diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
index 7f26c5c..e84e54b 100644
--- a/.github/workflows/testing.yaml
+++ b/.github/workflows/testing.yaml
@@ -26,14 +26,14 @@ jobs:
         run: |
           expected_file=./test-data/analysis-output.yaml
           actual_file=./output/output.yaml
-          sed 's/^[ \t-]*//' $expected_file | sort > /tmp/expected_file
-          sed 's/^[ \t-]*//' $actual_file | sort > /tmp/actual_file
+          sed 's/^[ \t-]*//' $expected_file | sort -s > /tmp/expected_file
+          sed 's/^[ \t-]*//' $actual_file | sort -s > /tmp/actual_file
           diff /tmp/expected_file /tmp/actual_file || diff $expected_file $actual_file
 
       - name: Fail if dependencies output does not match expected
         run: |
           expected_file=./test-data/deps-output.yaml
           actual_file=./output/dependencies.yaml
-          sed 's/^[ \t-]*//' $expected_file | sort > /tmp/expected_file
-          sed 's/^[ \t-]*//' $actual_file | sort > /tmp/actual_file
+          sed 's/^[ \t-]*//' $expected_file | sort -s > /tmp/expected_file
+          sed 's/^[ \t-]*//' $actual_file | sort -s > /tmp/actual_file
           diff /tmp/expected_file /tmp/actual_file || diff $expected_file $actual_file
\ No newline at end of file
diff --git a/cmd/analyze.go b/cmd/analyze.go
index 2cfeac5..3386ecd 100644
--- a/cmd/analyze.go
+++ b/cmd/analyze.go
@@ -16,7 +16,6 @@ import (
 	"sort"
 	"strings"
 
-	"github.com/apex/log"
 	"github.com/go-logr/logr"
 	"github.com/konveyor/analyzer-lsp/engine"
 	outputv1 "github.com/konveyor/analyzer-lsp/output/v1/konveyor"
@@ -82,6 +81,7 @@ func NewAnalyzeCmd(log logr.Logger) *cobra.Command {
 			}
 			err := analyzeCmd.Validate()
 			if err != nil {
+				log.Error(err, "failed to validate flags")
 				return err
 			}
 			return nil
@@ -90,31 +90,35 @@ func NewAnalyzeCmd(log logr.Logger) *cobra.Command {
 			if analyzeCmd.listSources || analyzeCmd.listTargets {
 				err := analyzeCmd.ListLabels(cmd.Context())
 				if err != nil {
-					log.V(5).Error(err, "failed to list rule labels")
+					log.Error(err, "failed to list rule labels")
 					return err
 				}
 				return nil
 			}
 			xmlOutputDir, err := analyzeCmd.ConvertXML(cmd.Context())
 			if err != nil {
-				log.V(5).Error(err, "failed to convert XML rules")
+				log.Error(err, "failed to convert xml rules")
 				return err
 			}
 			err = analyzeCmd.RunAnalysis(cmd.Context(), xmlOutputDir)
 			if err != nil {
-				log.V(5).Error(err, "failed to execute analysis")
+				log.Error(err, "failed to run analysis")
 				return err
 			}
 			err = analyzeCmd.GenerateStaticReport(cmd.Context())
 			if err != nil {
-				log.V(5).Error(err, "failed to generate static report")
+				log.Error(err, "failed to generate static report")
 				return err
 			}
 			return nil
 		},
 		PostRunE: func(cmd *cobra.Command, args []string) error {
+			if cmd.PersistentFlags().Changed(noCleanupFlag) {
+				return nil
+			}
 			err := analyzeCmd.Clean(cmd.Context())
 			if err != nil {
+				log.Error(err, "failed to generate static report")
 				return err
 			}
 			return nil
@@ -143,7 +147,7 @@ func (a *analyzeCommand) Validate() error {
 		if errors.Is(err, os.ErrNotExist) {
 			err = os.MkdirAll(a.output, os.ModePerm)
 			if err != nil {
-				return fmt.Errorf("failed to create output dir %s", a.output)
+				return fmt.Errorf("%w failed to create output dir %s", err, a.output)
 			}
 		} else {
 			return fmt.Errorf("failed to stat output directory %s", a.output)
@@ -154,14 +158,14 @@ func (a *analyzeCommand) Validate() error {
 	}
 	stat, err = os.Stat(a.input)
 	if err != nil {
-		return fmt.Errorf("failed to stat input path %s", a.input)
+		return fmt.Errorf("%w failed to stat input path %s", err, a.input)
 	}
 	// when input isn't a dir, it's pointing to a binary
 	// we need abs path to mount the file correctly
 	if !stat.Mode().IsDir() {
 		a.input, err = filepath.Abs(a.input)
 		if err != nil {
-			return fmt.Errorf("failed to get absolute path for input file %s", a.input)
+			return fmt.Errorf("%w failed to get absolute path for input file %s", err, a.input)
 		}
 		// make sure we mount a file and not a dir
 		SourceMountPath = filepath.Join(SourceMountPath, filepath.Base(a.input))
@@ -191,7 +195,7 @@ func (a *analyzeCommand) ListLabels(ctx context.Context) error {
 		if a.listSources {
 			sourceSlice, err := readRuleFilesForLabels(sourceLabel)
 			if err != nil {
-				a.log.V(5).Error(err, "failed to read rule labels")
+				a.log.Error(err, "failed to read rule labels")
 				return err
 			}
 			listOptionsFromLabels(sourceSlice, sourceLabel)
@@ -200,7 +204,7 @@ func (a *analyzeCommand) ListLabels(ctx context.Context) error {
 		if a.listTargets {
 			targetsSlice, err := readRuleFilesForLabels(targetLabel)
 			if err != nil {
-				a.log.V(5).Error(err, "failed to read rule labels")
+				a.log.Error(err, "failed to read rule labels")
 				return err
 			}
 			listOptionsFromLabels(targetsSlice, targetLabel)
@@ -209,6 +213,7 @@ func (a *analyzeCommand) ListLabels(ctx context.Context) error {
 	} else {
 		volumes, err := a.getRulesVolumes()
 		if err != nil {
+			a.log.Error(err, "failed getting rules volumes")
 			return err
 		}
 		args := []string{"analyze"}
@@ -217,7 +222,7 @@ func (a *analyzeCommand) ListLabels(ctx context.Context) error {
 		} else {
 			args = append(args, "--list-targets")
 		}
-		err = NewContainer().Run(
+		err = NewContainer(a.log).Run(
 			ctx,
 			WithEnv(runMode, runModeContainer),
 			WithVolumes(volumes),
@@ -225,6 +230,7 @@ func (a *analyzeCommand) ListLabels(ctx context.Context) error {
 			WithEntrypointArgs(args...),
 		)
 		if err != nil {
+			a.log.Error(err, "failed listing labels")
 			return err
 		}
 	}
@@ -308,9 +314,10 @@ func listOptionsFromLabels(sl []string, label string) {
 func (a *analyzeCommand) getConfigVolumes() (map[string]string, error) {
 	tempDir, err := os.MkdirTemp("", "analyze-config-")
 	if err != nil {
+		a.log.V(1).Error(err, "failed creating temp dir", "dir", tempDir)
 		return nil, err
 	}
-	a.log.V(5).Info("created directory for provider settings", "dir", tempDir)
+	a.log.V(1).Info("created directory for provider settings", "dir", tempDir)
 	a.tempDirs = append(a.tempDirs, tempDir)
 
 	otherProvsMountPath := SourceMountPath
@@ -364,10 +371,12 @@ func (a *analyzeCommand) getConfigVolumes() (map[string]string, error) {
 	}
 	jsonData, err := json.MarshalIndent(&provConfig, "", "	")
 	if err != nil {
+		a.log.V(1).Error(err, "failed to marshal provider config")
 		return nil, err
 	}
 	err = ioutil.WriteFile(filepath.Join(tempDir, "settings.json"), jsonData, os.ModePerm)
 	if err != nil {
+		a.log.V(1).Error(err, "failed to write provider config", "dir", tempDir, "file", "settings.json")
 		return nil, err
 	}
 	return map[string]string{
@@ -383,14 +392,15 @@ func (a *analyzeCommand) getRulesVolumes() (map[string]string, error) {
 	rulesetNeeded := false
 	tempDir, err := os.MkdirTemp("", "analyze-rules-")
 	if err != nil {
+		a.log.V(1).Error(err, "failed to create temp dir", "path", tempDir)
 		return nil, err
 	}
-	a.log.V(5).Info("created directory for rules", "dir", tempDir)
+	a.log.V(1).Info("created directory for rules", "dir", tempDir)
 	a.tempDirs = append(a.tempDirs, tempDir)
 	for i, r := range a.rules {
 		stat, err := os.Stat(r)
 		if err != nil {
-			log.Errorf("failed to stat rules %s", r)
+			a.log.V(1).Error(err, "failed to stat rules", "path", r)
 			return nil, err
 		}
 		// move rules files passed into dir to mount
@@ -403,7 +413,7 @@ func (a *analyzeCommand) getRulesVolumes() (map[string]string, error) {
 			destFile := filepath.Join(tempDir, fmt.Sprintf("rules%d.yaml", i))
 			err := copyFileContents(r, destFile)
 			if err != nil {
-				log.Errorf("failed to move rules file from %s to %s", r, destFile)
+				a.log.V(1).Error(err, "failed to move rules file", "src", r, "dest", destFile)
 				return nil, err
 			}
 
@@ -412,9 +422,10 @@ func (a *analyzeCommand) getRulesVolumes() (map[string]string, error) {
 		}
 	}
 	if rulesetNeeded {
-		err = createTempRuleSet(filepath.Join(tempDir, "ruleset.yaml"))
+		tempRulesetPath := filepath.Join(tempDir, "ruleset.yaml")
+		err = createTempRuleSet(tempRulesetPath)
 		if err != nil {
-			log.Error("failed to create ruleset for custom rules")
+			a.log.V(1).Error(err, "failed to create temp ruleset", "path", tempRulesetPath)
 			return nil, err
 		}
 		rulesVolumes[tempDir] = filepath.Join(RulesMountPath, filepath.Base(tempDir))
@@ -473,7 +484,7 @@ func (a *analyzeCommand) RunAnalysis(ctx context.Context, xmlOutputDir string) e
 
 	configVols, err := a.getConfigVolumes()
 	if err != nil {
-		a.log.V(5).Error(err, "failed to get config volumes for analysis")
+		a.log.V(1).Error(err, "failed to get config volumes for analysis")
 		return err
 	}
 	maps.Copy(volumes, configVols)
@@ -481,7 +492,7 @@ func (a *analyzeCommand) RunAnalysis(ctx context.Context, xmlOutputDir string) e
 	if len(a.rules) > 0 {
 		ruleVols, err := a.getRulesVolumes()
 		if err != nil {
-			a.log.V(5).Error(err, "failed to get rule volumes for analysis")
+			a.log.V(1).Error(err, "failed to get rule volumes for analysis")
 			return err
 		}
 		maps.Copy(volumes, ruleVols)
@@ -491,6 +502,7 @@ func (a *analyzeCommand) RunAnalysis(ctx context.Context, xmlOutputDir string) e
 		fmt.Sprintf("--provider-settings=%s", ProviderSettingsMountPath),
 		fmt.Sprintf("--rules=%s/", RulesetPath),
 		fmt.Sprintf("--output-file=%s", AnalysisOutputMountPath),
+		fmt.Sprintf("--context-lines=%d", 100),
 	}
 	if !a.analyzeKnownLibraries {
 		args = append(args,
@@ -518,7 +530,7 @@ func (a *analyzeCommand) RunAnalysis(ctx context.Context, xmlOutputDir string) e
 	a.log.Info("running source code analysis", "log", analysisLogFilePath,
 		"input", a.input, "output", a.output, "args", strings.Join(args, " "), "volumes", volumes)
 	// TODO (pgaikwad): run analysis & deps in parallel
-	err = NewContainer().Run(
+	err = NewContainer(a.log).Run(
 		ctx,
 		WithVolumes(volumes),
 		WithStdout(os.Stdout, analysisLog),
@@ -532,7 +544,7 @@ func (a *analyzeCommand) RunAnalysis(ctx context.Context, xmlOutputDir string) e
 
 	a.log.Info("running dependency analysis",
 		"log", depsLogFilePath, "input", a.input, "output", a.output, "args", strings.Join(args, " "))
-	err = NewContainer().Run(
+	err = NewContainer(a.log).Run(
 		ctx,
 		WithStdout(os.Stdout, dependencyLog),
 		WithStderr(os.Stderr, dependencyLog),
@@ -569,7 +581,7 @@ func (a *analyzeCommand) GenerateStaticReport(ctx context.Context) error {
 
 	a.log.Info("generating static report",
 		"output", a.output, "args", strings.Join(args, " "))
-	container := NewContainer()
+	container := NewContainer(a.log)
 	err := container.Run(
 		ctx,
 		WithEntrypointBin("/usr/local/bin/js-bundle-generator"),
@@ -599,7 +611,7 @@ func (a *analyzeCommand) Clean(ctx context.Context) error {
 	for _, path := range a.tempDirs {
 		err := os.RemoveAll(path)
 		if err != nil {
-			a.log.V(5).Error(err, "failed to delete temporary dir", "dir", path)
+			a.log.V(1).Error(err, "failed to delete temporary dir", "dir", path)
 			continue
 		}
 	}
@@ -665,7 +677,7 @@ func (a *analyzeCommand) getXMLRulesVolumes(tempRuleDir string) (map[string]stri
 	for _, r := range a.rules {
 		stat, err := os.Stat(r)
 		if err != nil {
-			a.log.V(5).Error(err, "failed to stat rules")
+			a.log.V(1).Error(err, "failed to stat rules")
 			return nil, err
 		}
 		// move xml rule files from user into dir to mount
@@ -678,7 +690,7 @@ func (a *analyzeCommand) getXMLRulesVolumes(tempRuleDir string) (map[string]stri
 			destFile := filepath.Join(tempRuleDir, xmlFileName)
 			err := copyFileContents(r, destFile)
 			if err != nil {
-				a.log.Error(err, "failed to move rules file from source to destination", "src", r, "dest", destFile)
+				a.log.V(1).Error(err, "failed to move rules file from source to destination", "src", r, "dest", destFile)
 				return nil, err
 			}
 		} else {
@@ -697,16 +709,16 @@ func (a *analyzeCommand) ConvertXML(ctx context.Context) (string, error) {
 	}
 	tempDir, err := os.MkdirTemp("", "transform-rules-")
 	if err != nil {
-		a.log.V(5).Error(err, "failed to create temp dir for rules")
+		a.log.V(1).Error(err, "failed to create temp dir for rules")
 		return "", err
 	}
-	a.log.V(5).Info("created directory for XML rules", "dir", tempDir)
+	a.log.V(1).Info("created directory for XML rules", "dir", tempDir)
 	tempOutputDir, err := os.MkdirTemp("", "transform-output-")
 	if err != nil {
-		a.log.V(5).Error(err, "failed to create temp dir for rules")
+		a.log.V(1).Error(err, "failed to create temp dir for rules")
 		return "", err
 	}
-	a.log.V(5).Info("created directory for converted XML rules", "dir", tempDir)
+	a.log.V(1).Info("created directory for converted XML rules", "dir", tempDir)
 	defer os.RemoveAll(tempDir)
 	volumes := map[string]string{
 		tempOutputDir: ShimOutputPath,
@@ -714,16 +726,17 @@ func (a *analyzeCommand) ConvertXML(ctx context.Context) (string, error) {
 
 	ruleVols, err := a.getXMLRulesVolumes(tempDir)
 	if err != nil {
-		a.log.V(5).Error(err, "failed to get XML rule volumes for analysis")
+		a.log.V(1).Error(err, "failed to get XML rule volumes for analysis")
 		return "", err
 	}
 	maps.Copy(volumes, ruleVols)
 
+	a.log.Info("running windup shim", "output", a.output)
 	args := []string{"convert",
 		fmt.Sprintf("--outputdir=%v", ShimOutputPath),
 		XMLRulePath,
 	}
-	err = NewContainer().Run(
+	err = NewContainer(a.log).Run(
 		ctx,
 		WithVolumes(volumes),
 		WithEntrypointArgs(args...),
diff --git a/cmd/container.go b/cmd/container.go
index f73322b..0e2ead8 100644
--- a/cmd/container.go
+++ b/cmd/container.go
@@ -12,6 +12,8 @@ import (
 	"runtime"
 	"strings"
 	"time"
+
+	"github.com/go-logr/logr"
 )
 
 type container struct {
@@ -27,6 +29,7 @@ type container struct {
 	cleanup bool
 	// map of source -> dest paths to mount
 	volumes map[string]string
+	log     logr.Logger
 }
 
 type Option func(c *container)
@@ -101,7 +104,7 @@ func randomName() string {
 	return string(b)
 }
 
-func NewContainer() *container {
+func NewContainer(log logr.Logger) *container {
 	return &container{
 		image:          Settings.RunnerImage,
 		entrypointArgs: []string{},
@@ -112,6 +115,7 @@ func NewContainer() *container {
 		name:           randomName(),
 		// by default, remove the container after run()
 		cleanup: true,
+		log:     log,
 	}
 }
 
@@ -121,7 +125,7 @@ func (c *container) Exists(ctx context.Context) (bool, error) {
 		"ps", "-a", "--format", "{{.Names}}")
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return false, fmt.Errorf("failed checking status of container %s", c.name)
+		return false, fmt.Errorf("%w failed checking status of container %s", err, c.name)
 	}
 	for _, found := range strings.Split(string(output), "\n") {
 		if found == c.name {
@@ -138,20 +142,16 @@ func (c *container) Run(ctx context.Context, opts ...Option) error {
 	}
 	exists, err := c.Exists(ctx)
 	if err != nil {
-		return fmt.Errorf("failed to check status of container %s", c.name)
+		return fmt.Errorf("%w failed to check status of container %s", err, c.name)
 	}
 	if exists {
 		return fmt.Errorf("container %s already exists, must remove existing before running", c.name)
 	}
-	if c.cleanup {
-		defer func() {
-			if rmErr := c.Rm(ctx); rmErr != nil {
-				err = rmErr
-			}
-		}()
-	}
 	args := []string{"run"}
 	os := runtime.GOOS
+	if c.cleanup {
+		args = append(args, "--rm")
+	}
 	if c.name != "" {
 		args = append(args, "--name")
 		args = append(args, c.name)
@@ -194,8 +194,11 @@ func (c *container) Run(ctx context.Context, opts ...Option) error {
 		cmd.Stderr = io.MultiWriter(
 			append(c.stderr, errBytes)...)
 	}
+	c.log.V(1).Info("executing podman command",
+		"podman", Settings.PodmanBinary, "cmd", c.entrypointBin, "args", strings.Join(args, " "))
 	err = cmd.Run()
 	if err != nil {
+		c.log.V(1).Error(err, "container run error")
 		if _, ok := err.(*exec.ExitError); ok {
 			return fmt.Errorf(errBytes.String())
 		}
@@ -210,7 +213,7 @@ func (c *container) Cp(ctx context.Context, src string, dest string) error {
 	}
 	exists, err := c.Exists(ctx)
 	if err != nil {
-		return fmt.Errorf("failed to check status of container %s", c.name)
+		return err
 	}
 	if !exists {
 		return fmt.Errorf("container %s does not exist, cannot copy from non-existing container", c.name)
@@ -219,13 +222,15 @@ func (c *container) Cp(ctx context.Context, src string, dest string) error {
 		ctx,
 		Settings.PodmanBinary,
 		"cp", fmt.Sprintf("%s:%s", c.name, src), dest)
+	c.log.V(1).Info("copying files from container",
+		"podman", Settings.PodmanBinary, "src", src, "dest", dest)
 	return cmd.Run()
 }
 
 func (c *container) Rm(ctx context.Context) error {
 	exists, err := c.Exists(ctx)
 	if err != nil {
-		return fmt.Errorf("failed to check status of container %s", c.name)
+		return err
 	}
 	if !exists {
 		return nil
@@ -234,5 +239,7 @@ func (c *container) Rm(ctx context.Context) error {
 		ctx,
 		Settings.PodmanBinary,
 		"rm", c.name)
+	c.log.V(1).Info("removing container",
+		"podman", Settings.PodmanBinary, "name", c.name)
 	return cmd.Run()
 }
diff --git a/cmd/openrewrite.go b/cmd/openrewrite.go
index babdd7c..633affa 100644
--- a/cmd/openrewrite.go
+++ b/cmd/openrewrite.go
@@ -38,12 +38,12 @@ func NewOpenRewriteCommand(log logr.Logger) *cobra.Command {
 		RunE: func(cmd *cobra.Command, args []string) error {
 			err := openRewriteCmd.Validate()
 			if err != nil {
-				log.V(5).Error(err, "failed validating input args")
+				log.Error(err, "failed validating input args")
 				return err
 			}
 			err = openRewriteCmd.Run(cmd.Context())
 			if err != nil {
-				log.V(5).Error(err, "failed executing openrewrite recipe")
+				log.Error(err, "failed executing openrewrite recipe")
 				return err
 			}
 			return nil
@@ -63,7 +63,7 @@ func (o *openRewriteCommand) Validate() error {
 	}
 	stat, err := os.Stat(o.input)
 	if err != nil {
-		return fmt.Errorf("failed to stat input directory %s", o.input)
+		return fmt.Errorf("%w failed to stat input directory %s", err, o.input)
 	}
 	if !stat.IsDir() {
 		return fmt.Errorf("input path %s is not a directory", o.input)
@@ -138,7 +138,7 @@ func (o *openRewriteCommand) Run(ctx context.Context) error {
 	}
 	o.log.Info("executing openrewrite recipe",
 		"recipe", o.target, "input", o.input, "args", strings.Join(args, " "))
-	err := NewContainer().Run(
+	err := NewContainer(o.log).Run(
 		ctx,
 		WithEntrypointArgs(args...),
 		WithEntrypointBin("/usr/bin/mvn"),
@@ -146,6 +146,7 @@ func (o *openRewriteCommand) Run(ctx context.Context) error {
 		WithWorkDir(InputPath),
 	)
 	if err != nil {
+		o.log.V(1).Error(err, "error running openrewrite")
 		return err
 	}
 	return nil
diff --git a/cmd/root.go b/cmd/root.go
index c222cfe..03ffd37 100644
--- a/cmd/root.go
+++ b/cmd/root.go
@@ -13,27 +13,39 @@ import (
 	"github.com/spf13/cobra"
 )
 
+const (
+	noCleanupFlag = "no-cleanup"
+)
+
+var logLevel uint32
+var logrusLog *logrus.Logger
+var noCleanup bool
+
 // rootCmd represents the base command when called without any subcommands
 var rootCmd = &cobra.Command{
 	// TODO: better descriptions
 	Short:        "A cli tool for analysis and transformation of applications",
 	Long:         ``,
 	SilenceUsage: true,
+	PersistentPreRun: func(cmd *cobra.Command, args []string) {
+		// TODO (pgaikwad): this is a hack to set log level
+		// this won't work if any subcommand ovverrides this func
+		_ = cmd.ParseFlags(args)
+		logrusLog.SetLevel(logrus.Level(logLevel))
+	},
 }
 
-var logLevel int
-
 func init() {
-	rootCmd.PersistentFlags().IntVar(&logLevel, "log-level", 5, "log level")
+	rootCmd.PersistentFlags().Uint32Var(&logLevel, "log-level", 4, "log level")
+	rootCmd.PersistentFlags().BoolVar(&noCleanup, noCleanupFlag, false, "do not cleanup temporary resources")
 
-	logrusLog := logrus.New()
+	logrusLog = logrus.New()
 	logrusLog.SetOutput(os.Stdout)
 	logrusLog.SetFormatter(&logrus.TextFormatter{})
-	logrusLog.SetLevel(logrus.InfoLevel)
-	log := logrusr.New(logrusLog)
 
-	rootCmd.AddCommand(NewTransformCommand(log))
-	rootCmd.AddCommand(NewAnalyzeCmd(log))
+	logger := logrusr.New(logrusLog)
+	rootCmd.AddCommand(NewTransformCommand(logger))
+	rootCmd.AddCommand(NewAnalyzeCmd(logger))
 }
 
 // Execute adds all child commands to the root command and sets flags appropriately.
@@ -41,7 +53,8 @@ func init() {
 func Execute() {
 	err := Settings.Load()
 	if err != nil {
-		log.Fatal("failed to load global settings")
+		log.Fatal(err, "failed to load global settings")
+		os.Exit(1)
 	}
 
 	ctx, cancelFunc := context.WithCancel(context.Background())
diff --git a/cmd/settings.go b/cmd/settings.go
index 09d332d..379cde0 100644
--- a/cmd/settings.go
+++ b/cmd/settings.go
@@ -26,10 +26,10 @@ type Config struct {
 
 func (c *Config) Load() error {
 	podmanPath, _ := exec.LookPath("podman")
-	if podmanPath != Settings.PodmanBinary && (podmanPath != "" || len(podmanPath) > 0) {
+	if podmanPath != c.PodmanBinary && (podmanPath != "" || len(podmanPath) > 0) {
 		os.Setenv("PODMAN_BIN", podmanPath)
 	}
-	err := env.Set(Settings)
+	err := env.Set(c)
 	if err != nil {
 		return err
 	}
diff --git a/cmd/shimconvert.go b/cmd/shimconvert.go
index f2c0c1c..a54333e 100644
--- a/cmd/shimconvert.go
+++ b/cmd/shimconvert.go
@@ -8,7 +8,6 @@ import (
 	"path/filepath"
 	"strings"
 
-	"github.com/apex/log"
 	"github.com/go-logr/logr"
 	"github.com/spf13/cobra"
 	"golang.org/x/exp/maps"
@@ -39,6 +38,7 @@ func NewWindupShimCommand(log logr.Logger) *cobra.Command {
 
 			err := windupShimCmd.Validate()
 			if err != nil {
+				log.Error(err, "failed to validate flags")
 				return err
 			}
 			return nil
@@ -46,6 +46,7 @@ func NewWindupShimCommand(log logr.Logger) *cobra.Command {
 		RunE: func(cmd *cobra.Command, args []string) error {
 			err := windupShimCmd.Run(cmd.Context())
 			if err != nil {
+				log.Error(err, "failed to execute windup shim")
 				return err
 			}
 			return nil
@@ -63,15 +64,14 @@ func (w *windupShimCommand) Validate() error {
 		if errors.Is(err, os.ErrNotExist) {
 			err = os.MkdirAll(w.output, os.ModePerm)
 			if err != nil {
-				return fmt.Errorf("failed to create output dir %s", w.output)
+				return fmt.Errorf("%w failed to create output dir %s", err, w.output)
 			}
 		} else {
 			return fmt.Errorf("failed to stat output directory %s", w.output)
 		}
 	}
 	if outputStat != nil && !outputStat.IsDir() {
-		log.Errorf("output path %s is not a directory", w.output)
-		return err
+		return fmt.Errorf("output path %s is not a directory", w.output)
 	}
 	if w.input == nil || len(w.input) == 0 {
 		return fmt.Errorf("input for rule file or directory must not be empty")
@@ -94,7 +94,7 @@ func (w *windupShimCommand) getRulesVolumes(tempRuleDir string) (map[string]stri
 	for _, r := range w.input {
 		stat, err := os.Stat(r)
 		if err != nil {
-			w.log.V(5).Error(err, "failed to stat rules")
+			w.log.V(1).Error(err, "failed to stat rules")
 			return nil, err
 		}
 		// move xml rule files from user into dir to mount
@@ -104,7 +104,7 @@ func (w *windupShimCommand) getRulesVolumes(tempRuleDir string) (map[string]stri
 			destFile := filepath.Join(tempRuleDir, xmlFileName)
 			err := copyFileContents(r, destFile)
 			if err != nil {
-				w.log.Error(err, "failed to move rules file from source to destination", "src", r, "dest", destFile)
+				w.log.V(1).Error(err, "failed to move rules file from source to destination", "src", r, "dest", destFile)
 				return nil, err
 			}
 		} else {
@@ -120,7 +120,7 @@ func (w *windupShimCommand) getRulesVolumes(tempRuleDir string) (map[string]stri
 func (w *windupShimCommand) Run(ctx context.Context) error {
 	tempDir, err := os.MkdirTemp("", "transform-rules-")
 	if err != nil {
-		w.log.V(5).Error(err, "failed to create temp dir for rules")
+		w.log.V(1).Error(err, "failed to create temp dir for rules")
 		return err
 	}
 	defer os.RemoveAll(tempDir)
@@ -129,7 +129,7 @@ func (w *windupShimCommand) Run(ctx context.Context) error {
 	}
 	ruleVols, err := w.getRulesVolumes(tempDir)
 	if err != nil {
-		w.log.V(5).Error(err, "failed to get xml rules for conversion")
+		w.log.V(1).Error(err, "failed to get xml rules for conversion")
 		return err
 	}
 	maps.Copy(volumes, ruleVols)
@@ -140,13 +140,14 @@ func (w *windupShimCommand) Run(ctx context.Context) error {
 	}
 	w.log.Info("running windup-shim convert command",
 		"args", strings.Join(args, " "), "volumes", volumes, "output", w.output, "inputs", strings.Join(w.input, ","))
-	err = NewContainer().Run(
+	err = NewContainer(w.log).Run(
 		ctx,
 		WithVolumes(volumes),
 		WithEntrypointArgs(args...),
 		WithEntrypointBin("/usr/local/bin/windup-shim"),
 	)
 	if err != nil {
+		w.log.V(1).Error(err, "failed to run convert command")
 		return err
 	}
 	return nil
diff --git a/cmd/transform.go b/cmd/transform.go
index 5973ee3..2a22cd0 100644
--- a/cmd/transform.go
+++ b/cmd/transform.go
@@ -7,12 +7,8 @@ import (
 
 func NewTransformCommand(log logr.Logger) *cobra.Command {
 	cmd := &cobra.Command{
-		Use: "transform",
-
+		Use:   "transform",
 		Short: "Transform application source code or windup XML rules",
-		PreRunE: func(cmd *cobra.Command, args []string) error {
-			return nil
-		},
 		Run: func(cmd *cobra.Command, args []string) {
 			cmd.Help()
 		},
diff --git a/test-data/analysis-output.yaml b/test-data/analysis-output.yaml
index 5ef740a..c9f0c89 100644
--- a/test-data/analysis-output.yaml
+++ b/test-data/analysis-output.yaml
@@ -142,24 +142,24 @@
       - uri: file:///opt/input/source/target/classes/persistence.properties
         message: When migrating environments, hard-coded IP addresses may need to be modified or eliminated.
         codeSnip: |2
-           1  jdbc.driverClassName=oracle.jdbc.driver.OracleDriver
-           2  jdbc.url=jdbc:oracle:thin:@169.60.225.216:1521/XEPDB1
-           3  jdbc.user=customers
-           4  jdbc.password=customers
-           5  hibernate.hbm2ddl.auto=create-drop
-           6  hibernate.dialect=org.hibernate.dialect.OracleDialect
+            1  jdbc.driverClassName=oracle.jdbc.driver.OracleDriver
+            2  jdbc.url=jdbc:oracle:thin:@169.60.225.216:1521/XEPDB1
+            3  jdbc.user=customers
+            4  jdbc.password=customers
+            5  hibernate.hbm2ddl.auto=create-drop
+            6  hibernate.dialect=org.hibernate.dialect.OracleDialect
         lineNumber: 2
         variables:
           matchingText: 169.60.225.216
       - uri: file:///opt/input/source/src/main/resources/persistence.properties
         message: When migrating environments, hard-coded IP addresses may need to be modified or eliminated.
         codeSnip: |2
-           1  jdbc.driverClassName=oracle.jdbc.driver.OracleDriver
-           2  jdbc.url=jdbc:oracle:thin:@169.60.225.216:1521/XEPDB1
-           3  jdbc.user=customers
-           4  jdbc.password=customers
-           5  hibernate.hbm2ddl.auto=create-drop
-           6  hibernate.dialect=org.hibernate.dialect.OracleDialect
+            1  jdbc.driverClassName=oracle.jdbc.driver.OracleDriver
+            2  jdbc.url=jdbc:oracle:thin:@169.60.225.216:1521/XEPDB1
+            3  jdbc.user=customers
+            4  jdbc.password=customers
+            5  hibernate.hbm2ddl.auto=create-drop
+            6  hibernate.dialect=org.hibernate.dialect.OracleDialect
         lineNumber: 2
         variables:
           matchingText: 169.60.225.216
@@ -1433,8 +1433,8 @@
   description: This ruleset detects the Java Mail API, which may be problematic when migrating an application to a cloud environment.
   tags:
   - Java Remote Method Invocation (RMI) service
-  - Java Remote Method Invocation (RMI) API
   - rmi
+  - Java Remote Method Invocation (RMI) API
   violations:
     jni-native-code-00000:
       description: |-
@@ -1448,7 +1448,7 @@
       incidents:
       - uri: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
         message: Java native libraries might not run in a cloud or container environment.. Recommendations. * Review the purpose of the native library in your application.. * Check whether the native library is compatible with a cloud environment.. * Reuse or embed the native library or application in a cloud environment, for example, in a JBoss module.. * Replace, remove, or rewrite the native library or application using a cloud-compatible equivalent.
-        codeSnip: " 3  import java.io.FileInputStream;\n 4  import java.io.InputStream;\n 5  import java.util.Properties;\n 6  \n 7  public class ApplicationConfiguration {\n 8  \n 9  \tprivate Properties config;\n10  \n11  \tpublic ApplicationConfiguration() {\n12  \t\tsuper();\n13  \t\tthis.config = loadProperties();\n14  \n15  \t}\n16  \n17  \tprivate Properties loadProperties() {\n18  \t\tProperties properties = new Properties();\n19  \n20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n21  \n22  \t\t\tproperties.load(inputStream);\n23  "
+        codeSnip: "  1  package io.konveyor.demo.config;\n  2  \n  3  import java.io.FileInputStream;\n  4  import java.io.InputStream;\n  5  import java.util.Properties;\n  6  \n  7  public class ApplicationConfiguration {\n  8  \n  9  \tprivate Properties config;\n 10  \n 11  \tpublic ApplicationConfiguration() {\n 12  \t\tsuper();\n 13  \t\tthis.config = loadProperties();\n 14  \n 15  \t}\n 16  \n 17  \tprivate Properties loadProperties() {\n 18  \t\tProperties properties = new Properties();\n 19  \n 20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n 21  \n 22  \t\t\tproperties.load(inputStream);\n 23  \n 24  \t\t} catch (Exception e) {\n 25  \t\t\tSystem.out.println(\"Exception: \" + e);\n 26  \t\t}\n 27  \n 28  \t\treturn properties;\n 29  \t}\n 30  \n 31  \tpublic String getProperty (String name) {\n 32  \t\treturn config.getProperty(name);\n 33  \t}\n 34  \n 35  \n 36  \n 37  }\n"
         lineNumber: 12
         variables:
           file: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
@@ -1456,7 +1456,7 @@
           name: ApplicationConfiguration
       - uri: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
         message: Java native libraries might not run in a cloud or container environment.. Recommendations. * Review the purpose of the native library in your application.. * Check whether the native library is compatible with a cloud environment.. * Reuse or embed the native library or application in a cloud environment, for example, in a JBoss module.. * Replace, remove, or rewrite the native library or application using a cloud-compatible equivalent.
-        codeSnip: "12  \t\tsuper();\n13  \t\tthis.config = loadProperties();\n14  \n15  \t}\n16  \n17  \tprivate Properties loadProperties() {\n18  \t\tProperties properties = new Properties();\n19  \n20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n21  \n22  \t\t\tproperties.load(inputStream);\n23  \n24  \t\t} catch (Exception e) {\n25  \t\t\tSystem.out.println(\"Exception: \" + e);\n26  \t\t}\n27  \n28  \t\treturn properties;\n29  \t}\n30  \n31  \tpublic String getProperty (String name) {\n32  \t\treturn config.getProperty(name);"
+        codeSnip: "  1  package io.konveyor.demo.config;\n  2  \n  3  import java.io.FileInputStream;\n  4  import java.io.InputStream;\n  5  import java.util.Properties;\n  6  \n  7  public class ApplicationConfiguration {\n  8  \n  9  \tprivate Properties config;\n 10  \n 11  \tpublic ApplicationConfiguration() {\n 12  \t\tsuper();\n 13  \t\tthis.config = loadProperties();\n 14  \n 15  \t}\n 16  \n 17  \tprivate Properties loadProperties() {\n 18  \t\tProperties properties = new Properties();\n 19  \n 20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n 21  \n 22  \t\t\tproperties.load(inputStream);\n 23  \n 24  \t\t} catch (Exception e) {\n 25  \t\t\tSystem.out.println(\"Exception: \" + e);\n 26  \t\t}\n 27  \n 28  \t\treturn properties;\n 29  \t}\n 30  \n 31  \tpublic String getProperty (String name) {\n 32  \t\treturn config.getProperty(name);\n 33  \t}\n 34  \n 35  \n 36  \n 37  }\n"
         lineNumber: 21
         variables:
           file: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
@@ -1481,7 +1481,7 @@
       incidents:
       - uri: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
         message: 'An application running inside a container could lose access to a file in local storage.. Recommendations. The following recommendations depend on the function of the file in local storage:. * Logging: Log to standard output and use a centralized log collector to analyze the logs.. * Caching: Use a cache backing service.. * Configuration: Store configuration settings in environment variables so that they can be updated without code changes.. * Data storage: Use a database backing service for relational data or use a persistent data storage system.. * Temporary data storage: Use the file system of a running container as a brief, single-transaction cache.'
-        codeSnip: "10  \n11  \tpublic ApplicationConfiguration() {\n12  \t\tsuper();\n13  \t\tthis.config = loadProperties();\n14  \n15  \t}\n16  \n17  \tprivate Properties loadProperties() {\n18  \t\tProperties properties = new Properties();\n19  \n20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n21  \n22  \t\t\tproperties.load(inputStream);\n23  \n24  \t\t} catch (Exception e) {\n25  \t\t\tSystem.out.println(\"Exception: \" + e);\n26  \t\t}\n27  \n28  \t\treturn properties;\n29  \t}\n30  "
+        codeSnip: "  1  package io.konveyor.demo.config;\n  2  \n  3  import java.io.FileInputStream;\n  4  import java.io.InputStream;\n  5  import java.util.Properties;\n  6  \n  7  public class ApplicationConfiguration {\n  8  \n  9  \tprivate Properties config;\n 10  \n 11  \tpublic ApplicationConfiguration() {\n 12  \t\tsuper();\n 13  \t\tthis.config = loadProperties();\n 14  \n 15  \t}\n 16  \n 17  \tprivate Properties loadProperties() {\n 18  \t\tProperties properties = new Properties();\n 19  \n 20  \t\ttry (InputStream inputStream = new FileInputStream(\"/opt/config/persistence.properties\")) {\n 21  \n 22  \t\t\tproperties.load(inputStream);\n 23  \n 24  \t\t} catch (Exception e) {\n 25  \t\t\tSystem.out.println(\"Exception: \" + e);\n 26  \t\t}\n 27  \n 28  \t\treturn properties;\n 29  \t}\n 30  \n 31  \tpublic String getProperty (String name) {\n 32  \t\treturn config.getProperty(name);\n 33  \t}\n 34  \n 35  \n 36  \n 37  }\n"
         lineNumber: 19
         variables:
           file: konveyor-jdt://contents/root/.m2/repository/io/konveyor/demo/config-utils/1.0.0/config-utils-1.0.0.jar?packageName=io.konveyor.demo.config.ApplicationConfiguration.class&source-range=true
@@ -1521,8 +1521,8 @@
   - logging-0000
   - logging-0001
   - jca-00000
-  - local-storage-00004
   - local-storage-00003
+  - local-storage-00004
   - session-00000
   - java-rmi-00000
   - logging-0001
@@ -1531,8 +1531,8 @@
   - socket-communication-00001
   - mail-00000
   - session-00001
-  - local-storage-00005
   - local-storage-00002
+  - local-storage-00005
   - socket-communication-00000
 - name: os/windows
   description: This is a ruleset for Windows operating system specific rules while migrating to Linux operating system.