Fixes for manifest with symlink (#2256)

## Description

Fixes the issue with symlinks inside of manifests, similar to that seen
in the [Big Bang Keycloak Helm
Chart](https://repo1.dso.mil/big-bang/product/packages/keycloak/-/blob/main/development/theme-custom/theme/custom-theme/account/resources?ref_type=heads).

## Related Issue

Fixes #2255

## Type of change

- [x] Bug fix (non-breaking change which fixes an issue)
- [ ] New feature (non-breaking change which adds functionality)
- [ ] Other (security config, docs update, etc)

## Checklist before merging

- [x] Test, docs, adr added or updated as needed
- [x] [Contributor Guide
Steps](https://github.com/defenseunicorns/zarf/blob/main/CONTRIBUTING.md#developer-workflow)
followed

---------

Co-authored-by: razzle <harry@razzle.cloud>
Co-authored-by: Wayne Starr <Racer159@users.noreply.github.com>

src/pkg/packager/create_stages.go

@@ -316,24 +316,41 @@ func (p *Packager) getFilesToSBOM(component types.ZarfComponent) (*layout.Compon
 		Component: componentPaths,
 	}
 
-	appendSBOMFiles := func(path string) {
+	appendSBOMFiles := func(path string) error {
 		if utils.IsDir(path) {
-			files, _ := utils.RecursiveFileList(path, nil, false)
+			files, err := utils.RecursiveFileList(path, nil, false)
+			if err != nil {
+				return err
+			}
 			componentSBOM.Files = append(componentSBOM.Files, files...)
 		} else {
-			componentSBOM.Files = append(componentSBOM.Files, path)
+			info, err := os.Lstat(path)
+			if err != nil {
+				return err
+			}
+			if info.Mode().IsRegular() {
+				componentSBOM.Files = append(componentSBOM.Files, path)
+			}
 		}
+
+		return nil
 	}
 
 	for filesIdx, file := range component.Files {
 		path := filepath.Join(componentPaths.Files, strconv.Itoa(filesIdx), filepath.Base(file.Target))
-		appendSBOMFiles(path)
+		err := appendSBOMFiles(path)
+		if err != nil {
+			return nil, err
+		}
 	}
 
 	for dataIdx, data := range component.DataInjections {
 		path := filepath.Join(componentPaths.DataInjections, strconv.Itoa(dataIdx), filepath.Base(data.Target.Path))
 
-		appendSBOMFiles(path)
+		err := appendSBOMFiles(path)
+		if err != nil {
+			return nil, err
+		}
 	}
 
 	return componentSBOM, nil

src/pkg/utils/io.go

@@ -218,7 +218,13 @@ func RecursiveFileList(dir string, pattern *regexp.Regexp, skipHidden bool) (fil
 			return err
 		}
 
-		if !d.IsDir() {
+		info, err := d.Info()
+
+		if err != nil {
+			return err
+		}
+
+		if info.Mode().IsRegular() {
 			if pattern != nil {
 				if len(pattern.FindStringIndex(path)) > 0 {
 					files = append(files, path)
@@ -442,8 +448,16 @@ func CreateReproducibleTarballFromDir(dirPath, dirPrefix, tarballPath string) er
 			return err
 		}
 
+		link := ""
+		if info.Mode().Type() == os.ModeSymlink {
+			link, err = os.Readlink(filePath)
+			if err != nil {
+				return fmt.Errorf("error reading symlink: %w", err)
+			}
+		}
+
 		// Create a new header
-		header, err := tar.FileInfoHeader(info, "")
+		header, err := tar.FileInfoHeader(info, link)
 		if err != nil {
 			return fmt.Errorf("error creating tar header: %w", err)
 		}
@@ -470,7 +484,7 @@ func CreateReproducibleTarballFromDir(dirPath, dirPrefix, tarballPath string) er
 		}
 
 		// If it's a file, write its content
-		if !info.IsDir() {
+		if info.Mode().IsRegular() {
 			file, err := os.Open(filePath)
 			if err != nil {
 				return fmt.Errorf("error opening file: %w", err)

src/test/e2e/34_manifest_with_symlink_test.go

@@ -0,0 +1,33 @@
+// SPDX-License-Identifier: Apache-2.0
+// SPDX-FileCopyrightText: 2021-Present The Zarf Authors
+
+// Package test provides e2e tests for Zarf.
+package test
+
+import (
+	"fmt"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+func TestManifestWithSymlink(t *testing.T) {
+	t.Log("E2E: Manifest With Symlink")
+	tmpdir := t.TempDir()
+	cachePath := filepath.Join(tmpdir, ".cache-location")
+
+	// Build the package, should succeed, even though there is a symlink in the package.
+	buildPath := filepath.Join("src", "test", "packages", "34-manifest-with-symlink")
+	stdOut, stdErr, err := e2e.Zarf("package", "create", buildPath, "--zarf-cache", cachePath, "-o=build", "--confirm")
+	require.NoError(t, err, stdOut, stdErr)
+
+	path := fmt.Sprintf("build/zarf-package-manifest-with-symlink-%s-0.0.1.tar.zst", e2e.Arch)
+	require.FileExists(t, path)
+	defer e2e.CleanFiles(path)
+
+	stdOut, stdErr, err = e2e.Zarf("package", "deploy", path, "--zarf-cache", cachePath, "--confirm")
+	defer e2e.CleanFiles("temp/manifests")
+	require.NoError(t, err, stdOut, stdErr)
+	require.FileExists(t, "temp/manifests/resources/img", "Symlink does not exist in the package as expected.")
+}

src/test/packages/34-manifest-with-symlink/manifests/img/test.txt

@@ -0,0 +1 @@
+test

src/test/packages/34-manifest-with-symlink/manifests/resources/img

@@ -0,0 +1 @@
+../img

src/test/packages/34-manifest-with-symlink/zarf.yaml

@@ -0,0 +1,12 @@
+kind: ZarfPackageConfig
+metadata:
+  name: manifest-with-symlink
+  description: Example with a symbolic link embedded in it
+  version: 0.0.1
+
+components:
+  - name: manifest-with-symlink
+    required: true
+    files:
+      - source: manifests
+        target: temp/manifests