Remove byte order masks when constructing variation trees

Author: ibbem

pom.xml

@@ -131,6 +131,12 @@
             <version>3.12.0</version>
         </dependency>
 
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.12.0</version>
+        </dependency>
+
         <dependency>
             <groupId>org.tinylog</groupId>
             <artifactId>tinylog-api</artifactId>

src/main/java/org/variantsync/diffdetective/validation/ConstructionValidation.java

@@ -12,6 +12,7 @@
 import java.util.Set;
 import java.util.function.BiConsumer;
 
+import org.apache.commons.io.input.CharacterFilterReader;
 import org.apache.commons.lang3.NotImplementedException;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.tinylog.Logger;
@@ -350,11 +351,13 @@ private void counts(DiffTree tree, DiffTreeStatistics statistics) {
 
     private DiffTree parseVariationTree(Analysis analysis, RevCommit commit) throws IOException, DiffParseException {
         try (BufferedReader afterFile =
-            GitDiffer.getBeforeFullFile(
-                analysis.getRepository().getGitRepo().run(),
-                commit,
-                analysis.getCurrentPatch().getFileName()
-            )
+            new BufferedReader(
+                new CharacterFilterReader(
+                    GitDiffer.getBeforeFullFile(
+                        analysis.getRepository().getGitRepo().run(),
+                        commit,
+                        analysis.getCurrentPatch().getFileName()),
+                    0xfeff)) // BOM, same as GitDiffer.BOM_PATTERN
         ) {
             return DiffTreeParser.createVariationTree(afterFile, analysis.getRepository().getParseOptions().diffTreeParseOptions());
         }