fix mod compilation

src/main/java/net/fabricmc/loom/AbstractPlugin.java

@@ -105,6 +105,7 @@ public class AbstractPlugin implements Plugin<Project> {
 					javaCompileTask.doFirst(task1 -> {
 						project.getLogger().lifecycle(":setting java compiler args");
 						try {
+							javaCompileTask.getClasspath().add(project.getConfigurations().getByName(Constants.CONFIG_MINECRAFT));
 							javaCompileTask.getClasspath().add(target.files(this.getClass().getProtectionDomain().getCodeSource().getLocation()));
 
 							javaCompileTask.getOptions().getCompilerArgs().add("-AinMapFilePomfIntermediary=" + Constants.MAPPINGS_TINY.get(extension).getCanonicalPath());

src/main/java/net/fabricmc/loom/task/SetupTask.java

@@ -43,6 +43,7 @@ public class SetupTask extends DefaultTask {
 	public void configureModRemapper(){
 		LoomGradleExtension extension = getProject().getExtensions().getByType(LoomGradleExtension.class);
 		Configuration inputConfig =  getProject().getConfigurations().getByName(Constants.COMPILE_MODS);
+
 		inputConfig.getResolvedConfiguration().getFiles().stream()
 			.filter(file -> file.getName().endsWith(".jar"))
 			.forEach(input -> {

src/main/java/net/fabricmc/loom/util/Constants.java

@@ -65,7 +65,6 @@ public class Constants {
 	public static final IDelayed<File> MINECRAFT_LIBS = new DelayedFile(extension -> new File(extension.getUserCache(), extension.version + "-libs"));
 	public static final IDelayed<File> MINECRAFT_NATIVES = new DelayedFile(extension -> new File(extension.getUserCache(), extension.version + "-natives"));
 	public static final IDelayed<File> MINECRAFT_JSON = new DelayedFile(extension -> new File(extension.getUserCache(), extension.version + "-info.json"));
-	public static final IDelayed<File> REF_MAP = new DelayedFile(extension -> new File(CACHE_FILES, "mixin-refmap.json"));
 
 	public static final IDelayed<File> VERSION_MANIFEST = new DelayedFile(extension -> new File(extension.getUserCache(), "version_manifest.json"));
 

src/main/java/net/fabricmc/loom/util/ModProcessor.java

@@ -53,10 +53,7 @@ import java.lang.reflect.Field;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.HashMap;
+import java.util.*;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
 import java.util.jar.JarFile;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
@@ -83,7 +80,11 @@ public class ModProcessor {
 		File mappingsFile = Constants.MAPPINGS_TINY.get(extension);
 		Path mappings = mappingsFile.toPath();
 		Path mc = Constants.MINECRAFT_INTERMEDIARY_JAR.get(extension).toPath();
-		Path[] classpath = project.getConfigurations().getByName(Constants.CONFIG_MC_DEPENDENCIES).getFiles().stream()
+		Path[] mcDeps = project.getConfigurations().getByName(Constants.CONFIG_MC_DEPENDENCIES).getFiles().stream()
+			.map(File::toPath)
+			.toArray(Path[]::new);
+		Collection<File> modCompileFiles = project.getConfigurations().getByName(Constants.COMPILE_MODS).getFiles();
+		Path[] modCompiles = modCompileFiles.stream()
 				.map(File::toPath)
 				.toArray(Path[]::new);
 
@@ -96,9 +97,12 @@ public class ModProcessor {
 		try {
 			OutputConsumerPath outputConsumer = new OutputConsumerPath(Paths.get(output.getAbsolutePath()));
 			outputConsumer.addNonClassFiles(input.toPath());
+			if (!modCompileFiles.contains(input)) {
 				remapper.read(input.toPath());
+			}
+			remapper.read(modCompiles);
 			remapper.read(mc);
-			remapper.read(classpath);
+			remapper.read(mcDeps);
 			remapper.apply(input.toPath(), outputConsumer);
 			outputConsumer.finish();
 		} catch (Exception e){
@@ -110,7 +114,6 @@ public class ModProcessor {
 		}
 
 		Gson gson = new GsonBuilder().setPrettyPrinting().create();
-		project.getLogger().lifecycle(":remapping " + input.getName() + " (Mixin reference map)");
 		// first, identify all of the mixin refmaps
 		Set<String> mixinRefmapFilenames = new HashSet<>();
 		// TODO: this is a lovely hack
@@ -139,6 +142,8 @@ public class ModProcessor {
 				throw new RuntimeException(e);
 			}
 
+			project.getLogger().lifecycle(":remapping " + input.getName() + " (Mixin reference maps)");
+
 			ZipUtil.transformEntries(
 					output,
 					mixinRefmapFilenames.stream()