diff --git a/internal/discovery/discovery.go b/internal/discovery/discovery.go
index ead782d..e4801d3 100644
--- a/internal/discovery/discovery.go
+++ b/internal/discovery/discovery.go
@@ -78,6 +78,10 @@ func findJavaFilesGit(root string) ([]string, error) {
 		if line == "" {
 			continue
 		}
+		if isExcludedInfraPath(line) {
+			continue
+		}
+
 		// ls-files output is relative to git root.
 		absPath := filepath.Join(gitRoot, line)
 		// Keep only files under target root (avoids picking up
@@ -91,11 +95,27 @@ func findJavaFilesGit(root string) ([]string, error) {
 	return files, nil
 }
 
+func isExcludedInfraPath(path string) bool {
+	parts := strings.FieldsFunc(filepath.Clean(path), func(r rune) bool {
+		return r == '/' || r == filepath.Separator
+	})
+	for i, part := range parts {
+		if part == "vendor" || part == "node_modules" || part == ".git" || part == ".mvn" || part == ".gradle" {
+			return true
+		}
+		if part == "wrapper" && i > 0 && parts[i-1] == "gradle" {
+			return true
+		}
+	}
+	return false
+}
+
 // findJavaFilesWalk is the recursive filesystem walk fallback.
 // It skips vendor/, node_modules/, .git/, .mvn/, .gradle/,
 // and gradle/wrapper/ (build-wrapper/infrastructure directories).
 func findJavaFilesWalk(root string) ([]string, error) {
 	var files []string
+	rootParent := filepath.Dir(filepath.Clean(root))
 
 	err := filepath.Walk(root, func(path string, info os.FileInfo, err error) error {
 		if err != nil {
@@ -103,13 +123,11 @@ func findJavaFilesWalk(root string) ([]string, error) {
 		}
 
 		if info.IsDir() {
-			name := info.Name()
-			// Skip common non-source and build-wrapper/infrastructure directories
-			if name == "vendor" || name == "node_modules" || name == ".git" || name == ".mvn" || name == ".gradle" {
-				return filepath.SkipDir
+			relPath, err := filepath.Rel(rootParent, path)
+			if err != nil {
+				return err
 			}
-			// Skip gradle/wrapper build wrapper infrastructure
-			if name == "wrapper" && filepath.Base(filepath.Dir(path)) == "gradle" {
+			if isExcludedInfraPath(relPath) {
 				return filepath.SkipDir
 			}
 			return nil
diff --git a/internal/discovery/discovery_test.go b/internal/discovery/discovery_test.go
new file mode 100644
index 0000000..18424fa
--- /dev/null
+++ b/internal/discovery/discovery_test.go
@@ -0,0 +1,125 @@
+package discovery
+
+import (
+	"os"
+	"os/exec"
+	"path/filepath"
+	"reflect"
+	"sort"
+	"testing"
+)
+
+func TestIsExcludedInfraPath(t *testing.T) {
+	t.Parallel()
+
+	tests := []struct {
+		name string
+		path string
+		want bool
+	}{
+		{name: "maven wrapper nested", path: "complete/.mvn/wrapper/MavenWrapperDownloader.java", want: true},
+		{name: "maven wrapper root", path: ".mvn/wrapper/X.java", want: true},
+		{name: "vendor", path: "vendor/foo/Bar.java", want: true},
+		{name: "node modules", path: "node_modules/pkg/Thing.java", want: true},
+		{name: "git dir", path: ".git/hooks/whatever.java", want: true},
+		{name: "gradle cache", path: ".gradle/cache/Y.java", want: true},
+		{name: "gradle wrapper", path: "proj/gradle/wrapper/GradleWrapperMain.java", want: true},
+		{name: "normal source true positive", path: "src/main/java/com/example/HotelServiceEvent.java", want: false},
+		{name: "normal app", path: "src/main/java/com/example/App.java", want: false},
+		{name: "mvn substring only", path: "mvnutil/src/Main.java", want: false},
+		{name: "gradle substring only", path: "mygradlestuff/src/X.java", want: false},
+		{name: "wrapper without gradle parent", path: "wrapper/Foo.java", want: false},
+		{name: "wrapper under src", path: "src/wrapper/Helper.java", want: false},
+	}
+
+	for _, tc := range tests {
+		tc := tc
+		t.Run(tc.name, func(t *testing.T) {
+			t.Parallel()
+			if got := isExcludedInfraPath(tc.path); got != tc.want {
+				t.Fatalf("isExcludedInfraPath(%q) = %v, want %v", tc.path, got, tc.want)
+			}
+		})
+	}
+}
+
+func TestFindJavaFilesWalkExcludesInfraPaths(t *testing.T) {
+	root := t.TempDir()
+
+	mustWriteFile(t, root, "src/main/java/Live.java")
+	mustWriteFile(t, root, ".mvn/wrapper/MavenWrapperDownloader.java")
+	mustWriteFile(t, root, "gradle/wrapper/GradleWrapperMain.java")
+	mustWriteFile(t, root, "vendor/x/V.java")
+
+	files, err := FindJavaFiles(root)
+	if err != nil {
+		t.Fatalf("FindJavaFiles() error = %v", err)
+	}
+
+	got := relPaths(t, root, files)
+	want := []string{"src/main/java/Live.java"}
+	if !reflect.DeepEqual(got, want) {
+		t.Fatalf("FindJavaFiles() = %v, want %v", got, want)
+	}
+}
+
+func TestFindJavaFilesWithGitExcludesInfraPaths(t *testing.T) {
+	if _, err := exec.LookPath("git"); err != nil {
+		t.Skip("git not available")
+	}
+
+	root := t.TempDir()
+	mustWriteFile(t, root, "src/main/java/Live.java")
+	mustWriteFile(t, root, ".mvn/wrapper/MavenWrapperDownloader.java")
+	mustWriteFile(t, root, "gradle/wrapper/GradleWrapperMain.java")
+	mustWriteFile(t, root, "vendor/x/V.java")
+
+	git(t, root, "init")
+	git(t, root, "add", ".")
+
+	files, err := FindJavaFilesWithGit(root, true)
+	if err != nil {
+		t.Fatalf("FindJavaFilesWithGit() error = %v", err)
+	}
+
+	got := relPaths(t, root, files)
+	want := []string{"src/main/java/Live.java"}
+	if !reflect.DeepEqual(got, want) {
+		t.Fatalf("FindJavaFilesWithGit() = %v, want %v", got, want)
+	}
+}
+
+func mustWriteFile(t *testing.T, root, rel string) {
+	t.Helper()
+	path := filepath.Join(root, filepath.FromSlash(rel))
+	if err := os.MkdirAll(filepath.Dir(path), 0o755); err != nil {
+		t.Fatalf("MkdirAll(%q) error = %v", filepath.Dir(path), err)
+	}
+	if err := os.WriteFile(path, []byte("class X {}\n"), 0o644); err != nil {
+		t.Fatalf("WriteFile(%q) error = %v", path, err)
+	}
+}
+
+func relPaths(t *testing.T, root string, files []string) []string {
+	t.Helper()
+	rel := make([]string, 0, len(files))
+	for _, file := range files {
+		p, err := filepath.Rel(root, file)
+		if err != nil {
+			t.Fatalf("filepath.Rel(%q, %q) error = %v", root, file, err)
+		}
+		rel = append(rel, filepath.ToSlash(p))
+	}
+	sort.Strings(rel)
+	return rel
+}
+
+func git(t *testing.T, dir string, args ...string) {
+	t.Helper()
+	cmd := exec.Command("git", args...)
+	cmd.Dir = dir
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("git %v failed: %v\n%s", args, err, out)
+	}
+}