Make fatjar allow remapping many files at once

build.gradle

@@ -83,18 +83,26 @@ managedVersioning {
     apply()
 }
 
+sourceSets {
+    cli {}
+}
+
 dependencies {
+    cliImplementation 'net.neoforged.jst:jst-cli:1.0.63'
+    cliImplementation 'net.neoforged.jst:jst-api:1.0.63'
+    cliCompileOnly sourceSets.main.output
+
+    cliCompileOnly cLibs.bundles.compileonly
+    cliAnnotationProcessor cLibs.bundles.annotationprocessor
+
     implementation 'net.neoforged.jst:jst-cli:1.0.63'
     implementation 'net.neoforged.jst:jst-api:1.0.63'
     implementation 'net.neoforged:srgutils:1.0.9'
     implementation 'org.ow2.asm:asm:9.7'
     implementation 'org.slf4j:slf4j-simple:2.0.13'
 
-    compileOnly 'org.jetbrains:annotations:24.1.0'
-    compileOnly 'org.jspecify:jspecify:1.0.0'
-    compileOnly 'com.google.auto.service:auto-service:1.1.1'
-
-    annotationProcessor 'com.google.auto.service:auto-service:1.1.1'
+    compileOnly cLibs.bundles.compileonly
+    annotationProcessor cLibs.bundles.annotationprocessor
 
     testImplementation platform('org.junit:junit-bom:5.10.3')
     testImplementation 'org.junit.jupiter:junit-jupiter'
@@ -112,10 +120,11 @@ configurations {
 }
 
 shadowJar {
+    from sourceSets.cli.output
     configurations = [project.configurations.include]
     mergeServiceFiles()
     manifest {
-        attributes 'Main-Class': 'net.neoforged.jst.cli.Main'
+        attributes 'Main-Class': 'dev.lukebemish.christen.cli.ChristenMain'
     }
 }
 

src/cli/java/dev/lukebemish/christen/cli/ChristenMain.java

@@ -0,0 +1,55 @@
+package dev.lukebemish.christen.cli;
+
+import dev.lukebemish.christen.ChristenTransformer;
+import net.neoforged.jst.api.SourceTransformer;
+import net.neoforged.jst.cli.Main;
+import picocli.CommandLine;
+
+import java.lang.invoke.MethodHandle;
+import java.lang.invoke.MethodHandles;
+import java.util.HashSet;
+import java.util.List;
+import java.util.concurrent.Callable;
+
+public class ChristenMain implements Callable<Integer> {
+    @CommandLine.ArgGroup(exclusive = false, multiplicity = "1")
+    ChristenTransformer plugin;
+
+    @CommandLine.ArgGroup(exclusive = false, multiplicity = "1..*")
+    List<Main> subcommands;
+
+    private static final MethodHandle ENABLED_TRANSFORMERS;
+
+    static {
+        try {
+            ENABLED_TRANSFORMERS = MethodHandles.lookup().findGetter(Main.class, "enabledTransformers", HashSet.class);
+        } catch (NoSuchFieldException | IllegalAccessException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    public static void main(String[] args) {
+        var commandLine = new CommandLine(new ChristenMain());
+        commandLine.setCaseInsensitiveEnumValuesAllowed(true);
+        System.exit(commandLine.execute(args));
+    }
+
+    @SuppressWarnings("unchecked")
+    @Override
+    public Integer call() throws Exception {
+        for (var main : subcommands) {
+            HashSet<SourceTransformer> enabledTransformers;
+            try {
+                enabledTransformers = (HashSet<SourceTransformer>) ENABLED_TRANSFORMERS.invoke(main);
+            } catch (Throwable e) {
+                throw new RuntimeException(e);
+            }
+            enabledTransformers.add(plugin);
+            var result = main.call();
+            if (!result.equals(0)) {
+                return result;
+            }
+        }
+        return 0;
+    }
+}