL for 3rd party
-  // packages
   repeated string boardManagerAdditionalUrls = 4;
 }
 
 message InitReq {
-  Configuration configuration = 1;
+  Configuration configuration = 1; // DEPRECATED this field will be ignored
   bool library_manager_only = 2;
 }