fix line number remapping, add option to disable mixin refmap remapping (unnecessary in loader 0.4.0+, but needs testting)

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

@@ -46,6 +46,7 @@ public class LoomGradleExtension {
 	public String refmapName;
 	public String loaderLaunchMethod;
 	public boolean remapMod = true;
+	public boolean remapDependencyMixinRefMaps = true;
 	public boolean autoGenIDERuns = true;
 	public boolean extractJars = false;
 

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

@@ -25,15 +25,20 @@
 package net.fabricmc.loom;
 
 import net.fabricmc.loom.providers.MappingsProvider;
+import net.fabricmc.loom.providers.MinecraftAssetsProvider;
 import net.fabricmc.loom.providers.MinecraftLibraryProvider;
 import net.fabricmc.loom.task.*;
 import net.fabricmc.loom.task.fernflower.FernFlowerTask;
 import net.fabricmc.loom.util.LineNumberRemapper;
+import net.fabricmc.loom.util.progress.ProgressLogger;
+import net.fabricmc.stitch.util.StitchUtil;
 import org.gradle.api.Project;
 import org.gradle.api.tasks.TaskContainer;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.Locale;
 
 public class LoomGradlePlugin extends AbstractPlugin {
@@ -71,8 +76,8 @@ public class LoomGradlePlugin extends AbstractPlugin {
 			MinecraftLibraryProvider libraryProvider = extension.getMinecraftProvider().libraryProvider;
 			MappingsProvider mappingsProvider = extension.getMappingsProvider();
 			File mappedJar = mappingsProvider.mappedProvider.getMappedJar();
-			File sourcesJar = getMappedByproduct(project, "-sources-tmp.jar");
+			File linemappedJarTmp = getMappedByproduct(project, "-linemapped.jar.tmp");
-			File sourcesFinalJar = getMappedByproduct(project, "-sources.jar");
+			File sourcesJar = getMappedByproduct(project, "-sources.jar");
 			File linemapFile = getMappedByproduct(project, "-sources.lmap");
 
 			task.setInput(mappedJar);
@@ -80,23 +85,33 @@ public class LoomGradlePlugin extends AbstractPlugin {
 			task.setLineMapFile(linemapFile);
 			task.setLibraries(libraryProvider.getLibraries());
 
-			if (sourcesJar.exists()) {
-				sourcesJar.delete();
-			}
-
 			task.doLast((tt) -> {
-				project.getLogger().lifecycle(":readjusting line numbers");
+				project.getLogger().lifecycle(":adjusting line numbers");
 				LineNumberRemapper remapper = new LineNumberRemapper();
 				remapper.readMappings(linemapFile);
 
-				try {
+				ProgressLogger progressLogger = ProgressLogger.getProgressFactory(project, FernFlowerTask.class.getName());
-					remapper.process(sourcesJar.toPath(), sourcesFinalJar.toPath());
+				progressLogger.start("Adjusting line numbers", "linemap");
+
+				try (StitchUtil.FileSystemDelegate inFs = StitchUtil.getJarFileSystem(mappedJar, true);
+				     StitchUtil.FileSystemDelegate outFs = StitchUtil.getJarFileSystem(linemappedJarTmp, true)) {
+					remapper.process(progressLogger, inFs.get().getPath("/"), outFs.get().getPath("/"));
 				} catch (IOException e) {
 					throw new RuntimeException(e);
 				}
 
-				if (sourcesJar.exists()) {
+				progressLogger.completed();
-					sourcesJar.delete();
+
+				Path mappedJarPath = mappedJar.toPath();
+				Path linemappedJarTmpPath = linemappedJarTmp.toPath();
+
+				if (Files.exists(linemappedJarTmpPath)) {
+					try {
+						Files.deleteIfExists(mappedJarPath);
+						Files.move(linemappedJarTmpPath, mappedJarPath);
+					} catch (IOException e) {
+						throw new RuntimeException(e);
+					}
 				}
 			});
 		});

src/main/java/net/fabricmc/loom/task/fernflower/ThreadSafeResultSaver.java

@@ -74,7 +74,7 @@ public class ThreadSafeResultSaver implements IResultSaver, IFabricResultSaver {
             try {
                 lineMapWriter = new PrintWriter(new FileWriter(lineMapFile.get()));
             } catch (IOException e) {
-                throw new RuntimeException("Unable to create LineMap file.", e);
+                throw new RuntimeException("Unable to create line mapping file: " + lineMapFile.get(), e);
             }
         }
     }
@@ -100,16 +100,15 @@ public class ThreadSafeResultSaver implements IResultSaver, IFabricResultSaver {
             }
             if (mapping != null && lineMapWriter != null) {
                 int maxLine = 0;
-                int maxLineDist = 0;
+                int maxLineDest = 0;
-                // 2 loops here is meh, perhaps merge with a buffer?
+                StringBuilder builder = new StringBuilder();
                 for (int i = 0; i < mapping.length; i += 2) {
                     maxLine = Math.max(maxLine, mapping[i]);
-                    maxLineDist = Math.max(maxLineDist, mapping[i + 1]);
+                    maxLineDest = Math.max(maxLineDest, mapping[i + 1]);
-                }
+                    builder.append("\t").append(mapping[i]).append("\t").append(mapping[i + 1]).append("\n");
-                lineMapWriter.println(qualifiedName + "\t" + maxLine + "\t" + maxLineDist);
-                for (int i = 0; i < mapping.length; i += 2) {
-                    lineMapWriter.println("\t" + mapping[i] + "\t" + mapping[i + 1]);
                 }
+                lineMapWriter.println(qualifiedName + "\t" + maxLine + "\t" + maxLineDest);
+                lineMapWriter.println(builder.toString());
             }
         });
     }

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

@@ -24,6 +24,8 @@
 
 package net.fabricmc.loom.util;
 
+import net.fabricmc.loom.util.progress.ProgressLogger;
+import org.gradle.api.logging.Logger;
 import org.objectweb.asm.*;
 
 import java.io.*;
@@ -56,9 +58,9 @@ public class LineNumberRemapper {
                     if (line.charAt(0) != '\t') {
                         clazz = lineMap.computeIfAbsent(segs[0], RClass::new);
                         clazz.maxLine = Integer.parseInt(segs[1]);
-                        clazz.maxLineDist = Integer.parseInt(segs[2]);
+                        clazz.maxLineDest = Integer.parseInt(segs[2]);
                     } else {
-                        clazz.lineMap.put(Integer.parseInt(segs[0]), (Integer) Integer.parseInt(segs[1]));
+                        clazz.lineMap.put(Integer.parseInt(segs[0]), Integer.parseInt(segs[1]));
                     }
                     i++;
                 }
@@ -70,7 +72,7 @@ public class LineNumberRemapper {
         }
     }
 
-    public void process(Path input, Path output) throws IOException {
+    public void process(ProgressLogger logger, Path input, Path output) throws IOException {
         Files.walkFileTree(input, new SimpleFileVisitor<Path>() {
             @Override
             public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
@@ -86,7 +88,11 @@ public class LineNumberRemapper {
                         Files.delete(dst);
                     }
                     String idx = rel.substring(0, rel.length() - 6);
-                    int dollarPos = idx.indexOf('$');//This makes the assumption that only Java classes are to be remapped.
+                    if (logger != null) {
+                        logger.progress("Remapping " + idx);
+                    }
+
+                    int dollarPos = idx.indexOf('$'); //This makes the assumption that only Java classes are to be remapped.
                     if (dollarPos >= 0) {
                         idx = idx.substring(0, dollarPos);
                     }
@@ -127,13 +133,13 @@ public class LineNumberRemapper {
                     if (tLine <= 0) {
                         super.visitLineNumber(line, start);
                     } else if (tLine >= rClass.maxLine) {
-                        super.visitLineNumber(rClass.maxLineDist, start);
+                        super.visitLineNumber(rClass.maxLineDest, start);
                     } else {
                         Integer matchedLine = null;
-                        while (tLine <= rClass.maxLine && ((matchedLine = rClass.lineMap.get(tLine)) != null)) {
+                        while (tLine <= rClass.maxLine && ((matchedLine = rClass.lineMap.get(tLine)) == null)) {
                             tLine++;
                         }
-                        super.visitLineNumber(matchedLine != null ? matchedLine : rClass.maxLineDist, start);
+                        super.visitLineNumber(matchedLine != null ? matchedLine : rClass.maxLineDest, start);
                     }
                 }
             };
@@ -144,7 +150,7 @@ public class LineNumberRemapper {
 
         private final String name;
         private int maxLine;
-        private int maxLineDist;
+        private int maxLineDest;
         private Map<Integer, Integer> lineMap = new HashMap<>();
 
         private RClass(String name) {

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

@@ -182,11 +182,13 @@ public class ModProcessor {
 			throw new RuntimeException("Failed to remap JAR to " + toM + " file not found: " + output.getAbsolutePath());
 		}
 
+		if (extension.remapDependencyMixinRefMaps) {
 			if (MixinRefmapHelper.transformRefmaps(remapper, output)) {
 				project.getLogger().lifecycle(":remapping " + input.getName() + " (Mixin reference maps)");
 				remapper.finish();
 			}
 		}
+	}
 
 	static void readInstallerJson(File file, Project project){
 		try {