diff --git a/pkg/prebuild/prebuild.go b/pkg/prebuild/prebuild.go
index 77ff86aef..56e1fc7b6 100644
--- a/pkg/prebuild/prebuild.go
+++ b/pkg/prebuild/prebuild.go
@@ -33,7 +33,7 @@ func init() {
 	case "ubuntu":
 		if cfg.Release["VERSION_CODENAME"] == "noble" {
 			builder.Register("abi3")
-			cfg.Overwrite = true
+			cfg.Overwrite.Enabled = true
 		}
 	}
 }
diff --git a/pkg/prebuild/prepare/flags.go b/pkg/prebuild/prepare/flags.go
index ee55a28ac..995b13916 100644
--- a/pkg/prebuild/prepare/flags.go
+++ b/pkg/prebuild/prepare/flags.go
@@ -32,27 +32,17 @@ func init() {
 
 func (p SetFlags) Apply() ([]string, error) {
 	res := []string{}
-	for _, name := range []string{"main.flags", cfg.Distribution + ".flags"} {
-		path := cfg.FlagDir.Join(name)
-		if !path.Exist() {
-			continue
-		}
-		lines, _ := path.ReadFileAsLines()
-		for _, line := range lines {
-			if strings.HasPrefix(line, "#") || line == "" {
-				continue
-			}
-			manifest := strings.Split(line, " ")
-			profile := manifest[0]
+	for _, name := range []string{"main", cfg.Distribution} {
+		for profile, flags := range cfg.Flags.Read(name) {
 			file := cfg.RootApparmord.Join(profile)
 			if !file.Exist() {
 				res = append(res, fmt.Sprintf("Profile %s not found, ignoring", profile))
 				continue
 			}
 
-			// If flags is set, overwrite profile flag
-			if len(manifest) > 1 {
-				flags := " flags=(" + manifest[1] + ") {"
+			// Overwrite profile flags
+			if len(flags) > 0 {
+				flagsStr := " flags=(" + strings.Join(flags, ",") + ") {"
 				content, err := file.ReadFile()
 				if err != nil {
 					return res, err
@@ -60,13 +50,13 @@ func (p SetFlags) Apply() ([]string, error) {
 
 				// Remove all flags definition, then set manifest' flags
 				out := regFlags.ReplaceAllLiteralString(string(content), "")
-				out = regProfileHeader.ReplaceAllLiteralString(out, flags)
+				out = regProfileHeader.ReplaceAllLiteralString(out, flagsStr)
 				if err := file.WriteFile([]byte(out)); err != nil {
 					return res, err
 				}
 			}
 		}
-		res = append(res, path.String())
+		res = append(res, cfg.FlagDir.Join(name+".flags").String())
 	}
 	return res, nil
 }
diff --git a/pkg/prebuild/prepare/ignore.go b/pkg/prebuild/prepare/ignore.go
index 23b144225..3fd01495d 100644
--- a/pkg/prebuild/prepare/ignore.go
+++ b/pkg/prebuild/prepare/ignore.go
@@ -5,8 +5,6 @@
 package prepare
 
 import (
-	"strings"
-
 	"github.com/arduino/go-paths-helper"
 	"github.com/roddhjav/apparmor.d/pkg/prebuild/cfg"
 )
@@ -26,19 +24,11 @@ func init() {
 
 func (p Ignore) Apply() ([]string, error) {
 	res := []string{}
-	for _, name := range []string{"main.ignore", cfg.Distribution + ".ignore"} {
-		path := cfg.DistDir.Join("ignore", name)
-		if !path.Exist() {
-			continue
-		}
-		lines, _ := path.ReadFileAsLines()
-		for _, line := range lines {
-			if strings.HasPrefix(line, "#") || line == "" {
-				continue
-			}
-			profile := cfg.Root.Join(line)
+	for _, name := range []string{"main", cfg.Distribution} {
+		for _, ignore := range cfg.Ignore.Read(name) {
+			profile := cfg.Root.Join(ignore)
 			if profile.NotExist() {
-				files, err := cfg.RootApparmord.ReadDirRecursiveFiltered(nil, paths.FilterNames(line))
+				files, err := cfg.RootApparmord.ReadDirRecursiveFiltered(nil, paths.FilterNames(ignore))
 				if err != nil {
 					return res, err
 				}
@@ -53,7 +43,7 @@ func (p Ignore) Apply() ([]string, error) {
 				}
 			}
 		}
-		res = append(res, path.String())
+		res = append(res, cfg.IgnoreDir.Join(name+".ignore").String())
 	}
 	return res, nil
 }
diff --git a/pkg/util/tools.go b/pkg/util/tools.go
index 64b71bd00..75a7258fe 100644
--- a/pkg/util/tools.go
+++ b/pkg/util/tools.go
@@ -94,4 +94,3 @@ func CopyTo(src *paths.Path, dst *paths.Path) error {
 	}
 	return nil
 }
-