diff --git a/pkg/prebuild/cli/cli.go b/pkg/prebuild/cli/cli.go
index d192dd664..2ae440afc 100644
--- a/pkg/prebuild/cli/cli.go
+++ b/pkg/prebuild/cli/cli.go
@@ -15,6 +15,7 @@ import (
 	"github.com/roddhjav/apparmor.d/pkg/prebuild/builder"
 	"github.com/roddhjav/apparmor.d/pkg/prebuild/directive"
 	"github.com/roddhjav/apparmor.d/pkg/prebuild/prepare"
+	"github.com/roddhjav/apparmor.d/pkg/util"
 )
 
 const (
diff --git a/pkg/prebuild/directive/exec.go b/pkg/prebuild/directive/exec.go
index 5aee73740..26722349a 100644
--- a/pkg/prebuild/directive/exec.go
+++ b/pkg/prebuild/directive/exec.go
@@ -8,10 +8,12 @@ package directive
 
 import (
 	"fmt"
+	"path/filepath"
 	"slices"
 	"strings"
 
 	"github.com/roddhjav/apparmor.d/pkg/aa"
+	"github.com/roddhjav/apparmor.d/pkg/paths"
 	"github.com/roddhjav/apparmor.d/pkg/prebuild"
 )
 
@@ -43,7 +45,14 @@ func (d Exec) Apply(opt *Option, profileRaw string) (string, error) {
 
 	rules := aa.Rules{}
 	for name := range opt.ArgMap {
-		profiletoTransition := prebuild.RootApparmord.Join(name).MustReadFileAsString()
+		match, err := filepath.Glob(prebuild.Root.String() + "/*/" + name)
+		if err != nil {
+			return "", err
+		}
+		if len(match) != 1 {
+			return "", fmt.Errorf("No profile found for %s", name)
+		}
+		profiletoTransition := paths.New(match[0]).MustReadFileAsString()
 		dstProfile := aa.DefaultTunables()
 		if _, err := dstProfile.Parse(profiletoTransition); err != nil {
 			return "", err
diff --git a/pkg/prebuild/directive/stack.go b/pkg/prebuild/directive/stack.go
index 03dd826e1..631c6f00f 100644
--- a/pkg/prebuild/directive/stack.go
+++ b/pkg/prebuild/directive/stack.go
@@ -6,10 +6,12 @@ package directive
 
 import (
 	"fmt"
+	"path/filepath"
 	"regexp"
 	"slices"
 	"strings"
 
+	"github.com/roddhjav/apparmor.d/pkg/paths"
 	"github.com/roddhjav/apparmor.d/pkg/prebuild"
 	"github.com/roddhjav/apparmor.d/pkg/util"
 )
@@ -55,7 +57,14 @@ func (s Stack) Apply(opt *Option, profile string) (string, error) {
 
 	res := ""
 	for name := range opt.ArgMap {
-		stackedProfile := prebuild.RootApparmord.Join(name).MustReadFileAsString()
+		match, err := filepath.Glob(prebuild.Root.String() + "/*/" + name)
+		if err != nil {
+			return "", err
+		}
+		if len(match) != 1 {
+			return "", fmt.Errorf("No profile found for %s", name)
+		}
+		stackedProfile := paths.New(match[0]).MustReadFileAsString()
 		m := regRules.FindStringSubmatch(stackedProfile)
 		if len(m) < 2 {
 			return "", fmt.Errorf("No profile found in %s", name)
diff --git a/pkg/prebuild/directories.go b/pkg/prebuild/directories.go
index 38f3f53e6..7859fa89d 100644
--- a/pkg/prebuild/directories.go
+++ b/pkg/prebuild/directories.go
@@ -66,7 +66,7 @@ func getRootBuild() *paths.Path {
 func getPackages() []string {
 	files, err := PkgDir.ReadDirRecursiveFiltered(nil, paths.FilterOutDirectories())
 	if err != nil {
-		panic(err)
+		return []string{}
 	}
 	packages := make([]string, 0, len(files))
 	for _, file := range files {
diff --git a/pkg/prebuild/prepare/ignore.go b/pkg/prebuild/prepare/ignore.go
index 2aece5174..4a7eb929a 100644
--- a/pkg/prebuild/prepare/ignore.go
+++ b/pkg/prebuild/prepare/ignore.go
@@ -5,6 +5,9 @@
 package prepare
 
 import (
+	"fmt"
+	"strings"
+
 	"github.com/roddhjav/apparmor.d/pkg/paths"
 	"github.com/roddhjav/apparmor.d/pkg/prebuild"
 )
@@ -26,21 +29,39 @@ func (p Ignore) Apply() ([]string, error) {
 	res := []string{}
 	for _, name := range []string{"main", prebuild.Distribution} {
 		for _, ignore := range prebuild.Ignore.Read(name) {
-			profile := prebuild.Root.Join(ignore)
-			if profile.NotExist() {
-				files, err := prebuild.RootApparmord.ReadDirRecursiveFiltered(nil, paths.FilterNames(ignore))
+			// Ignore file from share/
+			path := prebuild.Root.Join(ignore)
+			if path.Exist() {
+				if err := path.RemoveAll(); err != nil {
+					return res, err
+				}
+				continue
+			}
+
+			// Ignore file from apparmor.d/
+			profile := strings.TrimPrefix(ignore, prebuild.Src+"/")
+			if strings.HasPrefix(ignore, prebuild.Src) {
+				path = prebuild.RootApparmord.Join(profile)
+			}
+			if path.Exist() {
+				if err := path.RemoveAll(); err != nil {
+					return res, err
+				}
+
+			} else {
+				files, err := prebuild.RootApparmord.ReadDirRecursiveFiltered(nil, paths.FilterNames(profile))
 				if err != nil {
 					return res, err
 				}
+				if len(files) == 0 {
+					return res, fmt.Errorf("%s.ignore: no files found for '%s'", name, profile)
+				}
 				for _, path := range files {
 					if err := path.RemoveAll(); err != nil {
 						return res, err
 					}
 				}
-			} else {
-				if err := profile.RemoveAll(); err != nil {
-					return res, err
-				}
+
 			}
 		}
 		res = append(res, prebuild.IgnoreDir.Join(name+".ignore").String())
diff --git a/pkg/prebuild/prepare/merge.go b/pkg/prebuild/prepare/merge.go
index d2c720003..bc8be9062 100644
--- a/pkg/prebuild/prepare/merge.go
+++ b/pkg/prebuild/prepare/merge.go
@@ -48,7 +48,7 @@ func (p Merge) Apply() ([]string, error) {
 
 		files, err = filepath.Glob(prebuild.RootApparmord.Join(dirRemoved).String())
 		if err != nil {
-			return []string{}, err
+			return res, err
 		}
 		for _, file := range files {
 			if err := paths.New(file).RemoveAll(); err != nil {
diff --git a/pkg/prebuild/prepare/overwrite.go b/pkg/prebuild/prepare/overwrite.go
index 6f8951161..4f31fee70 100644
--- a/pkg/prebuild/prepare/overwrite.go
+++ b/pkg/prebuild/prepare/overwrite.go
@@ -50,7 +50,6 @@ func (p Overwrite) Apply() ([]string, error) {
 			continue
 		}
 		if err := origin.Rename(dest); err != nil {
-
 			return res, err
 		}
 		originRel, err := origin.RelFrom(dest)
diff --git a/pkg/prebuild/prepare/synchronise.go b/pkg/prebuild/prepare/synchronise.go
index b272388c7..6dbfd8bb8 100644
--- a/pkg/prebuild/prepare/synchronise.go
+++ b/pkg/prebuild/prepare/synchronise.go
@@ -33,14 +33,15 @@ func (p Synchronise) Apply() ([]string, error) {
 		}
 	}
 	if p.Path == "" {
-		for _, name := range []string{"apparmor.d", "share"} {
-			if err := paths.CopyTo(paths.New(name), prebuild.Root.Join(name)); err != nil {
-				return res, err
-			}
+		if err := paths.CopyTo(paths.New("share"), prebuild.Root.Join("share")); err != nil {
+			return res, err
+		}
+		if err := paths.CopyTo(prebuild.SrcApparmord, prebuild.RootApparmord); err != nil {
+			return res, err
 		}
 	} else {
 		file := paths.New(p.Path)
-		destination, err := file.RelFrom(paths.New("apparmor.d"))
+		destination, err := file.RelFrom(prebuild.SrcApparmord)
 		if err != nil {
 			return res, err
 		}