Fix vanilla classes not being filtered out of mods

Author: thecatcore

src/main/java/io/github/fabriccompatibilitylayers/modremappingapi/impl/context/ModDiscoverer.java

@@ -90,6 +90,7 @@ public void excludeClassEdits(List<ModCandidate> candidates, InternalCacheHandle
             var outputPath = tempDirectory.resolve(outputName);
 
             if (Files.isDirectory(modPath)) {
+                outputPath = tempDirectory.resolve(outputName + ".zip");
                 FileUtils.zipFolder(modPath, outputPath);
             } else {
                 Files.copy(modPath, outputPath);

src/main/java/io/github/fabriccompatibilitylayers/modremappingapi/impl/context/ModRemmaperV2Context.java

@@ -14,6 +14,7 @@
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.net.URISyntaxException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.util.*;
@@ -114,6 +115,16 @@ public List<ModRemapper> discoverMods(boolean remapClassEdits) {
         var config2Candidates = candidates.stream()
                 .collect(Collectors.groupingBy(ModCandidate::getDiscovererConfig));
 
+        for (var entry : config2Candidates.entrySet()) {
+            var config = entry.getKey();
+
+            try {
+                config2Discoverer.get(config).excludeClassEdits(entry.getValue(), this.cacheHandler, this.mappingsRegistry);
+            } catch (IOException | URISyntaxException e) {
+                throw new RuntimeException(e);
+            }
+        }
+
         for (var candidate : candidates) {
             mappingsRegistry.addModMappings(candidate.getPath());
         }

src/main/java/io/github/fabriccompatibilitylayers/modremappingapi/impl/utils/FileUtils.java

@@ -137,17 +137,29 @@ public static void emptyDir(Path dir) {
         }
     }
 
+    /* Define ZIP File System Properties in Map */
+    private static final Map<String, String> ZIPPING_PROPERTIES = Map.of(
+            /* We want to read an existing ZIP File, so we set this to False */
+            "create", "true",
+            /* Specify the encoding as UTF-8 */
+            "encoding", "UTF-8"
+    );
+
     /**
      * @author moehreag
      */
     @ApiStatus.Internal
     public static void zipFolder(Path in, Path out) throws IOException {
-        try (var outFs = FileSystems.newFileSystem(out)) {
+        try (var outFs = FileSystems.newFileSystem(out, ZIPPING_PROPERTIES)) {
             Files.walkFileTree(in, new SimpleFileVisitor<>(){
                 @Override
                 public @NotNull FileVisitResult visitFile(@NotNull Path file, @NotNull BasicFileAttributes attrs) throws IOException {
                     var outPath = outFs.getPath(in.relativize(file).toString());
-                    Files.createDirectories(outPath.getParent());
+
+                    if (outPath.getParent() != null) {
+                        Files.createDirectories(outPath.getParent());
+                    }
+
                     Files.copy(file, outPath);
                     return super.visitFile(file, attrs);
                 }