diff --git a/cli/cmd/lint_test.go b/cli/cmd/lint_test.go
index 13eaf2017..964e2ce93 100644
--- a/cli/cmd/lint_test.go
+++ b/cli/cmd/lint_test.go
@@ -16,90 +16,76 @@ import (
 	"github.com/spf13/cobra"
 )
 
-func TestLint_VerboseFlag(t *testing.T) {
-	// Create a temporary directory with a test chart
-	tmpDir := t.TempDir()
-	chartDir := filepath.Join(tmpDir, "test-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
+// getTestDataPath returns the absolute path to a test data file or directory.
+// This helper is used to locate fixture files in the testdata/ directory.
+func getTestDataPath(t *testing.T, relPath string) string {
+	t.Helper()
+	cwd, err := os.Getwd()
+	if err != nil {
+		t.Fatalf("failed to get working directory: %v", err)
 	}
 
-	// Create Chart.yaml
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: test-chart
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	// Navigate from cli/cmd/ to project root
+	projectRoot := filepath.Join(cwd, "..", "..")
+	absPath := filepath.Join(projectRoot, relPath)
 
-	// Create templates directory with a deployment
-	templatesDir := filepath.Join(chartDir, "templates")
-	if err := os.MkdirAll(templatesDir, 0755); err != nil {
-		t.Fatal(err)
+	// Verify the path exists
+	if _, err := os.Stat(absPath); err != nil {
+		t.Fatalf("test data path does not exist: %s (error: %v)", absPath, err)
 	}
 
-	deploymentYaml := filepath.Join(templatesDir, "deployment.yaml")
-	deploymentContent := `apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: test
-spec:
-  template:
-    spec:
-      containers:
-      - name: nginx
-        image: nginx:1.21
-`
-	if err := os.WriteFile(deploymentYaml, []byte(deploymentContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	return absPath
+}
 
-	// Create manifests directory with HelmChart
-	manifestsDir := filepath.Join(tmpDir, "manifests")
-	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
-		t.Fatal(err)
-	}
+// copyFixtureToTemp copies a fixture directory to a temporary directory for test isolation.
+// This ensures tests can modify files without affecting the original fixtures.
+func copyFixtureToTemp(t *testing.T, fixturePath string) string {
+	t.Helper()
+	tmpDir := t.TempDir()
+	destPath := filepath.Join(tmpDir, filepath.Base(fixturePath))
 
-	helmChartManifest := filepath.Join(manifestsDir, "helmchart.yaml")
-	helmChartContent := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: test-chart
-spec:
-  chart:
-    name: test-chart
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(helmChartManifest, []byte(helmChartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	// Copy the fixture directory recursively
+	if err := filepath.Walk(fixturePath, func(path string, info os.FileInfo, err error) error {
+		if err != nil {
+			return err
+		}
 
-	// Create .replicated config
-	configPath := filepath.Join(tmpDir, ".replicated")
-	configContent := `charts:
-  - path: ` + chartDir + `
-manifests:
-  - ` + manifestsDir + `/*.yaml
-repl-lint:
-  linters:
-    helm: {}
-    preflight:
-      disabled: true
-`
-	if err := os.WriteFile(configPath, []byte(configContent), 0644); err != nil {
-		t.Fatal(err)
+		// Calculate relative path from fixture root
+		relPath, err := filepath.Rel(fixturePath, path)
+		if err != nil {
+			return err
+		}
+
+		destFilePath := filepath.Join(destPath, relPath)
+
+		if info.IsDir() {
+			return os.MkdirAll(destFilePath, info.Mode())
+		}
+
+		// Copy file
+		data, err := os.ReadFile(path)
+		if err != nil {
+			return err
+		}
+		return os.WriteFile(destFilePath, data, info.Mode())
+	}); err != nil {
+		t.Fatalf("failed to copy fixture from %s to %s: %v", fixturePath, destPath, err)
 	}
 
-	// Change to temp directory for test
+	return destPath
+}
+
+func TestLint_VerboseFlag(t *testing.T) {
+	fixturePath := getTestDataPath(t, "testdata/lint/simple-chart")
+	testDir := copyFixtureToTemp(t, fixturePath)
+
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -190,7 +176,7 @@ repl-lint:
 func TestExtractAndDisplayImagesFromConfig_NoCharts(t *testing.T) {
 	tmpDir := t.TempDir()
 
-	// Create .replicated config with no charts
+	// Create .replicated config with no charts section
 	configPath := filepath.Join(tmpDir, ".replicated")
 	configContent := `repl-lint:
   linters:
@@ -200,7 +186,7 @@ func TestExtractAndDisplayImagesFromConfig_NoCharts(t *testing.T) {
 		t.Fatal(err)
 	}
 
-	// Change to temp directory
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
@@ -273,119 +259,16 @@ repl-lint:
 }
 
 func TestExtractAndDisplayImagesFromConfig_MultipleCharts(t *testing.T) {
-	// Create a temporary directory with multiple test charts
-	tmpDir := t.TempDir()
-
-	// Create first chart
-	chart1Dir := filepath.Join(tmpDir, "chart1")
-	if err := os.MkdirAll(filepath.Join(chart1Dir, "templates"), 0755); err != nil {
-		t.Fatal(err)
-	}
-	chart1Yaml := filepath.Join(chart1Dir, "Chart.yaml")
-	if err := os.WriteFile(chart1Yaml, []byte("apiVersion: v2\nname: chart1\nversion: 1.0.0\n"), 0644); err != nil {
-		t.Fatal(err)
-	}
-	dep1Yaml := filepath.Join(chart1Dir, "templates", "deployment.yaml")
-	dep1Content := `apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: test1
-spec:
-  template:
-    spec:
-      containers:
-      - name: nginx
-        image: nginx:1.21
-`
-	if err := os.WriteFile(dep1Yaml, []byte(dep1Content), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create second chart with different image
-	chart2Dir := filepath.Join(tmpDir, "chart2")
-	if err := os.MkdirAll(filepath.Join(chart2Dir, "templates"), 0755); err != nil {
-		t.Fatal(err)
-	}
-	chart2Yaml := filepath.Join(chart2Dir, "Chart.yaml")
-	if err := os.WriteFile(chart2Yaml, []byte("apiVersion: v2\nname: chart2\nversion: 1.0.0\n"), 0644); err != nil {
-		t.Fatal(err)
-	}
-	dep2Yaml := filepath.Join(chart2Dir, "templates", "deployment.yaml")
-	dep2Content := `apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: test2
-spec:
-  template:
-    spec:
-      containers:
-      - name: redis
-        image: redis:7.0
-`
-	if err := os.WriteFile(dep2Yaml, []byte(dep2Content), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create manifests directory with HelmChart manifests for both charts
-	manifestsDir := filepath.Join(tmpDir, "manifests")
-	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	helmChart1 := filepath.Join(manifestsDir, "chart1-helmchart.yaml")
-	helmChart1Content := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: chart1
-spec:
-  chart:
-    name: chart1
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(helmChart1, []byte(helmChart1Content), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	helmChart2 := filepath.Join(manifestsDir, "chart2-helmchart.yaml")
-	helmChart2Content := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: chart2
-spec:
-  chart:
-    name: chart2
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(helmChart2, []byte(helmChart2Content), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create .replicated config with both charts
-	configPath := filepath.Join(tmpDir, ".replicated")
-	configContent := `charts:
-  - path: ` + chart1Dir + `
-  - path: ` + chart2Dir + `
-manifests:
-  - ` + manifestsDir + `/*.yaml
-repl-lint:
-  linters:
-    helm: {}
-    preflight:
-      disabled: true
-`
-	if err := os.WriteFile(configPath, []byte(configContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	fixturePath := getTestDataPath(t, "testdata/lint/multi-chart-project")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Change to temp directory
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -451,27 +334,13 @@ repl-lint:
 
 // TestJSONOutputContainsAllToolVersions tests that JSON output includes all tool versions
 func TestJSONOutputContainsAllToolVersions(t *testing.T) {
-	// Create a temporary directory with a test chart
-	tmpDir := t.TempDir()
-	chartDir := filepath.Join(tmpDir, "test-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create minimal Chart.yaml
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: test-chart
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	fixturePath := getTestDataPath(t, "testdata/lint/simple-chart")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Create .replicated config with specific tool versions
-	configPath := filepath.Join(tmpDir, ".replicated")
+	// Update .replicated config to add tool versions and all linters
+	configPath := filepath.Join(testDir, ".replicated")
 	configContent := `charts:
-  - path: ` + chartDir + `
+  - path: chart
 repl-lint:
   version: 1
   linters:
@@ -487,13 +356,13 @@ repl-lint:
 		t.Fatal(err)
 	}
 
-	// Change to temp directory for test
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -673,27 +542,13 @@ repl-lint:
 
 // TestConfigMissingToolVersions tests that missing tool versions default to "latest"
 func TestConfigMissingToolVersions(t *testing.T) {
-	// Create a temporary directory with a test chart
-	tmpDir := t.TempDir()
-	chartDir := filepath.Join(tmpDir, "test-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create minimal Chart.yaml
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: test-chart
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	fixturePath := getTestDataPath(t, "testdata/lint/simple-chart")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Create .replicated config WITHOUT tool versions
-	configPath := filepath.Join(tmpDir, ".replicated")
+	// Update .replicated config WITHOUT tool versions
+	configPath := filepath.Join(testDir, ".replicated")
 	configContent := `charts:
-  - path: ` + chartDir + `
+  - path: chart
 repl-lint:
   version: 1
   linters:
@@ -703,13 +558,13 @@ repl-lint:
 		t.Fatal(err)
 	}
 
-	// Change to temp directory for test
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -788,53 +643,16 @@ func isValidSemVer(version string) bool {
 
 // TestLint_ChartValidationError tests that lint fails when a chart is missing its HelmChart manifest
 func TestLint_ChartValidationError(t *testing.T) {
-	tmpDir := t.TempDir()
-
-	// Create a chart
-	chartDir := filepath.Join(tmpDir, "test-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: test-app
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create empty manifests directory (no HelmChart manifest)
-	manifestsDir := filepath.Join(tmpDir, "manifests")
-	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create config with chart but no matching HelmChart manifest
-	configPath := filepath.Join(tmpDir, ".replicated")
-	configContent := `charts:
-  - path: ` + chartDir + `
-manifests:
-  - ` + manifestsDir + `/*.yaml
-repl-lint:
-  linters:
-    helm:
-      disabled: true
-    preflight:
-      disabled: true
-`
-	if err := os.WriteFile(configPath, []byte(configContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	fixturePath := getTestDataPath(t, "testdata/lint/chart-missing-helmchart")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Change to temp directory
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -878,103 +696,34 @@ repl-lint:
 
 // TestLint_ChartValidationWarning tests that lint succeeds but shows warning for orphaned HelmChart manifest
 func TestLint_ChartValidationWarning(t *testing.T) {
-	tmpDir := t.TempDir()
+	fixturePath := getTestDataPath(t, "testdata/lint/orphaned-helmchart")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Create a chart
-	chartDir := filepath.Join(tmpDir, "test-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
+	// Change to test directory
+	oldWd, err := os.Getwd()
+	if err != nil {
 		t.Fatal(err)
 	}
-
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: current-app
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
+	defer os.Chdir(oldWd)
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
-	// Create manifests directory with matching HelmChart + orphaned one
-	manifestsDir := filepath.Join(tmpDir, "manifests")
-	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
-		t.Fatal(err)
-	}
+	// Create output buffer
+	buf := new(bytes.Buffer)
+	w := tabwriter.NewWriter(buf, 0, 8, 4, ' ', 0)
 
-	// Matching HelmChart manifest
-	currentHelmChart := filepath.Join(manifestsDir, "current-app.yaml")
-	currentContent := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: current-app
-spec:
-  chart:
-    name: current-app
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(currentHelmChart, []byte(currentContent), 0644); err != nil {
-		t.Fatal(err)
+	r := &runners{
+		w:            w,
+		outputFormat: "table",
+		args: runnerArgs{
+			lintVerbose: false,
+		},
 	}
 
-	// Orphaned HelmChart manifest
-	oldHelmChart := filepath.Join(manifestsDir, "old-app.yaml")
-	oldContent := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: old-app
-spec:
-  chart:
-    name: old-app
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(oldHelmChart, []byte(oldContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create config
-	configPath := filepath.Join(tmpDir, ".replicated")
-	configContent := `charts:
-  - path: ` + chartDir + `
-manifests:
-  - ` + manifestsDir + `/*.yaml
-repl-lint:
-  linters:
-    helm:
-      disabled: true
-    preflight:
-      disabled: true
-`
-	if err := os.WriteFile(configPath, []byte(configContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Change to temp directory
-	oldWd, err := os.Getwd()
-	if err != nil {
-		t.Fatal(err)
-	}
-	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create output buffer
-	buf := new(bytes.Buffer)
-	w := tabwriter.NewWriter(buf, 0, 8, 4, ' ', 0)
-
-	r := &runners{
-		w:            w,
-		outputFormat: "table",
-		args: runnerArgs{
-			lintVerbose: false,
-		},
-	}
-
-	// Create a mock command with context
-	cmd := &cobra.Command{}
-	cmd.SetContext(context.Background())
+	// Create a mock command with context
+	cmd := &cobra.Command{}
+	cmd.SetContext(context.Background())
 
 	// Run the lint command - should succeed
 	err = r.runLint(cmd, []string{})
@@ -998,27 +747,13 @@ repl-lint:
 
 // TestLint_NoManifestsConfig tests error when charts configured but manifests section missing
 func TestLint_NoManifestsConfig(t *testing.T) {
-	tmpDir := t.TempDir()
-
-	// Create a chart
-	chartDir := filepath.Join(tmpDir, "test-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: test-app
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
+	fixturePath := getTestDataPath(t, "testdata/lint/chart-missing-helmchart")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Create config WITHOUT manifests section
-	configPath := filepath.Join(tmpDir, ".replicated")
+	// Update config to remove manifests section
+	configPath := filepath.Join(testDir, ".replicated")
 	configContent := `charts:
-  - path: ` + chartDir + `
+  - path: chart
 repl-lint:
   linters:
     helm:
@@ -1028,13 +763,13 @@ repl-lint:
 		t.Fatal(err)
 	}
 
-	// Change to temp directory
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -1079,96 +814,17 @@ repl-lint:
 // TestLint_AutodiscoveryWithMixedManifests tests that autodiscovery works
 // when manifests directory contains BOTH HelmChart manifests and Support Bundle specs,
 // and also includes Preflight specs.
-// This is the bug we're fixing - autodiscovery currently stores explicit paths which
-// causes strict validation to fail when processing mixed resource types.
 func TestLint_AutodiscoveryWithMixedManifests(t *testing.T) {
-	tmpDir := t.TempDir()
-
-	// Create a chart
-	chartDir := filepath.Join(tmpDir, "charts", "my-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: my-app
-version: 1.0.0
-description: Test chart for autodiscovery
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	valuesYaml := filepath.Join(chartDir, "values.yaml")
-	if err := os.WriteFile(valuesYaml, []byte("replicaCount: 1\n"), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create manifests directory with HelmChart, Support Bundle, and Preflight
-	manifestsDir := filepath.Join(tmpDir, "manifests")
-	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	// HelmChart manifest
-	helmChartFile := filepath.Join(manifestsDir, "helmchart.yaml")
-	helmChartContent := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: my-app-chart
-spec:
-  chart:
-    name: my-app
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(helmChartFile, []byte(helmChartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Support Bundle spec
-	sbFile := filepath.Join(manifestsDir, "support-bundle.yaml")
-	sbContent := `apiVersion: troubleshoot.sh/v1beta2
-kind: SupportBundle
-metadata:
-  name: my-support-bundle
-spec:
-  collectors:
-    - logs:
-        selector:
-          - app=my-app
-`
-	if err := os.WriteFile(sbFile, []byte(sbContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Preflight spec
-	preflightFile := filepath.Join(manifestsDir, "preflight.yaml")
-	preflightContent := `apiVersion: troubleshoot.sh/v1beta2
-kind: Preflight
-metadata:
-  name: my-preflight
-spec:
-  analyzers:
-    - clusterVersion:
-        outcomes:
-          - pass:
-              message: Kubernetes version is valid
-`
-	if err := os.WriteFile(preflightFile, []byte(preflightContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// NO .replicated config - trigger autodiscovery
+	fixturePath := getTestDataPath(t, "testdata/lint/mixed-manifests-autodiscovery")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Change to temp directory
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -1469,30 +1125,11 @@ spec:
 
 // TestLint_AutodiscoveryHiddenDirectories tests that hidden directories (.git, .github) are ignored
 func TestLint_AutodiscoveryHiddenDirectories(t *testing.T) {
-	tmpDir := t.TempDir()
-
-	// Create a real chart
-	chartDir := filepath.Join(tmpDir, "charts", "my-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: real-app
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	valuesYaml := filepath.Join(chartDir, "values.yaml")
-	if err := os.WriteFile(valuesYaml, []byte("replicaCount: 1\n"), 0644); err != nil {
-		t.Fatal(err)
-	}
+	fixturePath := getTestDataPath(t, "testdata/lint/hidden-dirs-test")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Create fake charts in hidden directories (should be ignored)
-	gitDir := filepath.Join(tmpDir, ".git", "charts")
+	// Create .git directory with fake chart (can't commit .git dirs to git, so create at runtime)
+	gitDir := filepath.Join(testDir, ".git", "charts")
 	if err := os.MkdirAll(gitDir, 0755); err != nil {
 		t.Fatal(err)
 	}
@@ -1501,52 +1138,13 @@ version: 1.0.0
 		t.Fatal(err)
 	}
 
-	githubDir := filepath.Join(tmpDir, ".github", "manifests")
-	if err := os.MkdirAll(githubDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-	githubSB := filepath.Join(githubDir, "support-bundle.yaml")
-	sbContent := `apiVersion: troubleshoot.sh/v1beta2
-kind: SupportBundle
-metadata:
-  name: fake-sb
-spec:
-  collectors: []
-`
-	if err := os.WriteFile(githubSB, []byte(sbContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Create real manifests
-	manifestsDir := filepath.Join(tmpDir, "manifests")
-	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	helmChartFile := filepath.Join(manifestsDir, "helmchart.yaml")
-	helmChartContent := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: real-app-chart
-spec:
-  chart:
-    name: real-app
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(helmChartFile, []byte(helmChartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// NO .replicated config - trigger autodiscovery
-
-	// Change to temp directory
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -1574,13 +1172,15 @@ spec:
 
 	// Verify only 1 chart discovered (hidden dirs ignored)
 	output := buf.String()
+	t.Logf("Output:\n%s", output)
 	if !strings.Contains(output, "1 Helm chart(s)") {
 		t.Error("expected to discover exactly 1 chart (hidden dirs should be ignored)")
 	}
 	if !strings.Contains(output, "1 HelmChart manifest(s)") {
 		t.Error("expected to discover exactly 1 HelmChart manifest")
 	}
-	if strings.Contains(output, "2 ") {
+	// Check for multiple charts/manifests being discovered (would indicate hidden dirs not ignored)
+	if strings.Contains(output, "2 Helm chart(s)") || strings.Contains(output, "2 HelmChart manifest(s)") {
 		t.Error("should not discover resources from hidden directories")
 	}
 
@@ -1589,93 +1189,16 @@ spec:
 
 // TestLint_AutodiscoveryBothYamlExtensions tests that both .yaml and .yml files are discovered
 func TestLint_AutodiscoveryBothYamlExtensions(t *testing.T) {
-	tmpDir := t.TempDir()
-
-	// Create a chart
-	chartDir := filepath.Join(tmpDir, "charts", "my-chart")
-	if err := os.MkdirAll(chartDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	// Helm requires Chart.yaml specifically (not .yml)
-	chartYaml := filepath.Join(chartDir, "Chart.yaml")
-	chartContent := `apiVersion: v2
-name: my-app
-version: 1.0.0
-`
-	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	valuesYaml := filepath.Join(chartDir, "values.yaml")
-	if err := os.WriteFile(valuesYaml, []byte("replicaCount: 1\n"), 0644); err != nil {
-		t.Fatal(err)
-	}
+	fixturePath := getTestDataPath(t, "testdata/lint/mixed-manifests-yaml-yml")
+	testDir := copyFixtureToTemp(t, fixturePath)
 
-	// Create manifests with mixed extensions
-	manifestsDir := filepath.Join(tmpDir, "manifests")
-	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
-		t.Fatal(err)
-	}
-
-	// HelmChart with .yaml
-	helmChartFile := filepath.Join(manifestsDir, "helmchart.yaml")
-	helmChartContent := `apiVersion: kots.io/v1beta2
-kind: HelmChart
-metadata:
-  name: my-app-chart
-spec:
-  chart:
-    name: my-app
-    chartVersion: 1.0.0
-  builder: {}
-`
-	if err := os.WriteFile(helmChartFile, []byte(helmChartContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Support Bundle with .yml
-	sbFile := filepath.Join(manifestsDir, "support-bundle.yml")
-	sbContent := `apiVersion: troubleshoot.sh/v1beta2
-kind: SupportBundle
-metadata:
-  name: my-support-bundle
-spec:
-  collectors:
-    - logs:
-        selector:
-          - app=my-app
-`
-	if err := os.WriteFile(sbFile, []byte(sbContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// Preflight with .yaml
-	preflightFile := filepath.Join(manifestsDir, "preflight.yaml")
-	preflightContent := `apiVersion: troubleshoot.sh/v1beta2
-kind: Preflight
-metadata:
-  name: my-preflight
-spec:
-  analyzers:
-    - clusterVersion:
-        outcomes:
-          - pass:
-              message: Valid
-`
-	if err := os.WriteFile(preflightFile, []byte(preflightContent), 0644); err != nil {
-		t.Fatal(err)
-	}
-
-	// NO .replicated config - trigger autodiscovery
-
-	// Change to temp directory
+	// Change to test directory
 	oldWd, err := os.Getwd()
 	if err != nil {
 		t.Fatal(err)
 	}
 	defer os.Chdir(oldWd)
-	if err := os.Chdir(tmpDir); err != nil {
+	if err := os.Chdir(testDir); err != nil {
 		t.Fatal(err)
 	}
 
@@ -1718,3 +1241,638 @@ spec:
 
 	t.Log("SUCCESS: Autodiscovery correctly handled both .yaml and .yml extensions for manifests")
 }
+
+// Tests for config discovery vs autodiscovery behavior
+
+// TestLint_SubdirectoryWithParentConfig tests that running lint from a subdirectory
+// uses the parent's .replicated config and does NOT trigger autodiscovery.
+func TestLint_SubdirectoryWithParentConfig(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Create chart1 in parent directory
+	chart1Dir := filepath.Join(tmpDir, "chart1")
+	if err := os.MkdirAll(chart1Dir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	chart1Yaml := filepath.Join(chart1Dir, "Chart.yaml")
+	chart1Content := `apiVersion: v2
+name: app1
+version: 1.0.0
+description: Chart in parent config
+`
+	if err := os.WriteFile(chart1Yaml, []byte(chart1Content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	valuesYaml := filepath.Join(chart1Dir, "values.yaml")
+	if err := os.WriteFile(valuesYaml, []byte("replicaCount: 1\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create HelmChart manifest for chart1
+	manifestsDir := filepath.Join(tmpDir, "manifests")
+	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	helmChartFile := filepath.Join(manifestsDir, "helmchart1.yaml")
+	helmChartContent := `apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: app1-chart
+spec:
+  chart:
+    name: app1
+    chartVersion: 1.0.0
+  builder: {}
+`
+	if err := os.WriteFile(helmChartFile, []byte(helmChartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create .replicated config in parent with chart1
+	configPath := filepath.Join(tmpDir, ".replicated")
+	configContent := `charts:
+  - path: ` + chart1Dir + `
+manifests:
+  - ` + manifestsDir + `/**
+repl-lint:
+  linters:
+    helm: {}
+`
+	if err := os.WriteFile(configPath, []byte(configContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create subdirectory with chart2 (NOT in parent config)
+	subDir := filepath.Join(tmpDir, "subdir")
+	if err := os.MkdirAll(subDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	chart2Dir := filepath.Join(subDir, "chart2")
+	if err := os.MkdirAll(chart2Dir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	chart2Yaml := filepath.Join(chart2Dir, "Chart.yaml")
+	chart2Content := `apiVersion: v2
+name: app2
+version: 1.0.0
+description: Chart NOT in parent config
+`
+	if err := os.WriteFile(chart2Yaml, []byte(chart2Content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	chart2Values := filepath.Join(chart2Dir, "values.yaml")
+	if err := os.WriteFile(chart2Values, []byte("replicaCount: 1\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Change to subdirectory
+	oldWd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer os.Chdir(oldWd)
+	if err := os.Chdir(subDir); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create output buffer
+	buf := new(bytes.Buffer)
+	w := tabwriter.NewWriter(buf, 0, 8, 4, ' ', 0)
+
+	r := &runners{
+		w:            w,
+		outputFormat: "table",
+		args: runnerArgs{
+			lintVerbose: false,
+		},
+	}
+
+	// Create a mock command with context
+	cmd := &cobra.Command{}
+	cmd.SetContext(context.Background())
+
+	// Run the lint command
+	err = r.runLint(cmd, []string{})
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	// Verify that autodiscovery did NOT trigger
+	output := buf.String()
+	if strings.Contains(output, "Auto-discovering lintable resources") {
+		t.Error("autodiscovery should NOT trigger when parent config exists with resources")
+	}
+
+	// Verify chart1 from parent config was linted
+	if !strings.Contains(output, chart1Dir) {
+		t.Errorf("expected chart1 from parent config to be linted, got output:\n%s", output)
+	}
+
+	// Verify chart2 was NOT linted (not in parent config)
+	if strings.Contains(output, "app2") {
+		t.Error("chart2 should NOT be linted (not in parent config)")
+	}
+
+	t.Log("SUCCESS: Subdirectory correctly used parent config instead of autodiscovery")
+}
+
+// TestLint_SubdirectoryWithEmptyParentConfig tests that running lint from a subdirectory
+// with an empty parent config DOES trigger autodiscovery.
+func TestLint_SubdirectoryWithEmptyParentConfig(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Create empty .replicated config in parent (no charts/preflights/manifests)
+	configPath := filepath.Join(tmpDir, ".replicated")
+	configContent := `repl-lint:
+  linters:
+    helm: {}
+    preflight: {}
+`
+	if err := os.WriteFile(configPath, []byte(configContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create subdirectory with resources
+	subDir := filepath.Join(tmpDir, "subdir")
+	if err := os.MkdirAll(subDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create chart in subdirectory
+	chartDir := filepath.Join(subDir, "my-chart")
+	if err := os.MkdirAll(chartDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	chartYaml := filepath.Join(chartDir, "Chart.yaml")
+	chartContent := `apiVersion: v2
+name: discovered-app
+version: 1.0.0
+description: Chart discovered by autodiscovery
+`
+	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	valuesYaml := filepath.Join(chartDir, "values.yaml")
+	if err := os.WriteFile(valuesYaml, []byte("replicaCount: 1\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create HelmChart manifest for the discovered chart
+	helmChartFile := filepath.Join(subDir, "helmchart.yaml")
+	helmChartContent := `apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: discovered-app-chart
+spec:
+  chart:
+    name: discovered-app
+    chartVersion: 1.0.0
+  builder: {}
+`
+	if err := os.WriteFile(helmChartFile, []byte(helmChartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create preflight in subdirectory
+	preflightFile := filepath.Join(subDir, "preflight.yaml")
+	preflightContent := `apiVersion: troubleshoot.sh/v1beta2
+kind: Preflight
+metadata:
+  name: discovered-preflight
+spec:
+  analyzers:
+    - clusterVersion:
+        outcomes:
+          - pass:
+              message: Valid
+`
+	if err := os.WriteFile(preflightFile, []byte(preflightContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Change to subdirectory
+	oldWd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer os.Chdir(oldWd)
+	if err := os.Chdir(subDir); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create output buffer
+	buf := new(bytes.Buffer)
+	w := tabwriter.NewWriter(buf, 0, 8, 4, ' ', 0)
+
+	r := &runners{
+		w:            w,
+		outputFormat: "table",
+		args: runnerArgs{
+			lintVerbose: false,
+		},
+	}
+
+	// Create a mock command with context
+	cmd := &cobra.Command{}
+	cmd.SetContext(context.Background())
+
+	// Run the lint command
+	err = r.runLint(cmd, []string{})
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	// Verify autodiscovery DID trigger
+	output := buf.String()
+	if !strings.Contains(output, "Auto-discovering lintable resources") {
+		t.Error("autodiscovery SHOULD trigger when parent config is empty")
+	}
+
+	// Verify resources were discovered
+	if !strings.Contains(output, "1 Helm chart(s)") {
+		t.Error("expected to discover 1 chart")
+	}
+	if !strings.Contains(output, "1 Preflight spec(s)") {
+		t.Error("expected to discover 1 preflight")
+	}
+
+	t.Log("SUCCESS: Empty parent config correctly triggered autodiscovery")
+}
+
+// TestLint_MonorepoMultipleConfigs tests that multiple .replicated configs
+// are merged correctly and autodiscovery does NOT trigger.
+func TestLint_MonorepoMultipleConfigs(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Create app1 chart at grandparent level
+	app1Dir := filepath.Join(tmpDir, "app1")
+	if err := os.MkdirAll(app1Dir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	app1Chart := filepath.Join(app1Dir, "Chart.yaml")
+	app1Content := `apiVersion: v2
+name: app1
+version: 1.0.0
+description: Grandparent app
+`
+	if err := os.WriteFile(app1Chart, []byte(app1Content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	if err := os.WriteFile(filepath.Join(app1Dir, "values.yaml"), []byte("replicaCount: 1\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create HelmChart manifest for app1
+	app1HelmChart := filepath.Join(tmpDir, "app1-helmchart.yaml")
+	app1HelmChartContent := `apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: app1-chart
+spec:
+  chart:
+    name: app1
+    chartVersion: 1.0.0
+  builder: {}
+`
+	if err := os.WriteFile(app1HelmChart, []byte(app1HelmChartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create grandparent .replicated with app1
+	grandparentConfig := filepath.Join(tmpDir, ".replicated")
+	grandparentContent := `charts:
+  - path: ` + app1Dir + `
+manifests:
+  - ` + tmpDir + `/*.yaml
+repl-lint:
+  linters:
+    helm: {}
+`
+	if err := os.WriteFile(grandparentConfig, []byte(grandparentContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create parent directory
+	parentDir := filepath.Join(tmpDir, "parent")
+	if err := os.MkdirAll(parentDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create app2 chart at parent level
+	app2Dir := filepath.Join(parentDir, "app2")
+	if err := os.MkdirAll(app2Dir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	app2Chart := filepath.Join(app2Dir, "Chart.yaml")
+	app2Content := `apiVersion: v2
+name: app2
+version: 1.0.0
+description: Parent app
+`
+	if err := os.WriteFile(app2Chart, []byte(app2Content), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	if err := os.WriteFile(filepath.Join(app2Dir, "values.yaml"), []byte("replicaCount: 1\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create HelmChart manifest for app2
+	app2HelmChart := filepath.Join(parentDir, "app2-helmchart.yaml")
+	app2HelmChartContent := `apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: app2-chart
+spec:
+  chart:
+    name: app2
+    chartVersion: 1.0.0
+  builder: {}
+`
+	if err := os.WriteFile(app2HelmChart, []byte(app2HelmChartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create parent .replicated with app2
+	parentConfig := filepath.Join(parentDir, ".replicated")
+	parentContent := `charts:
+  - path: ` + app2Dir + `
+manifests:
+  - ` + parentDir + `/*.yaml
+`
+	if err := os.WriteFile(parentConfig, []byte(parentContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create child directory
+	childDir := filepath.Join(parentDir, "child")
+	if err := os.MkdirAll(childDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	// Change to child directory
+	oldWd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer os.Chdir(oldWd)
+	if err := os.Chdir(childDir); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create output buffer
+	buf := new(bytes.Buffer)
+	w := tabwriter.NewWriter(buf, 0, 8, 4, ' ', 0)
+
+	r := &runners{
+		w:            w,
+		outputFormat: "table",
+		args: runnerArgs{
+			lintVerbose: false,
+		},
+	}
+
+	// Create a mock command with context
+	cmd := &cobra.Command{}
+	cmd.SetContext(context.Background())
+
+	// Run the lint command
+	err = r.runLint(cmd, []string{})
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	// Verify autodiscovery did NOT trigger
+	output := buf.String()
+	if strings.Contains(output, "Auto-discovering lintable resources") {
+		t.Error("autodiscovery should NOT trigger when merged configs have resources")
+	}
+
+	// Verify BOTH apps were linted (merged from grandparent and parent configs)
+	if !strings.Contains(output, "app1") {
+		t.Error("expected app1 from grandparent config to be linted")
+	}
+	if !strings.Contains(output, "app2") {
+		t.Error("expected app2 from parent config to be linted")
+	}
+
+	t.Log("SUCCESS: Multiple configs correctly merged and both apps linted")
+}
+
+// TestLint_AutodiscoveryOnlyWhenAllArraysEmpty tests that autodiscovery
+// only triggers when ALL resource arrays are empty.
+func TestLint_AutodiscoveryOnlyWhenAllArraysEmpty(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Create support bundle manifest
+	manifestsDir := filepath.Join(tmpDir, "manifests")
+	if err := os.MkdirAll(manifestsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	sbFile := filepath.Join(manifestsDir, "support-bundle.yaml")
+	sbContent := `apiVersion: troubleshoot.sh/v1beta2
+kind: SupportBundle
+metadata:
+  name: configured-sb
+spec:
+  collectors:
+    - logs:
+        selector:
+          - app=test
+`
+	if err := os.WriteFile(sbFile, []byte(sbContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create .replicated config with ONLY manifests (no charts/preflights)
+	configPath := filepath.Join(tmpDir, ".replicated")
+	configContent := `manifests:
+  - ` + manifestsDir + `/**
+repl-lint:
+  linters:
+    support-bundle: {}
+`
+	if err := os.WriteFile(configPath, []byte(configContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create subdirectory with a chart (NOT in config)
+	subDir := filepath.Join(tmpDir, "subdir")
+	if err := os.MkdirAll(subDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	chartDir := filepath.Join(subDir, "chart1")
+	if err := os.MkdirAll(chartDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	chartYaml := filepath.Join(chartDir, "Chart.yaml")
+	chartContent := `apiVersion: v2
+name: undiscovered-app
+version: 1.0.0
+description: Should NOT be discovered
+`
+	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	if err := os.WriteFile(filepath.Join(chartDir, "values.yaml"), []byte("replicaCount: 1\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Change to subdirectory
+	oldWd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer os.Chdir(oldWd)
+	if err := os.Chdir(subDir); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create output buffer
+	buf := new(bytes.Buffer)
+	w := tabwriter.NewWriter(buf, 0, 8, 4, ' ', 0)
+
+	r := &runners{
+		w:            w,
+		outputFormat: "table",
+		args: runnerArgs{
+			lintVerbose: false,
+		},
+	}
+
+	// Create a mock command with context
+	cmd := &cobra.Command{}
+	cmd.SetContext(context.Background())
+
+	// Run the lint command
+	err = r.runLint(cmd, []string{})
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	// Verify autodiscovery did NOT trigger
+	output := buf.String()
+	if strings.Contains(output, "Auto-discovering lintable resources") {
+		t.Error("autodiscovery should NOT trigger when manifests array is non-empty")
+	}
+
+	// Verify chart was NOT discovered
+	if strings.Contains(output, "undiscovered-app") {
+		t.Error("chart should NOT be discovered when config has manifests")
+	}
+
+	// Verify support bundle from config was used
+	if !strings.Contains(output, sbFile) {
+		t.Errorf("expected support bundle from parent config to be linted, got output:\n%s", output)
+	}
+
+	t.Log("SUCCESS: Autodiscovery correctly did NOT trigger with non-empty manifests array")
+}
+
+// TestLint_NoConfigAnywhere tests autodiscovery when no .replicated config
+// exists anywhere in the directory tree.
+func TestLint_NoConfigAnywhere(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Create deep nested directory structure with NO .replicated anywhere
+	deepDir := filepath.Join(tmpDir, "level1", "level2", "level3")
+	if err := os.MkdirAll(deepDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create chart in deep directory
+	chartDir := filepath.Join(deepDir, "my-chart")
+	if err := os.MkdirAll(chartDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	chartYaml := filepath.Join(chartDir, "Chart.yaml")
+	chartContent := `apiVersion: v2
+name: deep-app
+version: 1.0.0
+description: Chart in deep directory
+`
+	if err := os.WriteFile(chartYaml, []byte(chartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	if err := os.WriteFile(filepath.Join(chartDir, "values.yaml"), []byte("replicaCount: 1\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create HelmChart manifest
+	helmChartFile := filepath.Join(deepDir, "helmchart.yaml")
+	helmChartContent := `apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: deep-app-chart
+spec:
+  chart:
+    name: deep-app
+    chartVersion: 1.0.0
+  builder: {}
+`
+	if err := os.WriteFile(helmChartFile, []byte(helmChartContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Change to deep directory
+	oldWd, err := os.Getwd()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer os.Chdir(oldWd)
+	if err := os.Chdir(deepDir); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create output buffer
+	buf := new(bytes.Buffer)
+	w := tabwriter.NewWriter(buf, 0, 8, 4, ' ', 0)
+
+	r := &runners{
+		w:            w,
+		outputFormat: "table",
+		args: runnerArgs{
+			lintVerbose: false,
+		},
+	}
+
+	// Create a mock command with context
+	cmd := &cobra.Command{}
+	cmd.SetContext(context.Background())
+
+	// Run the lint command
+	err = r.runLint(cmd, []string{})
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	// Verify autodiscovery triggered
+	output := buf.String()
+	if !strings.Contains(output, "Auto-discovering lintable resources") {
+		t.Error("autodiscovery SHOULD trigger when no config exists anywhere")
+	}
+
+	// Verify chart was discovered
+	if !strings.Contains(output, "1 Helm chart(s)") {
+		t.Error("expected to discover 1 chart")
+	}
+
+	t.Log("SUCCESS: Autodiscovery correctly triggered with no config in directory tree")
+}
diff --git a/testdata/lint/chart-missing-helmchart/.replicated b/testdata/lint/chart-missing-helmchart/.replicated
new file mode 100644
index 000000000..f163d71d6
--- /dev/null
+++ b/testdata/lint/chart-missing-helmchart/.replicated
@@ -0,0 +1,10 @@
+charts:
+  - path: chart
+manifests:
+  - manifests/*.yaml
+repl-lint:
+  linters:
+    helm:
+      disabled: true
+    preflight:
+      disabled: true
diff --git a/testdata/lint/chart-missing-helmchart/chart/Chart.yaml b/testdata/lint/chart-missing-helmchart/chart/Chart.yaml
new file mode 100644
index 000000000..1f12b1d48
--- /dev/null
+++ b/testdata/lint/chart-missing-helmchart/chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: test-app
+version: 1.0.0
+description: Test chart without matching HelmChart manifest
diff --git a/testdata/lint/chart-missing-helmchart/manifests/.gitkeep b/testdata/lint/chart-missing-helmchart/manifests/.gitkeep
new file mode 100644
index 000000000..e5c70ee5a
--- /dev/null
+++ b/testdata/lint/chart-missing-helmchart/manifests/.gitkeep
@@ -0,0 +1 @@
+# Empty manifests directory - no HelmChart manifest
diff --git a/testdata/lint/configs/all-linters-enabled.yaml b/testdata/lint/configs/all-linters-enabled.yaml
new file mode 100644
index 000000000..4db87984a
--- /dev/null
+++ b/testdata/lint/configs/all-linters-enabled.yaml
@@ -0,0 +1,6 @@
+repl-lint:
+  version: 1
+  linters:
+    helm: {}
+    preflight: {}
+    support-bundle: {}
diff --git a/testdata/lint/configs/basic-helm-lint.yaml b/testdata/lint/configs/basic-helm-lint.yaml
new file mode 100644
index 000000000..014270583
--- /dev/null
+++ b/testdata/lint/configs/basic-helm-lint.yaml
@@ -0,0 +1,5 @@
+repl-lint:
+  linters:
+    helm: {}
+    preflight:
+      disabled: true
diff --git a/testdata/lint/configs/empty-config.yaml b/testdata/lint/configs/empty-config.yaml
new file mode 100644
index 000000000..97e9e0516
--- /dev/null
+++ b/testdata/lint/configs/empty-config.yaml
@@ -0,0 +1,8 @@
+charts: []
+manifests: []
+preflights: []
+repl-lint:
+  linters:
+    helm: {}
+    preflight:
+      disabled: true
diff --git a/testdata/lint/configs/helm-with-latest.yaml b/testdata/lint/configs/helm-with-latest.yaml
new file mode 100644
index 000000000..97a0c2722
--- /dev/null
+++ b/testdata/lint/configs/helm-with-latest.yaml
@@ -0,0 +1,9 @@
+repl-lint:
+  tools:
+    helm: "latest"
+    preflight: "latest"
+    support-bundle: "latest"
+  linters:
+    helm: {}
+    preflight:
+      disabled: true
diff --git a/testdata/lint/configs/helm-with-versions.yaml b/testdata/lint/configs/helm-with-versions.yaml
new file mode 100644
index 000000000..780f66f76
--- /dev/null
+++ b/testdata/lint/configs/helm-with-versions.yaml
@@ -0,0 +1,9 @@
+repl-lint:
+  tools:
+    helm: "3.14.4"
+    preflight: "0.123.9"
+    support-bundle: "0.123.9"
+  linters:
+    helm: {}
+    preflight:
+      disabled: true
diff --git a/testdata/lint/configs/manifests-only.yaml b/testdata/lint/configs/manifests-only.yaml
new file mode 100644
index 000000000..72f43f297
--- /dev/null
+++ b/testdata/lint/configs/manifests-only.yaml
@@ -0,0 +1,6 @@
+manifests:
+  - manifests/*.yaml
+repl-lint:
+  linters:
+    helm: {}
+    preflight: {}
diff --git a/testdata/lint/hidden-dirs-test/.github/manifests/fake-sb.yaml b/testdata/lint/hidden-dirs-test/.github/manifests/fake-sb.yaml
new file mode 100644
index 000000000..6f0c76360
--- /dev/null
+++ b/testdata/lint/hidden-dirs-test/.github/manifests/fake-sb.yaml
@@ -0,0 +1,7 @@
+# This should be ignored
+apiVersion: troubleshoot.sh/v1beta2
+kind: SupportBundle
+metadata:
+  name: fake
+spec:
+  collectors: []
diff --git a/testdata/lint/hidden-dirs-test/charts/my-chart/Chart.yaml b/testdata/lint/hidden-dirs-test/charts/my-chart/Chart.yaml
new file mode 100644
index 000000000..be9dd90ef
--- /dev/null
+++ b/testdata/lint/hidden-dirs-test/charts/my-chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: my-chart
+version: 1.0.0
+description: Test chart for hidden directory autodiscovery
diff --git a/testdata/lint/hidden-dirs-test/manifests/helmchart.yaml b/testdata/lint/hidden-dirs-test/manifests/helmchart.yaml
new file mode 100644
index 000000000..000b9b78e
--- /dev/null
+++ b/testdata/lint/hidden-dirs-test/manifests/helmchart.yaml
@@ -0,0 +1,9 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: my-chart
+spec:
+  chart:
+    name: my-chart
+    chartVersion: 1.0.0
+  weight: 1
diff --git a/testdata/lint/mixed-manifests-autodiscovery/charts/my-chart/Chart.yaml b/testdata/lint/mixed-manifests-autodiscovery/charts/my-chart/Chart.yaml
new file mode 100644
index 000000000..5e6e5b0cf
--- /dev/null
+++ b/testdata/lint/mixed-manifests-autodiscovery/charts/my-chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: my-app
+version: 1.0.0
+description: Test chart for autodiscovery with mixed manifests
diff --git a/testdata/lint/mixed-manifests-autodiscovery/manifests/helmchart.yaml b/testdata/lint/mixed-manifests-autodiscovery/manifests/helmchart.yaml
new file mode 100644
index 000000000..4561318f8
--- /dev/null
+++ b/testdata/lint/mixed-manifests-autodiscovery/manifests/helmchart.yaml
@@ -0,0 +1,9 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: my-app
+spec:
+  chart:
+    name: my-app
+    chartVersion: 1.0.0
+  weight: 1
diff --git a/testdata/lint/mixed-manifests-autodiscovery/manifests/preflight.yaml b/testdata/lint/mixed-manifests-autodiscovery/manifests/preflight.yaml
new file mode 100644
index 000000000..90651afad
--- /dev/null
+++ b/testdata/lint/mixed-manifests-autodiscovery/manifests/preflight.yaml
@@ -0,0 +1,13 @@
+apiVersion: troubleshoot.sh/v1beta2
+kind: Preflight
+metadata:
+  name: my-app-preflight
+spec:
+  analyzers:
+    - clusterVersion:
+        outcomes:
+          - fail:
+              when: "< 1.20.0"
+              message: Kubernetes version must be at least 1.20.0
+          - pass:
+              message: Kubernetes version is supported
diff --git a/testdata/lint/mixed-manifests-autodiscovery/manifests/support-bundle.yaml b/testdata/lint/mixed-manifests-autodiscovery/manifests/support-bundle.yaml
new file mode 100644
index 000000000..d3ab3e781
--- /dev/null
+++ b/testdata/lint/mixed-manifests-autodiscovery/manifests/support-bundle.yaml
@@ -0,0 +1,10 @@
+apiVersion: troubleshoot.sh/v1beta2
+kind: SupportBundle
+metadata:
+  name: my-app-support-bundle
+spec:
+  collectors:
+    - logs:
+        selector:
+          - app=my-app
+        namespace: default
diff --git a/testdata/lint/mixed-manifests-yaml-yml/charts/my-chart/Chart.yaml b/testdata/lint/mixed-manifests-yaml-yml/charts/my-chart/Chart.yaml
new file mode 100644
index 000000000..5e6e5b0cf
--- /dev/null
+++ b/testdata/lint/mixed-manifests-yaml-yml/charts/my-chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: my-app
+version: 1.0.0
+description: Test chart for autodiscovery with mixed manifests
diff --git a/testdata/lint/mixed-manifests-yaml-yml/manifests/helmchart.yaml b/testdata/lint/mixed-manifests-yaml-yml/manifests/helmchart.yaml
new file mode 100644
index 000000000..4561318f8
--- /dev/null
+++ b/testdata/lint/mixed-manifests-yaml-yml/manifests/helmchart.yaml
@@ -0,0 +1,9 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: my-app
+spec:
+  chart:
+    name: my-app
+    chartVersion: 1.0.0
+  weight: 1
diff --git a/testdata/lint/mixed-manifests-yaml-yml/manifests/preflight.yaml b/testdata/lint/mixed-manifests-yaml-yml/manifests/preflight.yaml
new file mode 100644
index 000000000..90651afad
--- /dev/null
+++ b/testdata/lint/mixed-manifests-yaml-yml/manifests/preflight.yaml
@@ -0,0 +1,13 @@
+apiVersion: troubleshoot.sh/v1beta2
+kind: Preflight
+metadata:
+  name: my-app-preflight
+spec:
+  analyzers:
+    - clusterVersion:
+        outcomes:
+          - fail:
+              when: "< 1.20.0"
+              message: Kubernetes version must be at least 1.20.0
+          - pass:
+              message: Kubernetes version is supported
diff --git a/testdata/lint/mixed-manifests-yaml-yml/manifests/support-bundle.yml b/testdata/lint/mixed-manifests-yaml-yml/manifests/support-bundle.yml
new file mode 100644
index 000000000..d3ab3e781
--- /dev/null
+++ b/testdata/lint/mixed-manifests-yaml-yml/manifests/support-bundle.yml
@@ -0,0 +1,10 @@
+apiVersion: troubleshoot.sh/v1beta2
+kind: SupportBundle
+metadata:
+  name: my-app-support-bundle
+spec:
+  collectors:
+    - logs:
+        selector:
+          - app=my-app
+        namespace: default
diff --git a/testdata/lint/multi-chart-project/.replicated b/testdata/lint/multi-chart-project/.replicated
new file mode 100644
index 000000000..93e29cd5e
--- /dev/null
+++ b/testdata/lint/multi-chart-project/.replicated
@@ -0,0 +1,10 @@
+charts:
+  - path: chart1
+  - path: chart2
+manifests:
+  - manifests/*.yaml
+repl-lint:
+  linters:
+    helm: {}
+    preflight:
+      disabled: true
diff --git a/testdata/lint/multi-chart-project/chart1/Chart.yaml b/testdata/lint/multi-chart-project/chart1/Chart.yaml
new file mode 100644
index 000000000..75e6b4f6f
--- /dev/null
+++ b/testdata/lint/multi-chart-project/chart1/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: chart1
+version: 1.0.0
+description: First chart for multi-chart testing
diff --git a/testdata/lint/multi-chart-project/chart1/templates/deployment.yaml b/testdata/lint/multi-chart-project/chart1/templates/deployment.yaml
new file mode 100644
index 000000000..1f352dd1d
--- /dev/null
+++ b/testdata/lint/multi-chart-project/chart1/templates/deployment.yaml
@@ -0,0 +1,18 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: nginx
+spec:
+  selector:
+    matchLabels:
+      app: nginx
+  template:
+    metadata:
+      labels:
+        app: nginx
+    spec:
+      containers:
+      - name: nginx
+        image: {{ .Values.image.repository }}:{{ .Values.image.tag }}
+        ports:
+        - containerPort: 80
diff --git a/testdata/lint/multi-chart-project/chart1/values.yaml b/testdata/lint/multi-chart-project/chart1/values.yaml
new file mode 100644
index 000000000..0022858fb
--- /dev/null
+++ b/testdata/lint/multi-chart-project/chart1/values.yaml
@@ -0,0 +1,3 @@
+image:
+  repository: nginx
+  tag: "1.21"
diff --git a/testdata/lint/multi-chart-project/chart2/Chart.yaml b/testdata/lint/multi-chart-project/chart2/Chart.yaml
new file mode 100644
index 000000000..24329c7d5
--- /dev/null
+++ b/testdata/lint/multi-chart-project/chart2/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: chart2
+version: 1.0.0
+description: Second chart for multi-chart testing
diff --git a/testdata/lint/multi-chart-project/chart2/templates/deployment.yaml b/testdata/lint/multi-chart-project/chart2/templates/deployment.yaml
new file mode 100644
index 000000000..dea1e9bea
--- /dev/null
+++ b/testdata/lint/multi-chart-project/chart2/templates/deployment.yaml
@@ -0,0 +1,18 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: redis
+spec:
+  selector:
+    matchLabels:
+      app: redis
+  template:
+    metadata:
+      labels:
+        app: redis
+    spec:
+      containers:
+      - name: redis
+        image: {{ .Values.image.repository }}:{{ .Values.image.tag }}
+        ports:
+        - containerPort: 6379
diff --git a/testdata/lint/multi-chart-project/chart2/values.yaml b/testdata/lint/multi-chart-project/chart2/values.yaml
new file mode 100644
index 000000000..7f1a50a8f
--- /dev/null
+++ b/testdata/lint/multi-chart-project/chart2/values.yaml
@@ -0,0 +1,3 @@
+image:
+  repository: redis
+  tag: "7.0"
diff --git a/testdata/lint/multi-chart-project/manifests/chart1-helmchart.yaml b/testdata/lint/multi-chart-project/manifests/chart1-helmchart.yaml
new file mode 100644
index 000000000..80b500abf
--- /dev/null
+++ b/testdata/lint/multi-chart-project/manifests/chart1-helmchart.yaml
@@ -0,0 +1,10 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: chart1
+spec:
+  chart:
+    name: chart1
+    chartVersion: 1.0.0
+  weight: 1
+  builder: {}
diff --git a/testdata/lint/multi-chart-project/manifests/chart2-helmchart.yaml b/testdata/lint/multi-chart-project/manifests/chart2-helmchart.yaml
new file mode 100644
index 000000000..04e200f74
--- /dev/null
+++ b/testdata/lint/multi-chart-project/manifests/chart2-helmchart.yaml
@@ -0,0 +1,10 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: chart2
+spec:
+  chart:
+    name: chart2
+    chartVersion: 1.0.0
+  weight: 2
+  builder: {}
diff --git a/testdata/lint/orphaned-helmchart/.replicated b/testdata/lint/orphaned-helmchart/.replicated
new file mode 100644
index 000000000..f163d71d6
--- /dev/null
+++ b/testdata/lint/orphaned-helmchart/.replicated
@@ -0,0 +1,10 @@
+charts:
+  - path: chart
+manifests:
+  - manifests/*.yaml
+repl-lint:
+  linters:
+    helm:
+      disabled: true
+    preflight:
+      disabled: true
diff --git a/testdata/lint/orphaned-helmchart/chart/Chart.yaml b/testdata/lint/orphaned-helmchart/chart/Chart.yaml
new file mode 100644
index 000000000..34886c6ab
--- /dev/null
+++ b/testdata/lint/orphaned-helmchart/chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: current-app
+version: 1.0.0
+description: Current active chart
diff --git a/testdata/lint/orphaned-helmchart/manifests/current-app-helmchart.yaml b/testdata/lint/orphaned-helmchart/manifests/current-app-helmchart.yaml
new file mode 100644
index 000000000..63e01ec72
--- /dev/null
+++ b/testdata/lint/orphaned-helmchart/manifests/current-app-helmchart.yaml
@@ -0,0 +1,9 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: current-app
+spec:
+  chart:
+    name: current-app
+    chartVersion: 1.0.0
+  weight: 1
diff --git a/testdata/lint/orphaned-helmchart/manifests/old-app-helmchart.yaml b/testdata/lint/orphaned-helmchart/manifests/old-app-helmchart.yaml
new file mode 100644
index 000000000..f474a62da
--- /dev/null
+++ b/testdata/lint/orphaned-helmchart/manifests/old-app-helmchart.yaml
@@ -0,0 +1,9 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: old-app
+spec:
+  chart:
+    name: old-app
+    chartVersion: 0.9.0
+  weight: 2
diff --git a/testdata/lint/simple-chart/.replicated b/testdata/lint/simple-chart/.replicated
new file mode 100644
index 000000000..b4975a7b2
--- /dev/null
+++ b/testdata/lint/simple-chart/.replicated
@@ -0,0 +1,9 @@
+charts:
+  - path: chart
+manifests:
+  - manifests/*.yaml
+repl-lint:
+  linters:
+    helm: {}
+    preflight:
+      disabled: true
diff --git a/testdata/lint/simple-chart/chart/Chart.yaml b/testdata/lint/simple-chart/chart/Chart.yaml
new file mode 100644
index 000000000..f4b224118
--- /dev/null
+++ b/testdata/lint/simple-chart/chart/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: test-chart
+version: 1.0.0
+description: A simple test chart for lint testing
diff --git a/testdata/lint/simple-chart/chart/templates/deployment.yaml b/testdata/lint/simple-chart/chart/templates/deployment.yaml
new file mode 100644
index 000000000..2ecaf9c3d
--- /dev/null
+++ b/testdata/lint/simple-chart/chart/templates/deployment.yaml
@@ -0,0 +1,19 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: test
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: test-chart
+  template:
+    metadata:
+      labels:
+        app: test-chart
+    spec:
+      containers:
+      - name: nginx
+        image: {{ .Values.image.repository }}:{{ .Values.image.tag }}
+        ports:
+        - containerPort: 80
diff --git a/testdata/lint/simple-chart/chart/values.yaml b/testdata/lint/simple-chart/chart/values.yaml
new file mode 100644
index 000000000..99bab5baf
--- /dev/null
+++ b/testdata/lint/simple-chart/chart/values.yaml
@@ -0,0 +1,6 @@
+replicaCount: 1
+
+image:
+  repository: nginx
+  tag: "1.21"
+  pullPolicy: IfNotPresent
diff --git a/testdata/lint/simple-chart/manifests/helmchart.yaml b/testdata/lint/simple-chart/manifests/helmchart.yaml
new file mode 100644
index 000000000..8ebd8f7f6
--- /dev/null
+++ b/testdata/lint/simple-chart/manifests/helmchart.yaml
@@ -0,0 +1,10 @@
+apiVersion: kots.io/v1beta2
+kind: HelmChart
+metadata:
+  name: test-chart
+spec:
+  chart:
+    name: test-chart
+    chartVersion: 1.0.0
+  weight: 1
+  builder: {}