Paper/patches/server/0020-Plugin-remapping.patch

From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
From: Jason Penilla <11360596+jpenilla@users.noreply.github.com>
Date: Sat, 29 Oct 2022 15:22:32 -0700
Subject: [PATCH] Plugin remapping

Co-authored-by: Nassim Jahnke <nassim@njahnke.dev>

diff --git a/build.gradle.kts b/build.gradle.kts
index 429fcd5927cf3259e8cdc83fadf78b41a38eb3bf..fa3476acb77ce5d1247244808ead5b2a994e5fc7 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -60,6 +60,7 @@ dependencies {
     testImplementation("org.ow2.asm:asm-tree:9.7.1")
     testImplementation("org.junit-pioneer:junit-pioneer:2.2.0") // Paper - CartesianTest
     implementation("net.neoforged:srgutils:1.0.9") // Paper - mappings handling
+    implementation("net.neoforged:AutoRenamingTool:2.0.3") // Paper - remap plugins
 }
 
 paperweight {
@@ -187,20 +188,41 @@ val runtimeClasspathWithoutVanillaServer = configurations.runtimeClasspath.flatM
         runtime.filterNot { it.asFile.absolutePath == vanilla }
     }
 
-tasks.registerRunTask("runServerJar") {
-    description = "Spin up a test server from the serverJar archiveFile"
-    classpath(tasks.serverJar.flatMap { it.archiveFile })
+tasks.registerRunTask("runServer") {
+    description = "Spin up a test server from the Mojang mapped server jar"
+    classpath(tasks.includeMappings.flatMap { it.outputJar })
     classpath(runtimeClasspathWithoutVanillaServer)
 }
 
-tasks.registerRunTask("runReobf") {
+tasks.registerRunTask("runReobfServer") {
     description = "Spin up a test server from the reobfJar output jar"
     classpath(tasks.reobfJar.flatMap { it.outputJar })
     classpath(runtimeClasspathWithoutVanillaServer)
 }
 
-tasks.registerRunTask("runDev") {
-    description = "Spin up a non-relocated Mojang-mapped test server"
+tasks.registerRunTask("runDevServer") {
+    description = "Spin up a test server without assembling a jar"
     classpath(sourceSets.main.map { it.runtimeClasspath })
     jvmArgs("-DPaper.pushPaperAssetsRoot=true")
 }
+
+tasks.registerRunTask("runBundler") {
+    description = "Spin up a test server from the Mojang mapped bundler jar"
+    classpath(rootProject.tasks.named<io.papermc.paperweight.tasks.CreateBundlerJar>("createMojmapBundlerJar").flatMap { it.outputZip })
+    mainClass.set(null as String?)
+}
+tasks.registerRunTask("runReobfBundler") {
+    description = "Spin up a test server from the reobf bundler jar"
+    classpath(rootProject.tasks.named<io.papermc.paperweight.tasks.CreateBundlerJar>("createReobfBundlerJar").flatMap { it.outputZip })
+    mainClass.set(null as String?)
+}
+tasks.registerRunTask("runPaperclip") {
+    description = "Spin up a test server from the Mojang mapped Paperclip jar"
+    classpath(rootProject.tasks.named<io.papermc.paperweight.tasks.CreatePaperclipJar>("createMojmapPaperclipJar").flatMap { it.outputZip })
+    mainClass.set(null as String?)
+}
+tasks.registerRunTask("runReobfPaperclip") {
+    description = "Spin up a test server from the reobf Paperclip jar"
+    classpath(rootProject.tasks.named<io.papermc.paperweight.tasks.CreatePaperclipJar>("createReobfPaperclipJar").flatMap { it.outputZip })
+    mainClass.set(null as String?)
+}
diff --git a/src/main/java/io/papermc/paper/plugin/PluginInitializerManager.java b/src/main/java/io/papermc/paper/plugin/PluginInitializerManager.java
index 708e5bb9bbf0476fcc2c4b92c6830b094703b43e..49d8e207795997e5deaf830eb971067f84bfc791 100644
--- a/src/main/java/io/papermc/paper/plugin/PluginInitializerManager.java
+++ b/src/main/java/io/papermc/paper/plugin/PluginInitializerManager.java
@@ -6,10 +6,12 @@ import io.papermc.paper.plugin.entrypoint.Entrypoint;
 import io.papermc.paper.plugin.entrypoint.LaunchEntryPointHandler;
 import io.papermc.paper.plugin.provider.PluginProvider;
 import io.papermc.paper.plugin.provider.type.paper.PaperPluginParent;
+import io.papermc.paper.pluginremap.PluginRemapper;
+import java.util.function.Function;
 import joptsimple.OptionSet;
 import net.minecraft.server.dedicated.DedicatedServer;
 import org.bukkit.configuration.file.YamlConfiguration;
-import org.bukkit.craftbukkit.CraftServer;
+import org.bukkit.plugin.java.LibraryLoader;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.slf4j.Logger;
@@ -25,10 +27,15 @@ public class PluginInitializerManager {
     private static PluginInitializerManager impl;
     private final Path pluginDirectory;
     private final Path updateDirectory;
+    public final io.papermc.paper.pluginremap.@org.checkerframework.checker.nullness.qual.MonotonicNonNull PluginRemapper pluginRemapper; // Paper
 
     PluginInitializerManager(final Path pluginDirectory, final Path updateDirectory) {
         this.pluginDirectory = pluginDirectory;
         this.updateDirectory = updateDirectory;
+        this.pluginRemapper = Boolean.getBoolean("paper.disablePluginRemapping")
+            ? null
+            : PluginRemapper.create(pluginDirectory);
+        LibraryLoader.REMAPPER = this.pluginRemapper == null ? Function.identity() : this.pluginRemapper::remapLibraries;
     }
 
     private static PluginInitializerManager parse(@NotNull final OptionSet minecraftOptionSet) throws Exception {
@@ -96,6 +103,7 @@ public class PluginInitializerManager {
     public static void load(OptionSet optionSet) throws Exception {
         // We have to load the bukkit configuration inorder to get the update folder location.
         io.papermc.paper.plugin.PluginInitializerManager pluginSystem = io.papermc.paper.plugin.PluginInitializerManager.init(optionSet);
+        if (pluginSystem.pluginRemapper != null) pluginSystem.pluginRemapper.loadingPlugins();
 
         // Register the default plugin directory
         io.papermc.paper.plugin.util.EntrypointUtil.registerProvidersFromSource(io.papermc.paper.plugin.provider.source.DirectoryProviderSource.INSTANCE, pluginSystem.pluginDirectoryPath());
diff --git a/src/main/java/io/papermc/paper/plugin/loader/PaperClasspathBuilder.java b/src/main/java/io/papermc/paper/plugin/loader/PaperClasspathBuilder.java
index f38ecd7f65dc24e4a3f0bc675e3730287ac353f1..f576060c8fe872772bbafe2016fc9b83a3c095f1 100644
--- a/src/main/java/io/papermc/paper/plugin/loader/PaperClasspathBuilder.java
+++ b/src/main/java/io/papermc/paper/plugin/loader/PaperClasspathBuilder.java
@@ -1,5 +1,6 @@
 package io.papermc.paper.plugin.loader;
 
+import io.papermc.paper.plugin.PluginInitializerManager;
 import io.papermc.paper.plugin.bootstrap.PluginProviderContext;
 import io.papermc.paper.plugin.loader.library.ClassPathLibrary;
 import io.papermc.paper.plugin.loader.library.PaperLibraryStore;
@@ -45,9 +46,12 @@ public class PaperClasspathBuilder implements PluginClasspathBuilder {
         }
 
         List<Path> paths = paperLibraryStore.getPaths();
+        if (PluginInitializerManager.instance().pluginRemapper != null) {
+            paths = PluginInitializerManager.instance().pluginRemapper.remapLibraries(paths);
+        }
         URL[] urls = new URL[paths.size()];
         for (int i = 0; i < paths.size(); i++) {
-            Path path = paperLibraryStore.getPaths().get(i);
+            Path path = paths.get(i);
             try {
                 urls[i] = path.toUri().toURL();
             } catch (MalformedURLException e) {
diff --git a/src/main/java/io/papermc/paper/plugin/provider/source/DirectoryProviderSource.java b/src/main/java/io/papermc/paper/plugin/provider/source/DirectoryProviderSource.java
index 226f457db6c1461c943c157b2b91e7450abc9dc6..0846d3a904e470ae1920c5c8be3df9c5dfc3de27 100644
--- a/src/main/java/io/papermc/paper/plugin/provider/source/DirectoryProviderSource.java
+++ b/src/main/java/io/papermc/paper/plugin/provider/source/DirectoryProviderSource.java
@@ -17,7 +17,7 @@ import org.slf4j.Logger;
 public class DirectoryProviderSource implements ProviderSource<Path, List<Path>> {
 
     public static final DirectoryProviderSource INSTANCE = new DirectoryProviderSource();
-    private static final FileProviderSource FILE_PROVIDER_SOURCE = new FileProviderSource("Directory '%s'"::formatted);
+    private static final FileProviderSource FILE_PROVIDER_SOURCE = new FileProviderSource("Directory '%s'"::formatted, false); // Paper - Remap plugins
     private static final Logger LOGGER = LogUtils.getClassLogger();
 
     @Override
@@ -37,6 +37,11 @@ public class DirectoryProviderSource implements ProviderSource<Path, List<Path>>
                 LOGGER.error("Error preparing plugin context: " + e.getMessage(), e);
             }
         });
+        // Paper start - Remap plugins
+        if (io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper != null) {
+            return io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper.rewritePluginDirectory(files);
+        }
+        // Paper end - Remap plugins
         return files;
     }
 
diff --git a/src/main/java/io/papermc/paper/plugin/provider/source/FileProviderSource.java b/src/main/java/io/papermc/paper/plugin/provider/source/FileProviderSource.java
index 5b58df8df7efca0f67e3a14dd71051dfd7a26079..6b8ed8a0baaf4a57d20e57cec3400af5561ddd79 100644
--- a/src/main/java/io/papermc/paper/plugin/provider/source/FileProviderSource.java
+++ b/src/main/java/io/papermc/paper/plugin/provider/source/FileProviderSource.java
@@ -24,9 +24,15 @@ import java.util.jar.JarFile;
 public class FileProviderSource implements ProviderSource<Path, Path> {
 
     private final Function<Path, String> contextChecker;
+    private final boolean applyRemap;
 
-    public FileProviderSource(Function<Path, String> contextChecker) {
+    public FileProviderSource(Function<Path, String> contextChecker, boolean applyRemap) {
         this.contextChecker = contextChecker;
+        this.applyRemap = applyRemap;
+    }
+
+    public FileProviderSource(Function<Path, String> contextChecker) {
+        this(contextChecker, true);
     }
 
     @Override
@@ -50,6 +56,11 @@ public class FileProviderSource implements ProviderSource<Path, Path> {
         } catch (Exception exception) {
             throw new RuntimeException(source + " failed to update!", exception);
         }
+        // Paper start - Remap plugins
+        if (this.applyRemap && io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper != null) {
+            context = io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper.rewritePlugin(context);
+        }
+        // Paper end - Remap plugins
         return context;
     }
 
diff --git a/src/main/java/io/papermc/paper/plugin/provider/source/PluginFlagProviderSource.java b/src/main/java/io/papermc/paper/plugin/provider/source/PluginFlagProviderSource.java
index ac55ae0e30119556f01e2e36c20fc63a111fae5f..c2b60c74513544e5d96110c7c3ff80e8f1b686d1 100644
--- a/src/main/java/io/papermc/paper/plugin/provider/source/PluginFlagProviderSource.java
+++ b/src/main/java/io/papermc/paper/plugin/provider/source/PluginFlagProviderSource.java
@@ -14,7 +14,7 @@ import java.util.List;
 public class PluginFlagProviderSource implements ProviderSource<List<Path>, List<Path>> {
 
     public static final PluginFlagProviderSource INSTANCE = new PluginFlagProviderSource();
-    private static final FileProviderSource FILE_PROVIDER_SOURCE = new FileProviderSource("File '%s' specified through 'add-plugin' argument"::formatted);
+    private static final FileProviderSource FILE_PROVIDER_SOURCE = new FileProviderSource("File '%s' specified through 'add-plugin' argument"::formatted, false);
     private static final Logger LOGGER = LogUtils.getClassLogger();
 
     @Override
@@ -27,6 +27,11 @@ public class PluginFlagProviderSource implements ProviderSource<List<Path>, List
                 LOGGER.error("Error preparing plugin context: " + e.getMessage(), e);
             }
         }
+        // Paper start - Remap plugins
+        if (io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper != null && !files.isEmpty()) {
+            return io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper.rewriteExtraPlugins(files);
+        }
+        // Paper end - Remap plugins
         return files;
     }
 
diff --git a/src/main/java/io/papermc/paper/plugin/provider/type/PluginFileType.java b/src/main/java/io/papermc/paper/plugin/provider/type/PluginFileType.java
index 87128685015d550440a798028f50be24bc755f6c..8d0da6e46d4eb5eb05c3144510c4ef083559d0ec 100644
--- a/src/main/java/io/papermc/paper/plugin/provider/type/PluginFileType.java
+++ b/src/main/java/io/papermc/paper/plugin/provider/type/PluginFileType.java
@@ -22,9 +22,10 @@ import java.util.jar.JarFile;
  */
 public abstract class PluginFileType<T, C extends PluginMeta> {
 
+    public static final String PAPER_PLUGIN_YML = "paper-plugin.yml";
     private static final List<String> CONFIG_TYPES = new ArrayList<>();
     
-    public static final PluginFileType<PaperPluginParent, PaperPluginMeta> PAPER = new PluginFileType<>("paper-plugin.yml", PaperPluginParent.FACTORY) {
+    public static final PluginFileType<PaperPluginParent, PaperPluginMeta> PAPER = new PluginFileType<>(PAPER_PLUGIN_YML, PaperPluginParent.FACTORY) {
         @Override
         protected void register(EntrypointHandler entrypointHandler, PaperPluginParent parent) {
             PaperPluginParent.PaperBootstrapProvider bootstrapPluginProvider = null;
diff --git a/src/main/java/io/papermc/paper/pluginremap/DebugLogger.java b/src/main/java/io/papermc/paper/pluginremap/DebugLogger.java
new file mode 100644
index 0000000000000000000000000000000000000000..99e658e3a0f08dbd90b3cf48609613e8a085fd64
--- /dev/null
+++ b/src/main/java/io/papermc/paper/pluginremap/DebugLogger.java
@@ -0,0 +1,63 @@
+package io.papermc.paper.pluginremap;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.function.Consumer;
+import org.checkerframework.checker.nullness.qual.NonNull;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.checkerframework.framework.qual.DefaultQualifier;
+
+/**
+ * {@link PrintWriter}-backed logger implementation for use with {@link net.neoforged.art.api.Renamer} which
+ * only opens the backing writer and logs messages when the {@link PluginRemapper#DEBUG_LOGGING} system property
+ * is set to true.
+ */
+@DefaultQualifier(NonNull.class)
+final class DebugLogger implements Consumer<String>, AutoCloseable {
+    private final @Nullable PrintWriter writer;
+
+    DebugLogger(final Path logFile) {
+        try {
+            this.writer = createWriter(logFile);
+        } catch (final IOException ex) {
+            throw new RuntimeException("Failed to initialize DebugLogger for file '" + logFile + "'", ex);
+        }
+    }
+
+    @Override
+    public void accept(final String line) {
+        this.useWriter(writer -> writer.println(line));
+    }
+
+    @Override
+    public void close() {
+        this.useWriter(PrintWriter::close);
+    }
+
+    private void useWriter(final Consumer<PrintWriter> op) {
+        final @Nullable PrintWriter writer = this.writer;
+        if (writer != null) {
+            op.accept(writer);
+        }
+    }
+
+    Consumer<String> debug() {
+        return line -> this.accept("[debug]: " + line);
+    }
+
+    static DebugLogger forOutputFile(final Path outputFile) {
+        return new DebugLogger(outputFile.resolveSibling(outputFile.getFileName() + ".log"));
+    }
+
+    private static @Nullable PrintWriter createWriter(final Path logFile) throws IOException {
+        if (!PluginRemapper.DEBUG_LOGGING) {
+            return null;
+        }
+        if (!Files.exists(logFile.getParent())) {
+            Files.createDirectories(logFile.getParent());
+        }
+        return new PrintWriter(logFile.toFile());
+    }
+}
diff --git a/src/main/java/io/papermc/paper/pluginremap/InsertManifestAttribute.java b/src/main/java/io/papermc/paper/pluginremap/InsertManifestAttribute.java
new file mode 100644
index 0000000000000000000000000000000000000000..d738b31f0005aca352a511c1a57e76b627fca2dd
--- /dev/null
+++ b/src/main/java/io/papermc/paper/pluginremap/InsertManifestAttribute.java
@@ -0,0 +1,69 @@
+package io.papermc.paper.pluginremap;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+import java.util.jar.Attributes;
+import java.util.jar.Manifest;
+import net.neoforged.art.api.Transformer;
+
+final class InsertManifestAttribute implements Transformer {
+    static final String PAPERWEIGHT_NAMESPACE_MANIFEST_KEY = "paperweight-mappings-namespace";
+    static final String MOJANG_NAMESPACE = "mojang";
+    static final String MOJANG_PLUS_YARN_NAMESPACE = "mojang+yarn";
+    static final String SPIGOT_NAMESPACE = "spigot";
+    static final Set<String> KNOWN_NAMESPACES = Set.of(MOJANG_NAMESPACE, MOJANG_PLUS_YARN_NAMESPACE, SPIGOT_NAMESPACE);
+
+    private final String mainAttributesKey;
+    private final String namespace;
+    private final boolean createIfMissing;
+    private volatile boolean visitedManifest = false;
+
+    static Transformer addNamespaceManifestAttribute(final String namespace) {
+        return new InsertManifestAttribute(PAPERWEIGHT_NAMESPACE_MANIFEST_KEY, namespace, true);
+    }
+
+    InsertManifestAttribute(
+        final String mainAttributesKey,
+        final String namespace,
+        final boolean createIfMissing
+    ) {
+        this.mainAttributesKey = mainAttributesKey;
+        this.namespace = namespace;
+        this.createIfMissing = createIfMissing;
+    }
+
+    @Override
+    public ManifestEntry process(final ManifestEntry entry) {
+        this.visitedManifest = true;
+        try {
+            final Manifest manifest = new Manifest(new ByteArrayInputStream(entry.getData()));
+            manifest.getMainAttributes().putValue(this.mainAttributesKey, this.namespace);
+            final ByteArrayOutputStream out = new ByteArrayOutputStream();
+            manifest.write(out);
+            return ManifestEntry.create(Entry.STABLE_TIMESTAMP, out.toByteArray());
+        } catch (final IOException e) {
+            throw new RuntimeException("Failed to modify manifest", e);
+        }
+    }
+
+    @Override
+    public Collection<? extends Entry> getExtras() {
+        if (!this.visitedManifest && this.createIfMissing) {
+            final Manifest manifest = new Manifest();
+            manifest.getMainAttributes().put(Attributes.Name.MANIFEST_VERSION, "1.0");
+            manifest.getMainAttributes().putValue(this.mainAttributesKey, this.namespace);
+            final ByteArrayOutputStream out = new ByteArrayOutputStream();
+            try {
+                manifest.write(out);
+            } catch (final IOException e) {
+                throw new RuntimeException("Failed to write manifest", e);
+            }
+            return List.of(ManifestEntry.create(Entry.STABLE_TIMESTAMP, out.toByteArray()));
+        }
+        return Transformer.super.getExtras();
+    }
+}
diff --git a/src/main/java/io/papermc/paper/pluginremap/PluginRemapper.java b/src/main/java/io/papermc/paper/pluginremap/PluginRemapper.java
new file mode 100644
index 0000000000000000000000000000000000000000..28857d0c9b53f2068d51b8f09ef40df7a2b97502
--- /dev/null
+++ b/src/main/java/io/papermc/paper/pluginremap/PluginRemapper.java
@@ -0,0 +1,438 @@
+package io.papermc.paper.pluginremap;
+
+import com.google.common.util.concurrent.ThreadFactoryBuilder;
+import com.mojang.logging.LogUtils;
+import io.papermc.paper.plugin.provider.type.PluginFileType;
+import io.papermc.paper.util.AtomicFiles;
+import io.papermc.paper.util.MappingEnvironment;
+import io.papermc.paper.util.concurrent.ScalingThreadPool;
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.CompletionException;
+import java.util.concurrent.Executor;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
+import java.util.function.Predicate;
+import java.util.function.Supplier;
+import java.util.jar.Manifest;
+import java.util.stream.Stream;
+import net.minecraft.DefaultUncaughtExceptionHandlerWithName;
+import net.minecraft.util.ExceptionCollector;
+import net.neoforged.art.api.Renamer;
+import net.neoforged.art.api.SignatureStripperConfig;
+import net.neoforged.art.api.Transformer;
+import net.neoforged.srgutils.IMappingFile;
+import org.checkerframework.checker.nullness.qual.NonNull;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.checkerframework.framework.qual.DefaultQualifier;
+import org.slf4j.Logger;
+
+import static io.papermc.paper.pluginremap.InsertManifestAttribute.addNamespaceManifestAttribute;
+
+@DefaultQualifier(NonNull.class)
+public final class PluginRemapper {
+    public static final boolean DEBUG_LOGGING = Boolean.getBoolean("Paper.PluginRemapperDebug");
+    private static final String PAPER_REMAPPED = ".paper-remapped";
+    private static final String UNKNOWN_ORIGIN = "unknown-origin";
+    private static final String LIBRARIES = "libraries";
+    private static final String EXTRA_PLUGINS = "extra-plugins";
+    private static final String REMAP_CLASSPATH = "remap-classpath";
+    private static final String REVERSED_MAPPINGS = "mappings/reversed";
+    private static final Logger LOGGER = LogUtils.getClassLogger();
+
+    private final ExecutorService threadPool;
+    private final ReobfServer reobf;
+    private final RemappedPluginIndex remappedPlugins;
+    private final RemappedPluginIndex extraPlugins;
+    private final UnknownOriginRemappedPluginIndex unknownOrigin;
+    private final UnknownOriginRemappedPluginIndex libraries;
+    private @Nullable CompletableFuture<IMappingFile> reversedMappings;
+
+    public PluginRemapper(final Path pluginsDir) {
+        this.threadPool = createThreadPool();
+        final CompletableFuture<IMappingFile> mappings = CompletableFuture.supplyAsync(PluginRemapper::loadReobfMappings, this.threadPool);
+        final Path remappedPlugins = pluginsDir.resolve(PAPER_REMAPPED);
+        this.reversedMappings = this.reversedMappingsFuture(() -> mappings, remappedPlugins, this.threadPool);
+        this.reobf = new ReobfServer(remappedPlugins.resolve(REMAP_CLASSPATH), mappings, this.threadPool);
+        this.remappedPlugins = new RemappedPluginIndex(remappedPlugins, false);
+        this.extraPlugins = new RemappedPluginIndex(this.remappedPlugins.dir().resolve(EXTRA_PLUGINS), true);
+        this.unknownOrigin = new UnknownOriginRemappedPluginIndex(this.remappedPlugins.dir().resolve(UNKNOWN_ORIGIN));
+        this.libraries = new UnknownOriginRemappedPluginIndex(this.remappedPlugins.dir().resolve(LIBRARIES));
+    }
+
+    public static @Nullable PluginRemapper create(final Path pluginsDir) {
+        if (MappingEnvironment.reobf() || !MappingEnvironment.hasMappings()) {
+            return null;
+        }
+
+        return new PluginRemapper(pluginsDir);
+    }
+
+    public void shutdown() {
+        this.threadPool.shutdown();
+        this.save(true);
+        boolean didShutdown;
+        try {
+            didShutdown = this.threadPool.awaitTermination(3L, TimeUnit.SECONDS);
+        } catch (final InterruptedException ex) {
+            didShutdown = false;
+        }
+        if (!didShutdown) {
+            this.threadPool.shutdownNow();
+        }
+    }
+
+    public void save(final boolean clean) {
+        this.remappedPlugins.write();
+        this.extraPlugins.write();
+        this.unknownOrigin.write(clean);
+        this.libraries.write(clean);
+    }
+
+    // Called on startup and reload
+    public void loadingPlugins() {
+        if (this.reversedMappings == null) {
+            this.reversedMappings = this.reversedMappingsFuture(
+                () -> CompletableFuture.supplyAsync(PluginRemapper::loadReobfMappings, this.threadPool),
+                this.remappedPlugins.dir(),
+                this.threadPool
+            );
+        }
+    }
+
+    // Called after all plugins enabled during startup/reload
+    public void pluginsEnabled() {
+        this.reversedMappings = null;
+        this.save(false);
+    }
+
+    public List<Path> remapLibraries(final List<Path> libraries) {
+        final List<CompletableFuture<Path>> tasks = new ArrayList<>();
+        for (final Path lib : libraries) {
+            if (!lib.getFileName().toString().endsWith(".jar")) {
+                if (DEBUG_LOGGING) {
+                    LOGGER.info("Library '{}' is not a jar.", lib);
+                }
+                tasks.add(CompletableFuture.completedFuture(lib));
+                continue;
+            }
+            final @Nullable Path cached = this.libraries.getIfPresent(lib);
+            if (cached != null) {
+                if (DEBUG_LOGGING) {
+                    LOGGER.info("Library '{}' has not changed since last remap.", lib);
+                }
+                tasks.add(CompletableFuture.completedFuture(cached));
+                continue;
+            }
+            tasks.add(this.remapLibrary(this.libraries, lib));
+        }
+        return waitForAll(tasks);
+    }
+
+    public Path rewritePlugin(final Path plugin) {
+        // Already remapped
+        if (plugin.getParent().equals(this.remappedPlugins.dir())
+            || plugin.getParent().equals(this.extraPlugins.dir())) {
+            return plugin;
+        }
+
+        final @Nullable Path cached = this.unknownOrigin.getIfPresent(plugin);
+        if (cached != null) {
+            if (DEBUG_LOGGING) {
+                LOGGER.info("Plugin '{}' has not changed since last remap.", plugin);
+            }
+            return cached;
+        }
+
+        return this.remapPlugin(this.unknownOrigin, plugin).join();
+    }
+
+    public List<Path> rewriteExtraPlugins(final List<Path> plugins) {
+        final @Nullable List<Path> allCached = this.extraPlugins.getAllIfPresent(plugins);
+        if (allCached != null) {
+            if (DEBUG_LOGGING) {
+                LOGGER.info("All extra plugins have a remapped variant cached.");
+            }
+            return allCached;
+        }
+
+        final List<CompletableFuture<Path>> tasks = new ArrayList<>();
+        for (final Path file : plugins) {
+            final @Nullable Path cached = this.extraPlugins.getIfPresent(file);
+            if (cached != null) {
+                if (DEBUG_LOGGING) {
+                    LOGGER.info("Extra plugin '{}' has not changed since last remap.", file);
+                }
+                tasks.add(CompletableFuture.completedFuture(cached));
+                continue;
+            }
+            tasks.add(this.remapPlugin(this.extraPlugins, file));
+        }
+        return waitForAll(tasks);
+    }
+
+    public List<Path> rewritePluginDirectory(final List<Path> jars) {
+        final @Nullable List<Path> remappedJars = this.remappedPlugins.getAllIfPresent(jars);
+        if (remappedJars != null) {
+            if (DEBUG_LOGGING) {
+                LOGGER.info("All plugins have a remapped variant cached.");
+            }
+            return remappedJars;
+        }
+
+        final List<CompletableFuture<Path>> tasks = new ArrayList<>();
+        for (final Path file : jars) {
+            final @Nullable Path existingFile = this.remappedPlugins.getIfPresent(file);
+            if (existingFile != null) {
+                if (DEBUG_LOGGING) {
+                    LOGGER.info("Plugin '{}' has not changed since last remap.", file);
+                }
+                tasks.add(CompletableFuture.completedFuture(existingFile));
+                continue;
+            }
+
+            tasks.add(this.remapPlugin(this.remappedPlugins, file));
+        }
+        return waitForAll(tasks);
+    }
+
+    private static IMappingFile reverse(final IMappingFile mappings) {
+        if (DEBUG_LOGGING) {
+            LOGGER.info("Reversing mappings...");
+        }
+        final long start = System.currentTimeMillis();
+        final IMappingFile reversed = mappings.reverse();
+        if (DEBUG_LOGGING) {
+            LOGGER.info("Done reversing mappings in {}ms.", System.currentTimeMillis() - start);
+        }
+        return reversed;
+    }
+
+    private CompletableFuture<IMappingFile> reversedMappingsFuture(
+        final Supplier<CompletableFuture<IMappingFile>> mappingsFuture,
+        final Path remappedPlugins,
+        final Executor executor
+    ) {
+        return CompletableFuture.supplyAsync(() -> {
+            try {
+                final String mappingsHash = MappingEnvironment.mappingsHash();
+                final String fName = mappingsHash + ".tiny";
+                final Path reversedMappings1 = remappedPlugins.resolve(REVERSED_MAPPINGS);
+                final Path file = reversedMappings1.resolve(fName);
+                if (Files.isDirectory(reversedMappings1)) {
+                    if (Files.isRegularFile(file)) {
+                        return CompletableFuture.completedFuture(
+                            loadMappings("Reversed", Files.newInputStream(file))
+                        );
+                    } else {
+                        for (final Path oldFile : list(reversedMappings1, Files::isRegularFile)) {
+                            Files.delete(oldFile);
+                        }
+                    }
+                } else {
+                    Files.createDirectories(reversedMappings1);
+                }
+                return mappingsFuture.get().thenApply(loadedMappings -> {
+                    final IMappingFile reversed = reverse(loadedMappings);
+                    try {
+                        AtomicFiles.atomicWrite(file, writeTo -> {
+                            reversed.write(writeTo, IMappingFile.Format.TINY, false);
+                        });
+                    } catch (final IOException e) {
+                        throw new RuntimeException("Failed to write reversed mappings", e);
+                    }
+                    return reversed;
+                });
+            } catch (final IOException e) {
+                throw new RuntimeException("Failed to load reversed mappings", e);
+            }
+        }, executor).thenCompose(f -> f);
+    }
+
+    private CompletableFuture<Path> remapPlugin(
+        final RemappedPluginIndex index,
+        final Path inputFile
+    ) {
+        return this.remap(index, inputFile, false);
+    }
+
+    private CompletableFuture<Path> remapLibrary(
+        final RemappedPluginIndex index,
+        final Path inputFile
+    ) {
+        return this.remap(index, inputFile, true);
+    }
+
+    /**
+     * Returns the remapped file if remapping was necessary, otherwise null.
+     *
+     * @param index     remapped plugin index
+     * @param inputFile input file
+     * @return remapped file, or inputFile if no remapping was necessary
+     */
+    private CompletableFuture<Path> remap(
+        final RemappedPluginIndex index,
+        final Path inputFile,
+        final boolean library
+    ) {
+        final Path destination = index.input(inputFile);
+
+        try (final FileSystem fs = FileSystems.newFileSystem(inputFile, new HashMap<>())) {
+            // Leave dummy files if no remapping is required, so that we can check if they exist without copying the whole file
+            final Path manifestPath = fs.getPath("META-INF/MANIFEST.MF");
+            final @Nullable String ns;
+            if (Files.exists(manifestPath)) {
+                final Manifest manifest;
+                try (final InputStream in = new BufferedInputStream(Files.newInputStream(manifestPath))) {
+                    manifest = new Manifest(in);
+                }
+                ns = manifest.getMainAttributes().getValue(InsertManifestAttribute.PAPERWEIGHT_NAMESPACE_MANIFEST_KEY);
+            } else {
+                ns = null;
+            }
+
+            if (ns != null && !InsertManifestAttribute.KNOWN_NAMESPACES.contains(ns)) {
+                throw new RuntimeException("Failed to remap plugin " + inputFile + " with unknown mapping namespace '" + ns + "'");
+            }
+
+            final boolean mojangMappedManifest = ns != null && (ns.equals(InsertManifestAttribute.MOJANG_NAMESPACE) || ns.equals(InsertManifestAttribute.MOJANG_PLUS_YARN_NAMESPACE));
+            if (library) {
+                if (mojangMappedManifest) {
+                    if (DEBUG_LOGGING) {
+                        LOGGER.info("Library '{}' is already Mojang mapped.", inputFile);
+                    }
+                    index.skip(inputFile);
+                    return CompletableFuture.completedFuture(inputFile);
+                } else if (ns == null) {
+                    if (DEBUG_LOGGING) {
+                        LOGGER.info("Library '{}' does not specify a mappings namespace (not remapping).", inputFile);
+                    }
+                    index.skip(inputFile);
+                    return CompletableFuture.completedFuture(inputFile);
+                }
+            } else {
+                if (mojangMappedManifest) {
+                    if (DEBUG_LOGGING) {
+                        LOGGER.info("Plugin '{}' is already Mojang mapped.", inputFile);
+                    }
+                    index.skip(inputFile);
+                    return CompletableFuture.completedFuture(inputFile);
+                } else if (ns == null && Files.exists(fs.getPath(PluginFileType.PAPER_PLUGIN_YML))) {
+                    if (DEBUG_LOGGING) {
+                        LOGGER.info("Plugin '{}' is a Paper plugin with no namespace specified.", inputFile);
+                    }
+                    index.skip(inputFile);
+                    return CompletableFuture.completedFuture(inputFile);
+                }
+            }
+        } catch (final IOException ex) {
+            return CompletableFuture.failedFuture(new RuntimeException("Failed to open plugin jar " + inputFile, ex));
+        }
+
+        return this.reobf.remapped().thenApplyAsync(reobfServer -> {
+            LOGGER.info("Remapping {} '{}'...", library ? "library" : "plugin", inputFile);
+            final long start = System.currentTimeMillis();
+            try (final DebugLogger logger = DebugLogger.forOutputFile(destination)) {
+                try (final Renamer renamer = Renamer.builder()
+                    .add(Transformer.renamerFactory(this.mappings(), false))
+                    .add(addNamespaceManifestAttribute(InsertManifestAttribute.MOJANG_PLUS_YARN_NAMESPACE))
+                    .add(Transformer.signatureStripperFactory(SignatureStripperConfig.ALL))
+                    .lib(reobfServer.toFile())
+                    .threads(1)
+                    .logger(logger)
+                    .debug(logger.debug())
+                    .build()) {
+                    renamer.run(inputFile.toFile(), destination.toFile());
+                }
+            } catch (final Exception ex) {
+                throw new RuntimeException("Failed to remap plugin jar '" + inputFile + "'", ex);
+            }
+            LOGGER.info("Done remapping {} '{}' in {}ms.", library ? "library" : "plugin", inputFile, System.currentTimeMillis() - start);
+            return destination;
+        }, this.threadPool);
+    }
+
+    private IMappingFile mappings() {
+        final @Nullable CompletableFuture<IMappingFile> mappings = this.reversedMappings;
+        if (mappings == null) {
+            return this.reversedMappingsFuture(
+                () -> CompletableFuture.supplyAsync(PluginRemapper::loadReobfMappings, Runnable::run),
+                this.remappedPlugins.dir(),
+                Runnable::run
+            ).join();
+        }
+        return mappings.join();
+    }
+
+    private static IMappingFile loadReobfMappings() {
+        return loadMappings("Reobf", MappingEnvironment.mappingsStream());
+    }
+
+    private static IMappingFile loadMappings(final String name, final InputStream stream) {
+        try (stream) {
+            if (DEBUG_LOGGING) {
+                LOGGER.info("Loading {} mappings...", name);
+            }
+            final long start = System.currentTimeMillis();
+            final IMappingFile load = IMappingFile.load(stream);
+            if (DEBUG_LOGGING) {
+                LOGGER.info("Done loading {} mappings in {}ms.", name, System.currentTimeMillis() - start);
+            }
+            return load;
+        } catch (final IOException ex) {
+            throw new RuntimeException("Failed to load " + name + " mappings", ex);
+        }
+    }
+
+    static List<Path> list(final Path dir, final Predicate<Path> filter) {
+        try (final Stream<Path> stream = Files.list(dir)) {
+            return stream.filter(filter).toList();
+        } catch (final IOException ex) {
+            throw new RuntimeException("Failed to list directory '" + dir + "'", ex);
+        }
+    }
+
+    private static List<Path> waitForAll(final List<CompletableFuture<Path>> tasks) {
+        final ExceptionCollector<Exception> collector = new ExceptionCollector<>();
+        final List<Path> ret = new ArrayList<>();
+        for (final CompletableFuture<Path> task : tasks) {
+            try {
+                ret.add(task.join());
+            } catch (final CompletionException ex) {
+                collector.add(ex);
+            }
+        }
+        try {
+            collector.throwIfPresent();
+        } catch (final Exception ex) {
+            // Don't hard fail during bootstrap/plugin loading. The plugin(s) in question will be skipped
+            LOGGER.error("Encountered exception remapping plugins", ex);
+        }
+        return ret;
+    }
+
+    private static ThreadPoolExecutor createThreadPool() {
+        return new ThreadPoolExecutor(
+            0,
+            4,
+            5L,
+            TimeUnit.SECONDS,
+            ScalingThreadPool.createUnboundedQueue(),
+            new ThreadFactoryBuilder()
+                .setNameFormat("Paper Plugin Remapper Thread - %1$d")
+                .setUncaughtExceptionHandler(new DefaultUncaughtExceptionHandlerWithName(LOGGER))
+                .build(),
+            ScalingThreadPool.defaultReEnqueuePolicy()
+        );
+    }
+}
diff --git a/src/main/java/io/papermc/paper/pluginremap/RemappedPluginIndex.java b/src/main/java/io/papermc/paper/pluginremap/RemappedPluginIndex.java
new file mode 100644
index 0000000000000000000000000000000000000000..86fc60452404d1f4609c25a90c4803ffb80dc8ab
--- /dev/null
+++ b/src/main/java/io/papermc/paper/pluginremap/RemappedPluginIndex.java
@@ -0,0 +1,212 @@
+package io.papermc.paper.pluginremap;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import com.mojang.logging.LogUtils;
+import io.papermc.paper.util.Hashing;
+import io.papermc.paper.util.MappingEnvironment;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.function.Function;
+import org.checkerframework.checker.nullness.qual.NonNull;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.checkerframework.framework.qual.DefaultQualifier;
+import org.slf4j.Logger;
+import org.spongepowered.configurate.loader.AtomicFiles;
+
+@DefaultQualifier(NonNull.class)
+class RemappedPluginIndex {
+    private static final Logger LOGGER = LogUtils.getLogger();
+    private static final Gson GSON = new GsonBuilder()
+        .setPrettyPrinting()
+        .create();
+    private static final String INDEX_FILE_NAME = "index.json";
+
+    protected final State state;
+    private final Path dir;
+    private final Path indexFile;
+    private final boolean handleDuplicateFileNames;
+
+    // todo maybe hash remapped variants to ensure they haven't changed? probably unneeded
+    static final class State {
+        final Map<String, String> hashes = new HashMap<>();
+        final Set<String> skippedHashes = new HashSet<>();
+        private final String mappingsHash = MappingEnvironment.mappingsHash();
+    }
+
+    RemappedPluginIndex(final Path dir, final boolean handleDuplicateFileNames) {
+        this.dir = dir;
+        this.handleDuplicateFileNames = handleDuplicateFileNames;
+        if (!Files.exists(this.dir)) {
+            try {
+                Files.createDirectories(this.dir);
+            } catch (final IOException ex) {
+                throw new RuntimeException(ex);
+            }
+        }
+
+        this.indexFile = dir.resolve(INDEX_FILE_NAME);
+        if (Files.isRegularFile(this.indexFile)) {
+            try {
+                this.state = this.readIndex();
+            } catch (final IOException e) {
+                throw new RuntimeException(e);
+            }
+        } else {
+            this.state = new State();
+        }
+    }
+
+    private State readIndex() throws IOException {
+        final State state;
+        try (final BufferedReader reader = Files.newBufferedReader(this.indexFile)) {
+            state = GSON.fromJson(reader, State.class);
+        }
+
+        // If mappings have changed, delete all cached files and create a new index
+        if (!state.mappingsHash.equals(MappingEnvironment.mappingsHash())) {
+            for (final String fileName : state.hashes.values()) {
+                Files.deleteIfExists(this.dir.resolve(fileName));
+            }
+            return new State();
+        }
+        return state;
+    }
+
+    Path dir() {
+        return this.dir;
+    }
+
+    /**
+     * Returns a list of cached paths if all of the input paths are present in the cache.
+     * The returned list may contain paths from different directories.
+     *
+     * @param paths plugin jar paths to check
+     * @return null if any of the paths are not present in the cache, otherwise a list of the cached paths
+     */
+    @Nullable List<Path> getAllIfPresent(final List<Path> paths) {
+        final Map<Path, String> hashCache = new HashMap<>();
+        final Function<Path, String> inputFileHash = path -> hashCache.computeIfAbsent(path, Hashing::sha256);
+
+        // Delete cached entries we no longer need
+        final Iterator<Map.Entry<String, String>> iterator = this.state.hashes.entrySet().iterator();
+        while (iterator.hasNext()) {
+            final Map.Entry<String, String> entry = iterator.next();
+            final String inputHash = entry.getKey();
+            final String fileName = entry.getValue();
+            if (paths.stream().anyMatch(path -> inputFileHash.apply(path).equals(inputHash))) {
+                // Hash is used, keep it
+                continue;
+            }
+
+            iterator.remove();
+            try {
+                Files.deleteIfExists(this.dir.resolve(fileName));
+            } catch (final IOException ex) {
+                throw new RuntimeException(ex);
+            }
+        }
+
+        // Also clear hashes of skipped files
+        this.state.skippedHashes.removeIf(hash -> paths.stream().noneMatch(path -> inputFileHash.apply(path).equals(hash)));
+
+        final List<Path> ret = new ArrayList<>();
+        for (final Path path : paths) {
+            final String inputHash = inputFileHash.apply(path);
+            if (this.state.skippedHashes.contains(inputHash)) {
+                // Add the original path
+                ret.add(path);
+                continue;
+            }
+
+            final @Nullable Path cached = this.getIfPresent(inputHash);
+            if (cached == null) {
+                // Missing the remapped file
+                return null;
+            }
+            ret.add(cached);
+        }
+        return ret;
+    }
+
+    private String createCachedFileName(final Path in) {
+        if (this.handleDuplicateFileNames) {
+            final String fileName = in.getFileName().toString();
+            final int i = fileName.lastIndexOf(".jar");
+            return fileName.substring(0, i) + "-" + System.currentTimeMillis() + ".jar";
+        }
+        return in.getFileName().toString();
+    }
+
+    /**
+     * Returns the given path if the file was previously skipped for being remapped, otherwise the cached path or null.
+     *
+     * @param in input file
+     * @return {@code in} if already remapped, the cached path if present, otherwise null
+     */
+    @Nullable Path getIfPresent(final Path in) {
+        final String inHash = Hashing.sha256(in);
+        if (this.state.skippedHashes.contains(inHash)) {
+            return in;
+        }
+        return this.getIfPresent(inHash);
+    }
+
+    /**
+     * Returns the cached path if a remapped file is present for the given hash, otherwise null.
+     *
+     * @param inHash hash of the input file
+     * @return the cached path if present, otherwise null
+     * @see #getIfPresent(Path)
+     */
+    protected @Nullable Path getIfPresent(final String inHash) {
+        final @Nullable String fileName = this.state.hashes.get(inHash);
+        if (fileName == null) {
+            return null;
+        }
+
+        final Path path = this.dir.resolve(fileName);
+        if (Files.exists(path)) {
+            return path;
+        }
+        return null;
+    }
+
+    Path input(final Path in) {
+        return this.input(in, Hashing.sha256(in));
+    }
+
+    /**
+     * Marks the given file as skipped for remapping.
+     *
+     * @param in input file
+     */
+    void skip(final Path in) {
+        this.state.skippedHashes.add(Hashing.sha256(in));
+    }
+
+    protected Path input(final Path in, final String hashString) {
+        final String name = this.createCachedFileName(in);
+        this.state.hashes.put(hashString, name);
+        return this.dir.resolve(name);
+    }
+
+    void write() {
+        try (final BufferedWriter writer = AtomicFiles.atomicBufferedWriter(this.indexFile, StandardCharsets.UTF_8)) {
+            GSON.toJson(this.state, writer);
+        } catch (final IOException ex) {
+            LOGGER.warn("Failed to write index file '{}'", this.indexFile, ex);
+        }
+    }
+}
diff --git a/src/main/java/io/papermc/paper/pluginremap/ReobfServer.java b/src/main/java/io/papermc/paper/pluginremap/ReobfServer.java
new file mode 100644
index 0000000000000000000000000000000000000000..aa5bf7ae042f3d43f7612d027ebef0e5c758ffc9
--- /dev/null
+++ b/src/main/java/io/papermc/paper/pluginremap/ReobfServer.java
@@ -0,0 +1,92 @@
+package io.papermc.paper.pluginremap;
+
+import com.mojang.logging.LogUtils;
+import io.papermc.paper.util.AtomicFiles;
+import io.papermc.paper.util.MappingEnvironment;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.Executor;
+import net.neoforged.art.api.Renamer;
+import net.neoforged.art.api.Transformer;
+import net.neoforged.art.internal.RenamerImpl;
+import net.neoforged.srgutils.IMappingFile;
+import org.checkerframework.checker.nullness.qual.NonNull;
+import org.checkerframework.framework.qual.DefaultQualifier;
+import org.slf4j.Logger;
+
+import static io.papermc.paper.pluginremap.InsertManifestAttribute.addNamespaceManifestAttribute;
+
+@DefaultQualifier(NonNull.class)
+final class ReobfServer {
+    private static final Logger LOGGER = LogUtils.getClassLogger();
+
+    private final Path remapClasspathDir;
+    private final CompletableFuture<Void> load;
+
+    ReobfServer(final Path remapClasspathDir, final CompletableFuture<IMappingFile> mappings, final Executor executor) {
+        this.remapClasspathDir = remapClasspathDir;
+        if (this.mappingsChanged()) {
+            this.load = mappings.thenAcceptAsync(this::remap, executor);
+        } else {
+            if (PluginRemapper.DEBUG_LOGGING) {
+				LOGGER.info("Have cached reobf server for current mappings.");
+			}
+            this.load = CompletableFuture.completedFuture(null);
+        }
+    }
+
+    CompletableFuture<Path> remapped() {
+        return this.load.thenApply($ -> this.remappedPath());
+    }
+
+    private Path remappedPath() {
+        return this.remapClasspathDir.resolve(MappingEnvironment.mappingsHash() + ".jar");
+    }
+
+    private boolean mappingsChanged() {
+        return !Files.exists(this.remappedPath());
+    }
+
+    private void remap(final IMappingFile mappings) {
+        try {
+            if (!Files.exists(this.remapClasspathDir)) {
+                Files.createDirectories(this.remapClasspathDir);
+            }
+            for (final Path file : PluginRemapper.list(this.remapClasspathDir, Files::isRegularFile)) {
+                Files.delete(file);
+            }
+        } catch (final IOException ex) {
+            throw new RuntimeException(ex);
+        }
+
+        LOGGER.info("Remapping server...");
+        final long startRemap = System.currentTimeMillis();
+        try (final DebugLogger log = DebugLogger.forOutputFile(this.remappedPath())) {
+            AtomicFiles.atomicWrite(this.remappedPath(), writeTo -> {
+                try (final RenamerImpl renamer = (RenamerImpl) Renamer.builder()
+                    .logger(log)
+                    .debug(log.debug())
+                    .threads(1)
+                    .add(Transformer.renamerFactory(mappings, false))
+                    .add(addNamespaceManifestAttribute(InsertManifestAttribute.SPIGOT_NAMESPACE))
+                    .build()) {
+                    renamer.run(serverJar().toFile(), writeTo.toFile(), true);
+                }
+            });
+        } catch (final Exception ex) {
+            throw new RuntimeException("Failed to remap server jar", ex);
+        }
+        LOGGER.info("Done remapping server in {}ms.", System.currentTimeMillis() - startRemap);
+    }
+
+    private static Path serverJar() {
+        try {
+            return Path.of(ReobfServer.class.getProtectionDomain().getCodeSource().getLocation().toURI());
+        } catch (final URISyntaxException ex) {
+            throw new RuntimeException(ex);
+        }
+    }
+}
diff --git a/src/main/java/io/papermc/paper/pluginremap/UnknownOriginRemappedPluginIndex.java b/src/main/java/io/papermc/paper/pluginremap/UnknownOriginRemappedPluginIndex.java
new file mode 100644
index 0000000000000000000000000000000000000000..ad53aab4fee16b76f6e4fd44e4b28d06fef80de4
--- /dev/null
+++ b/src/main/java/io/papermc/paper/pluginremap/UnknownOriginRemappedPluginIndex.java
@@ -0,0 +1,72 @@
+package io.papermc.paper.pluginremap;
+
+import com.mojang.logging.LogUtils;
+import io.papermc.paper.util.Hashing;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+import org.checkerframework.checker.nullness.qual.NonNull;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.checkerframework.framework.qual.DefaultQualifier;
+import org.slf4j.Logger;
+
+@DefaultQualifier(NonNull.class)
+final class UnknownOriginRemappedPluginIndex extends RemappedPluginIndex {
+    private static final Logger LOGGER = LogUtils.getLogger();
+
+    private final Set<String> used = new HashSet<>();
+
+    UnknownOriginRemappedPluginIndex(final Path dir) {
+        super(dir, true);
+    }
+
+    @Override
+    @Nullable Path getIfPresent(final Path in) {
+        final String hash = Hashing.sha256(in);
+        if (this.state.skippedHashes.contains(hash)) {
+            return in;
+        }
+
+        final @Nullable Path path = super.getIfPresent(hash);
+        if (path != null) {
+            this.used.add(hash);
+        }
+        return path;
+    }
+
+    @Override
+    Path input(final Path in) {
+        final String hash = Hashing.sha256(in);
+        this.used.add(hash);
+        return super.input(in, hash);
+    }
+
+    void write(final boolean clean) {
+        if (!clean) {
+            super.write();
+            return;
+        }
+
+        final Iterator<Map.Entry<String, String>> it = this.state.hashes.entrySet().iterator();
+        while (it.hasNext()) {
+            final Map.Entry<String, String> next = it.next();
+            if (this.used.contains(next.getKey())) {
+                continue;
+            }
+
+            // Remove unused mapped file
+            it.remove();
+            final Path file = this.dir().resolve(next.getValue());
+            try {
+                Files.deleteIfExists(file);
+            } catch (final IOException ex) {
+                LOGGER.warn("Failed to delete no longer needed cached jar '{}'", file, ex);
+            }
+        }
+        super.write();
+    }
+}
diff --git a/src/main/java/io/papermc/paper/util/AtomicFiles.java b/src/main/java/io/papermc/paper/util/AtomicFiles.java
new file mode 100644
index 0000000000000000000000000000000000000000..944250d2b8e1969f221b2f24cce7b1019c55fe01
--- /dev/null
+++ b/src/main/java/io/papermc/paper/util/AtomicFiles.java
@@ -0,0 +1,96 @@
+package io.papermc.paper.util;
+
+import java.io.IOException;
+import java.nio.file.AccessDeniedException;
+import java.nio.file.AtomicMoveNotSupportedException;
+import java.nio.file.CopyOption;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.util.concurrent.ThreadLocalRandom;
+import java.util.function.Consumer;
+import org.spongepowered.configurate.util.CheckedConsumer;
+
+// Stripped down version of https://github.com/jpenilla/squaremap/blob/7d7994b4096e5fc61364ea2d87e9aa4e14edf5c6/common/src/main/java/xyz/jpenilla/squaremap/common/util/FileUtil.java
+public final class AtomicFiles {
+
+    private AtomicFiles() {
+    }
+
+    public static void atomicWrite(final Path path, final CheckedConsumer<Path, IOException> op) throws IOException {
+        final Path tmp = tempFile(path);
+
+        try {
+            op.accept(tmp);
+            atomicMove(tmp, path, true);
+        } catch (final IOException ex) {
+            try {
+                Files.deleteIfExists(tmp);
+            } catch (final IOException ex1) {
+                ex.addSuppressed(ex1);
+            }
+            throw ex;
+        }
+    }
+
+    private static Path tempFile(final Path path) {
+        return path.resolveSibling("." + System.nanoTime() + "-" + ThreadLocalRandom.current().nextInt() + "-" + path.getFileName().toString() + ".tmp");    }
+
+    @SuppressWarnings("BusyWait") // not busy waiting
+    public static void atomicMove(final Path from, final Path to, final boolean replaceExisting) throws IOException {
+        final int maxRetries = 2;
+
+        try {
+            atomicMoveIfPossible(from, to, replaceExisting);
+        } catch (final AccessDeniedException ex) {
+            // Sometimes because of file locking this will fail... Let's just try again and hope for the best
+            // Thanks Windows!
+            int retries = 1;
+            while (true) {
+                try {
+                    // Pause for a bit
+                    Thread.sleep(10L * retries);
+                    atomicMoveIfPossible(from, to, replaceExisting);
+                    break; // success
+                } catch (final AccessDeniedException ex1) {
+                    ex.addSuppressed(ex1);
+                    if (retries == maxRetries) {
+                        throw ex;
+                    }
+                } catch (final InterruptedException interruptedException) {
+                    ex.addSuppressed(interruptedException);
+                    Thread.currentThread().interrupt();
+                    throw ex;
+                }
+                ++retries;
+            }
+        }
+    }
+
+    private static void atomicMoveIfPossible(final Path from, final Path to, final boolean replaceExisting) throws IOException {
+        final CopyOption[] options = replaceExisting
+            ? new CopyOption[]{StandardCopyOption.ATOMIC_MOVE, StandardCopyOption.REPLACE_EXISTING}
+            : new CopyOption[]{StandardCopyOption.ATOMIC_MOVE};
+
+        try {
+            Files.move(from, to, options);
+        } catch (final AtomicMoveNotSupportedException ex) {
+            Files.move(from, to, replaceExisting ? new CopyOption[]{StandardCopyOption.REPLACE_EXISTING} : new CopyOption[]{});
+        }
+    }
+
+    private static <T, X extends Throwable> Consumer<T> sneaky(final CheckedConsumer<T, X> consumer) {
+        return t -> {
+            try {
+                consumer.accept(t);
+            } catch (final Throwable thr) {
+                rethrow(thr);
+            }
+        };
+    }
+
+    @SuppressWarnings("unchecked")
+    private static <X extends Throwable> RuntimeException rethrow(final Throwable t) throws X {
+        throw (X) t;
+    }
+}
diff --git a/src/main/java/io/papermc/paper/util/Hashing.java b/src/main/java/io/papermc/paper/util/Hashing.java
new file mode 100644
index 0000000000000000000000000000000000000000..54c1324faa190a06bfa2b3b8f86928b4c51a57f8
--- /dev/null
+++ b/src/main/java/io/papermc/paper/util/Hashing.java
@@ -0,0 +1,50 @@
+package io.papermc.paper.util;
+
+import com.google.common.hash.HashCode;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Locale;
+import org.apache.commons.io.IOUtils;
+import org.checkerframework.checker.nullness.qual.NonNull;
+import org.checkerframework.framework.qual.DefaultQualifier;
+
+@DefaultQualifier(NonNull.class)
+public final class Hashing {
+    private Hashing() {
+    }
+
+    /**
+     * Hash the provided {@link InputStream} using SHA-256. Stream will be closed.
+     *
+     * @param stream input stream
+     * @return SHA-256 hash string
+     */
+    public static String sha256(final InputStream stream) {
+        try (stream) {
+            return com.google.common.hash.Hashing.sha256().hashBytes(IOUtils.toByteArray(stream)).toString().toUpperCase(Locale.ROOT);
+        } catch (final IOException ex) {
+            throw new RuntimeException("Failed to take hash of InputStream", ex);
+        }
+    }
+
+    /**
+     * Hash the provided file using SHA-256.
+     *
+     * @param file file
+     * @return SHA-256 hash string
+     */
+    public static String sha256(final Path file) {
+        if (!Files.isRegularFile(file)) {
+            throw new IllegalArgumentException("'" + file + "' is not a regular file!");
+        }
+        final HashCode hash;
+        try {
+            hash = com.google.common.io.Files.asByteSource(file.toFile()).hash(com.google.common.hash.Hashing.sha256());
+        } catch (final IOException ex) {
+            throw new RuntimeException("Failed to take hash of file '" + file + "'", ex);
+        }
+        return hash.toString().toUpperCase(Locale.ROOT);
+    }
+}
diff --git a/src/main/java/io/papermc/paper/util/MappingEnvironment.java b/src/main/java/io/papermc/paper/util/MappingEnvironment.java
new file mode 100644
index 0000000000000000000000000000000000000000..8e4229634d41a42b3d93948eebb77def7c0c72b1
--- /dev/null
+++ b/src/main/java/io/papermc/paper/util/MappingEnvironment.java
@@ -0,0 +1,65 @@
+package io.papermc.paper.util;
+
+import java.io.InputStream;
+import java.util.Objects;
+import java.util.jar.Manifest;
+import net.minecraft.world.entity.MobCategory;
+import org.checkerframework.checker.nullness.qual.NonNull;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.checkerframework.framework.qual.DefaultQualifier;
+
+@DefaultQualifier(NonNull.class)
+public final class MappingEnvironment {
+    private static final @Nullable String MAPPINGS_HASH = readMappingsHash();
+    private static final boolean REOBF = checkReobf();
+
+    private MappingEnvironment() {
+    }
+
+    public static boolean reobf() {
+        return REOBF;
+    }
+
+    public static boolean hasMappings() {
+        return MAPPINGS_HASH != null;
+    }
+
+    public static InputStream mappingsStream() {
+        return Objects.requireNonNull(mappingsStreamIfPresent(), "Missing mappings!");
+    }
+
+    public static @Nullable InputStream mappingsStreamIfPresent() {
+        return MappingEnvironment.class.getClassLoader().getResourceAsStream("META-INF/mappings/reobf.tiny");
+    }
+
+    public static String mappingsHash() {
+        return Objects.requireNonNull(MAPPINGS_HASH, "MAPPINGS_HASH");
+    }
+
+    private static @Nullable String readMappingsHash() {
+        final @Nullable Manifest manifest = JarManifests.manifest(MappingEnvironment.class);
+        if (manifest != null) {
+            final Object hash = manifest.getMainAttributes().getValue("Included-Mappings-Hash");
+            if (hash != null) {
+                return hash.toString();
+            }
+        }
+
+        final @Nullable InputStream stream = mappingsStreamIfPresent();
+        if (stream == null) {
+            return null;
+        }
+        return Hashing.sha256(stream);
+    }
+
+    @SuppressWarnings("ConstantConditions")
+    private static boolean checkReobf() {
+        final Class<?> clazz = MobCategory.class;
+        if (clazz.getSimpleName().equals("MobCategory")) {
+            return false;
+        } else if (clazz.getSimpleName().equals("EnumCreatureType")) {
+            return true;
+        }
+        throw new IllegalStateException();
+    }
+}
diff --git a/src/main/java/io/papermc/paper/util/ObfHelper.java b/src/main/java/io/papermc/paper/util/ObfHelper.java
index 9e6d48335b37fa5204bfebf396d748089884555b..6067be951c4c52c4b1da51efc01436b2c90ea3bf 100644
--- a/src/main/java/io/papermc/paper/util/ObfHelper.java
+++ b/src/main/java/io/papermc/paper/util/ObfHelper.java
@@ -80,10 +80,10 @@ public enum ObfHelper {
     }
 
     private static @Nullable Set<ClassMapping> loadMappingsIfPresent() {
-        try (final @Nullable InputStream mappingsInputStream = ObfHelper.class.getClassLoader().getResourceAsStream("META-INF/mappings/reobf.tiny")) {
-            if (mappingsInputStream == null) {
-                return null;
-            }
+        if (!MappingEnvironment.hasMappings()) {
+            return null;
+        }
+        try (final InputStream mappingsInputStream = MappingEnvironment.mappingsStream()) {
             final IMappingFile mappings = IMappingFile.load(mappingsInputStream); // Mappings are mojang->spigot
             final Set<ClassMapping> classes = new HashSet<>();
 
diff --git a/src/main/java/io/papermc/paper/util/concurrent/ScalingThreadPool.java b/src/main/java/io/papermc/paper/util/concurrent/ScalingThreadPool.java
new file mode 100644
index 0000000000000000000000000000000000000000..badff5d6ae6dd8d209c82bc7e8afe370db6148f2
--- /dev/null
+++ b/src/main/java/io/papermc/paper/util/concurrent/ScalingThreadPool.java
@@ -0,0 +1,85 @@
+package io.papermc.paper.util.concurrent;
+
+import java.util.concurrent.BlockingQueue;
+import java.util.concurrent.LinkedBlockingQueue;
+import java.util.concurrent.RejectedExecutionHandler;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
+
+/**
+ * Utilities for scaling thread pools.
+ *
+ * @see <a href="https://medium.com/@uditharosha/java-scale-first-executorservice-4245a63222df">Java Scale First ExecutorService — A myth or a reality</a>
+ */
+public final class ScalingThreadPool {
+    private ScalingThreadPool() {
+    }
+
+    public static RejectedExecutionHandler defaultReEnqueuePolicy() {
+        return reEnqueuePolicy(new ThreadPoolExecutor.AbortPolicy());
+    }
+
+    public static RejectedExecutionHandler reEnqueuePolicy(final RejectedExecutionHandler original) {
+        return new ReEnqueuePolicy(original);
+    }
+
+    public static <E> BlockingQueue<E> createUnboundedQueue() {
+        return new Queue<>();
+    }
+
+    public static <E> BlockingQueue<E> createQueue(final int capacity) {
+        return new Queue<>(capacity);
+    }
+
+    private static final class Queue<E> extends LinkedBlockingQueue<E> {
+        private final AtomicInteger idleThreads = new AtomicInteger(0);
+
+        private Queue() {
+            super();
+        }
+
+        private Queue(final int capacity) {
+            super(capacity);
+        }
+
+        @Override
+        public boolean offer(final E e) {
+            return this.idleThreads.get() > 0 && super.offer(e);
+        }
+
+        @Override
+        public E take() throws InterruptedException {
+            this.idleThreads.incrementAndGet();
+            try {
+                return super.take();
+            } finally {
+                this.idleThreads.decrementAndGet();
+            }
+        }
+
+        @Override
+        public E poll(final long timeout, final TimeUnit unit) throws InterruptedException {
+            this.idleThreads.incrementAndGet();
+            try {
+                return super.poll(timeout, unit);
+            } finally {
+                this.idleThreads.decrementAndGet();
+            }
+        }
+
+        @Override
+        public boolean add(final E e) {
+            return super.offer(e);
+        }
+    }
+
+    private record ReEnqueuePolicy(RejectedExecutionHandler originalHandler) implements RejectedExecutionHandler {
+        @Override
+        public void rejectedExecution(final Runnable r, final ThreadPoolExecutor executor) {
+            if (!executor.getQueue().add(r)) {
+                this.originalHandler.rejectedExecution(r, executor);
+            }
+        }
+    }
+}
diff --git a/src/main/java/net/minecraft/server/MinecraftServer.java b/src/main/java/net/minecraft/server/MinecraftServer.java
index afb67956031f4bcccee12f0ece4bb8a7e6f02cfc..3322865949fe5ddaab2dffc39260b75093f0f204 100644
--- a/src/main/java/net/minecraft/server/MinecraftServer.java
+++ b/src/main/java/net/minecraft/server/MinecraftServer.java
@@ -657,6 +657,7 @@ public abstract class MinecraftServer extends ReentrantBlockableEventLoop<TickTa
         }
 
         this.server.enablePlugins(org.bukkit.plugin.PluginLoadOrder.POSTWORLD);
+        if (io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper != null) io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper.pluginsEnabled(); // Paper - Remap plugins
         this.server.getPluginManager().callEvent(new ServerLoadEvent(ServerLoadEvent.LoadType.STARTUP));
         this.connection.acceptConnections();
     }
@@ -930,6 +931,7 @@ public abstract class MinecraftServer extends ReentrantBlockableEventLoop<TickTa
             this.server.disablePlugins();
         }
         // CraftBukkit end
+        if (io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper != null) io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper.shutdown(); // Paper - Plugin remapping
         this.getConnection().stop();
         this.isSaving = true;
         if (this.playerList != null) {
diff --git a/src/main/java/net/minecraft/server/dedicated/DedicatedServer.java b/src/main/java/net/minecraft/server/dedicated/DedicatedServer.java
index 3b403e9edf4e860160dd230977870f21a0e32a7a..9d6be455c3bbcdbcb9d3d24b0bad79f46ba6a8cb 100644
--- a/src/main/java/net/minecraft/server/dedicated/DedicatedServer.java
+++ b/src/main/java/net/minecraft/server/dedicated/DedicatedServer.java
@@ -318,6 +318,12 @@ public class DedicatedServer extends MinecraftServer implements ServerInterface
         }
     }
 
+    // Paper start
+    public java.io.File getPluginsFolder() {
+        return (java.io.File) this.options.valueOf("plugins");
+    }
+    // Paper end
+
     @Override
     public boolean isSpawningMonsters() {
         return this.settings.getProperties().spawnMonsters && super.isSpawningMonsters();
diff --git a/src/main/java/net/neoforged/art/internal/RenamerImpl.java b/src/main/java/net/neoforged/art/internal/RenamerImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..73b20a92f330311e3fef8f03b51a098513afafc1
--- /dev/null
+++ b/src/main/java/net/neoforged/art/internal/RenamerImpl.java
@@ -0,0 +1,308 @@
+/*
+ * Forge Auto Renaming Tool
+ * Copyright (c) 2021
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation version 2.1
+ * of the License.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ */
+
+package net.neoforged.art.internal;
+
+import java.io.BufferedOutputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.file.Files;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.function.Consumer;
+import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+import java.util.zip.ZipOutputStream;
+
+import net.neoforged.cliutils.JarUtils;
+import net.neoforged.cliutils.progress.ProgressReporter;
+import org.objectweb.asm.Opcodes;
+
+import net.neoforged.art.api.ClassProvider;
+import net.neoforged.art.api.Renamer;
+import net.neoforged.art.api.Transformer;
+import net.neoforged.art.api.Transformer.ClassEntry;
+import net.neoforged.art.api.Transformer.Entry;
+import net.neoforged.art.api.Transformer.ManifestEntry;
+import net.neoforged.art.api.Transformer.ResourceEntry;
+
+public class RenamerImpl implements Renamer { // Paper - public
+    private static final ProgressReporter PROGRESS = ProgressReporter.getDefault();
+    static final int MAX_ASM_VERSION = Opcodes.ASM9;
+    private static final String MANIFEST_NAME = "META-INF/MANIFEST.MF";
+    private final List<File> libraries;
+    private final List<Transformer> transformers;
+    private final SortedClassProvider sortedClassProvider;
+    private final List<ClassProvider> classProviders;
+    private final int threads;
+    private final Consumer<String> logger;
+    private final Consumer<String> debug;
+    private boolean setup = false;
+    private ClassProvider libraryClasses;
+
+    RenamerImpl(List<File> libraries, List<Transformer> transformers, SortedClassProvider sortedClassProvider, List<ClassProvider> classProviders,
+                int threads, Consumer<String> logger, Consumer<String> debug) {
+        this.libraries = libraries;
+        this.transformers = transformers;
+        this.sortedClassProvider = sortedClassProvider;
+        this.classProviders = Collections.unmodifiableList(classProviders);
+        this.threads = threads;
+        this.logger = logger;
+        this.debug = debug;
+    }
+
+    private void setup() {
+        if (this.setup)
+            return;
+
+        this.setup = true;
+
+        ClassProvider.Builder libraryClassesBuilder = ClassProvider.builder().shouldCacheAll(true);
+        this.logger.accept("Adding Libraries to Inheritance");
+        this.libraries.forEach(f -> libraryClassesBuilder.addLibrary(f.toPath()));
+
+        this.libraryClasses = libraryClassesBuilder.build();
+    }
+
+    @Override
+    public void run(File input, File output) {
+        // Paper start - Add remappingSelf
+        this.run(input, output, false);
+    }
+    public void run(File input, File output, boolean remappingSelf) {
+        // Paper end
+        if (!this.setup)
+            this.setup();
+
+        if (Boolean.getBoolean(ProgressReporter.ENABLED_PROPERTY)) {
+            try {
+                PROGRESS.setMaxProgress(JarUtils.getFileCountInZip(input));
+            } catch (IOException e) {
+                logger.accept("Failed to read zip file count: " + e);
+            }
+        }
+
+        input = Objects.requireNonNull(input).getAbsoluteFile();
+        output = Objects.requireNonNull(output).getAbsoluteFile();
+
+        if (!input.exists())
+            throw new IllegalArgumentException("Input file not found: " + input.getAbsolutePath());
+
+        logger.accept("Reading Input: " + input.getAbsolutePath());
+        PROGRESS.setStep("Reading input jar");
+        // Read everything from the input jar!
+        List<Entry> oldEntries = new ArrayList<>();
+        try (ZipFile in = new ZipFile(input)) {
+            int amount = 0;
+            for (Enumeration<? extends ZipEntry> entries = in.entries(); entries.hasMoreElements();) {
+                final ZipEntry e = entries.nextElement();
+                if (e.isDirectory())
+                    continue;
+                String name = e.getName();
+                byte[] data;
+                try (InputStream entryInput = in.getInputStream(e)) {
+                    data = entryInput.readAllBytes(); // Paper - Use readAllBytes
+                }
+
+                if (name.endsWith(".class") && !name.contains("META-INF/")) // Paper - Skip META-INF entries
+                    oldEntries.add(ClassEntry.create(name, e.getTime(), data));
+                else if (name.equals(MANIFEST_NAME))
+                    oldEntries.add(ManifestEntry.create(e.getTime(), data));
+                else if (name.equals("javadoctor.json"))
+                    oldEntries.add(Transformer.JavadoctorEntry.create(e.getTime(), data));
+                else
+                    oldEntries.add(ResourceEntry.create(name, e.getTime(), data));
+
+                if ((++amount) % 10 == 0) {
+                    PROGRESS.setProgress(amount);
+                }
+            }
+        } catch (IOException e) {
+            throw new RuntimeException("Could not parse input: " + input.getAbsolutePath(), e);
+        }
+
+        this.sortedClassProvider.clearCache();
+        ArrayList<ClassProvider> classProviders = new ArrayList<>(this.classProviders);
+        classProviders.add(0, this.libraryClasses);
+        this.sortedClassProvider.classProviders = classProviders;
+
+        AsyncHelper async = new AsyncHelper(threads);
+        try {
+
+            /* Disabled until we do something with it
+            // Gather original file Hashes, so that we can detect changes and update the manifest if necessary
+            log("Gathering original hashes");
+            Map<String, String> oldHashes = async.invokeAll(oldEntries,
+                e -> new Pair<>(e.getName(), HashFunction.SHA256.hash(e.getData()))
+            ).stream().collect(Collectors.toMap(Pair::getLeft, Pair::getRight));
+            */
+
+            PROGRESS.setProgress(0);
+            PROGRESS.setIndeterminate(true);
+            PROGRESS.setStep("Processing entries");
+
+            List<ClassEntry> ourClasses = oldEntries.stream()
+                .filter(e -> e instanceof ClassEntry && !e.getName().startsWith("META-INF/"))
+                .map(ClassEntry.class::cast)
+                .collect(Collectors.toList());
+
+            // Add the original classes to the inheritance map, TODO: Multi-Release somehow?
+            logger.accept("Adding input to inheritance map");
+            ClassProvider.Builder inputClassesBuilder = ClassProvider.builder();
+            async.consumeAll(ourClasses, ClassEntry::getClassName, c ->
+                inputClassesBuilder.addClass(c.getName().substring(0, c.getName().length() - 6), c.getData())
+            );
+            classProviders.add(0, inputClassesBuilder.build());
+
+            // Process everything
+            logger.accept("Processing entries");
+            List<Entry> newEntries = async.invokeAll(oldEntries, Entry::getName, this::processEntry);
+
+            logger.accept("Adding extras");
+            // Paper start - I'm pretty sure the duplicates are because the input is already on the classpath
+            List<Entry> finalNewEntries = newEntries;
+            transformers.forEach(t -> finalNewEntries.addAll(t.getExtras()));
+
+            Set<String> seen = new HashSet<>();
+            if (remappingSelf) {
+                // deduplicate
+                List<Entry> n = new ArrayList<>();
+                for (final Entry e : newEntries) {
+                    if (seen.add(e.getName())) {
+                        n.add(e);
+                    }
+                }
+                newEntries = n;
+            } else {
+            String dupes = newEntries.stream().map(Entry::getName)
+                .filter(n -> !seen.add(n))
+                .sorted()
+                .collect(Collectors.joining(", "));
+            if (!dupes.isEmpty())
+                throw new IllegalStateException("Duplicate entries detected: " + dupes);
+            }
+            // Paper end
+
+            // We care about stable output, so sort, and single thread write.
+            logger.accept("Sorting");
+            Collections.sort(newEntries, this::compare);
+
+            if (!output.getParentFile().exists())
+                output.getParentFile().mkdirs();
+
+            seen.clear();
+
+            PROGRESS.setMaxProgress(newEntries.size());
+            PROGRESS.setStep("Writing output");
+
+            logger.accept("Writing Output: " + output.getAbsolutePath());
+            try (OutputStream fos = new BufferedOutputStream(Files.newOutputStream(output.toPath()));
+                 ZipOutputStream zos = new ZipOutputStream(fos)) {
+
+                int amount = 0;
+                for (Entry e : newEntries) {
+                    String name = e.getName();
+                    int idx = name.lastIndexOf('/');
+                    if (idx != -1)
+                        addDirectory(zos, seen, name.substring(0, idx));
+
+                    logger.accept("  " + name);
+                    ZipEntry entry = new ZipEntry(name);
+                    entry.setTime(e.getTime());
+                    zos.putNextEntry(entry);
+                    zos.write(e.getData());
+                    zos.closeEntry();
+
+                    if ((++amount) % 10 == 0) {
+                        PROGRESS.setProgress(amount);
+                    }
+                }
+
+                PROGRESS.setProgress(amount);
+            }
+        } catch (final IOException e) {
+            throw new RuntimeException("Could not write to file " + output.getAbsolutePath(), e);
+        } finally {
+            async.shutdown();
+        }
+    }
+
+    private byte[] readAllBytes(InputStream in, long size) throws IOException {
+        // This program will crash if size exceeds MAX_INT anyway since arrays are limited to 32-bit indices
+        ByteArrayOutputStream tmp = new ByteArrayOutputStream(size >= 0 ? (int) size : 0);
+
+        byte[] buffer = new byte[8192];
+        int read;
+        while ((read = in.read(buffer)) != -1) {
+            tmp.write(buffer, 0, read);
+        }
+
+        return tmp.toByteArray();
+    }
+
+    // Tho Directory entries are not strictly necessary, we add them because some bad implementations of Zip extractors
+    // attempt to extract files without making sure the parents exist.
+    private void addDirectory(ZipOutputStream zos, Set<String> seen, String path) throws IOException {
+        if (!seen.add(path))
+            return;
+
+        int idx = path.lastIndexOf('/');
+        if (idx != -1)
+            addDirectory(zos, seen, path.substring(0, idx));
+
+        logger.accept("  " + path + '/');
+        ZipEntry dir = new ZipEntry(path + '/');
+        dir.setTime(Entry.STABLE_TIMESTAMP);
+        zos.putNextEntry(dir);
+        zos.closeEntry();
+    }
+
+    private Entry processEntry(final Entry start) {
+        Entry entry = start;
+        for (Transformer transformer : RenamerImpl.this.transformers) {
+            entry = entry.process(transformer);
+            if (entry == null)
+                return null;
+        }
+        return entry;
+    }
+
+    private int compare(Entry o1, Entry o2) {
+        // In order for JarInputStream to work, MANIFEST has to be the first entry, so make it first!
+        if (MANIFEST_NAME.equals(o1.getName()))
+            return MANIFEST_NAME.equals(o2.getName()) ? 0 : -1;
+        if (MANIFEST_NAME.equals(o2.getName()))
+            return MANIFEST_NAME.equals(o1.getName()) ? 0 :  1;
+        return o1.getName().compareTo(o2.getName());
+    }
+
+    @Override
+    public void close() throws IOException {
+        this.sortedClassProvider.close();
+    }
+}
diff --git a/src/main/java/org/bukkit/craftbukkit/CraftServer.java b/src/main/java/org/bukkit/craftbukkit/CraftServer.java
index 600e865688b423d9bb4338f413dc28418ba37748..ad699a4ad555a4d7c85727bd835ebacd24d02c2b 100644
--- a/src/main/java/org/bukkit/craftbukkit/CraftServer.java
+++ b/src/main/java/org/bukkit/craftbukkit/CraftServer.java
@@ -1005,6 +1005,7 @@ public final class CraftServer implements Server {
         this.loadPlugins();
         this.enablePlugins(PluginLoadOrder.STARTUP);
         this.enablePlugins(PluginLoadOrder.POSTWORLD);
+        if (io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper != null) io.papermc.paper.plugin.PluginInitializerManager.instance().pluginRemapper.pluginsEnabled(); // Paper - Remap plugins
         this.getPluginManager().callEvent(new ServerLoadEvent(ServerLoadEvent.LoadType.RELOAD));
     }