fix a lot of stuff

cmd/commands/app.go

@@ -49,9 +49,6 @@ func NewAppCommand() *cobra.Command {
 		Use:     "application",
 		Aliases: []string{"app"},
 		Short:   "Manage applications",
-		PersistentPreRun: func(_ *cobra.Command, _ []string) {
-			cloneOpts.Parse()
-		},
 		Run: func(cmd *cobra.Command, args []string) {
 			cmd.HelpFunc()(cmd, args)
 			exit(1)
@@ -93,6 +90,7 @@ func NewAppCreateCommand(cloneOpts *git.CloneOptions) *cobra.Command {
 
 	<BIN> app create <new_app_name> --app github.com/some_org/some_repo/manifests?ref=v1.2.3 --project project_name
 `),
+		PreRun: func(cmd *cobra.Command, args []string) { cloneOpts.Parse() },
 		RunE: func(cmd *cobra.Command, args []string) error {
 			if len(args) < 1 {
 				log.G().Fatal("must enter application name")
@@ -180,6 +178,7 @@ func setAppOptsDefaults(ctx context.Context, repofs fs.FS, opts *AppCreateOption
 			Auth: opts.CloneOpts.Auth,
 			FS:   memfs.New(),
 		}
+		cloneOpts.Parse()
 		_, fsys, err = clone(ctx, cloneOpts)
 		if err != nil {
 			return err
@@ -230,6 +229,7 @@ func NewAppListCommand(cloneOpts *git.CloneOptions) *cobra.Command {
 
 	<BIN> app list <project_name>
 `),
+		PreRun: func(cmd *cobra.Command, args []string) { cloneOpts.Parse() },
 		RunE: func(cmd *cobra.Command, args []string) error {
 			if len(args) < 1 {
 				log.G().Fatal("must enter a project name")
@@ -313,6 +313,7 @@ func NewAppDeleteCommand(cloneOpts *git.CloneOptions) *cobra.Command {
 
 	<BIN> app delete <app_name> --project <project_name>
 `),
+		PreRun: func(cmd *cobra.Command, args []string) { cloneOpts.Parse() },
 		RunE: func(cmd *cobra.Command, args []string) error {
 			if len(args) < 1 {
 				log.G().Fatal("must enter application name")

cmd/commands/project.go

@@ -65,9 +65,6 @@ func NewProjectCommand() *cobra.Command {
 		Use:     "project",
 		Aliases: []string{"proj"},
 		Short:   "Manage projects",
-		PersistentPreRun: func(_ *cobra.Command, _ []string) {
-			cloneOpts.Parse()
-		},
 		Run: func(cmd *cobra.Command, args []string) {
 			cmd.HelpFunc()(cmd, args)
 			exit(1)
@@ -107,6 +104,7 @@ func NewProjectCreateCommand(cloneOpts *git.CloneOptions) *cobra.Command {
 
 	<BIN> project create <PROJECT_NAME>
 `),
+		PreRun: func(cmd *cobra.Command, args []string) { cloneOpts.Parse() },
 		RunE: func(cmd *cobra.Command, args []string) error {
 			if len(args) < 1 {
 				log.G().Fatal("must enter project name")
@@ -341,6 +339,7 @@ func NewProjectListCommand(cloneOpts *git.CloneOptions) *cobra.Command {
 
 	<BIN> project list
 `),
+		PreRun: func(cmd *cobra.Command, args []string) { cloneOpts.Parse() },
 		RunE: func(cmd *cobra.Command, args []string) error {
 			return RunProjectList(cmd.Context(), &ProjectListOptions{
 				CloneOpts: cloneOpts,
@@ -408,6 +407,7 @@ func NewProjectDeleteCommand(cloneOpts *git.CloneOptions) *cobra.Command {
 	
 	<BIN> project delete <project_name>
 `),
+		PreRun: func(cmd *cobra.Command, args []string) { cloneOpts.Parse() },
 		RunE: func(cmd *cobra.Command, args []string) error {
 			if len(args) < 1 {
 				log.G().Fatal("must enter project name")

cmd/commands/repo.go

@@ -165,9 +165,8 @@ func NewRepoBootstrapCommand() *cobra.Command {
 
 	<BIN> repo bootstrap --repo https://github.com/example/repo/path/to/installation_root
 `),
-		PersistentPreRun: func(_ *cobra.Command, _ []string) {
-			cloneOpts.Parse()
-		}, RunE: func(cmd *cobra.Command, args []string) error {
+		PreRun: func(cmd *cobra.Command, args []string) { cloneOpts.Parse() },
+		RunE: func(cmd *cobra.Command, args []string) error {
 			return RunRepoBootstrap(cmd.Context(), &RepoBootstrapOptions{
 				AppSpecifier:     appSpecifier,
 				InstallationMode: installationMode,
@@ -306,7 +305,7 @@ func RunRepoBootstrap(ctx context.Context, opts *RepoBootstrapOptions) error {
 		return nil
 	}
 
-	log.G().Infof("cloning repo: %s", opts.CloneOptions.URL)
+	log.G().Infof("cloning repo: %s", opts.CloneOptions.URL())
 
 	// clone GitOps repo
 	r, repofs, err := clone(ctx, opts.CloneOptions)

pkg/application/application.go

@@ -454,20 +454,24 @@ func checkBaseCollision(repofs fs.FS, orgBasePath string, newBase *kusttypes.Kus
 }
 
 // fixResourcesPaths adjusts all relative paths in the kustomization file to the specified
-// `kustomizationPath`.
-func fixResourcesPaths(k *kusttypes.Kustomization, kustomizationPath string) error {
+// newKustDir.
+func fixResourcesPaths(k *kusttypes.Kustomization, newKustDir string) error {
 	for i, path := range k.Resources {
-		// if path is a local file
+		// if path is a remote resource ignore it
 		if _, err := os.Stat(path); err != nil && os.IsNotExist(err) {
 			continue
 		}
 
-		ap, err := filepath.Abs(path)
+		absRes, err := filepath.Abs(path)
 		if err != nil {
 			return err
 		}
 
-		k.Resources[i], err = filepath.Rel(kustomizationPath, ap)
+		k.Resources[i], err = filepath.Rel(newKustDir, absRes)
+		log.G().WithFields(log.Fields{
+			"from": absRes,
+			"to":   k.Resources[i],
+		}).Debug("adjusting kustomization paths to local filesystem")
 		if err != nil {
 			return err
 		}
@@ -477,14 +481,18 @@ func fixResourcesPaths(k *kusttypes.Kustomization, kustomizationPath string) err
 }
 
 var generateManifests = func(k *kusttypes.Kustomization) ([]byte, error) {
-	td, err := ioutil.TempDir("", "auto-pilot")
+	td, err := ioutil.TempDir(".", "auto-pilot")
 	if err != nil {
 		return nil, err
 	}
 	defer os.RemoveAll(td)
 
-	kustomizationPath := filepath.Join(td, "kustomization.yaml")
-	if err = fixResourcesPaths(k, kustomizationPath); err != nil {
+	absTd, err := filepath.Abs(td)
+	if err != nil {
+		return nil, err
+	}
+
+	if err = fixResourcesPaths(k, absTd); err != nil {
 		return nil, err
 	}
 
@@ -493,6 +501,7 @@ var generateManifests = func(k *kusttypes.Kustomization) ([]byte, error) {
 		return nil, err
 	}
 
+	kustomizationPath := filepath.Join(td, "kustomization.yaml")
 	if err = ioutil.WriteFile(kustomizationPath, kyaml, 0400); err != nil {
 		return nil, err
 	}

pkg/git/repository.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"io"
 	"os"
 	"strings"
 
@@ -39,6 +40,7 @@ type (
 		Repo     string
 		Auth     Auth
 		FS       billy.Filesystem
+		Progress io.Writer
 		url      string
 		revision string
 		path     string
@@ -126,6 +128,10 @@ func (o *CloneOptions) Clone(ctx context.Context) (Repository, fs.FS, error) {
 		return nil, nil, ErrNoParse
 	}
 
+	if o.Progress == nil {
+		o.Progress = os.Stderr
+	}
+
 	r, err := clone(ctx, o)
 	if err != nil {
 		if err == transport.ErrEmptyRemoteRepository {
@@ -197,7 +203,7 @@ var clone = func(ctx context.Context, opts *CloneOptions) (*repo, error) {
 		URL:      opts.url,
 		Auth:     getAuth(opts.Auth),
 		Depth:    1,
-		Progress: os.Stderr,
+		Progress: opts.Progress,
 		Tags:     gg.NoTags,
 	}