set the jakartaPackages flag via a gradle property

gradle-conjure-api/src/main/java/com/palantir/gradle/conjure/api/ConjureExtension.java

@@ -20,6 +20,7 @@
 import groovy.lang.DelegatesTo;
 import java.util.HashMap;
 import java.util.Map;
+import org.gradle.api.Project;
 
 public class ConjureExtension {
 
@@ -31,12 +32,16 @@ public class ConjureExtension {
     private final GeneratorOptions pythonOptions = new GeneratorOptions();
     private final Map<String, GeneratorOptions> genericOptions = new HashMap<>();
 
-    public ConjureExtension() {
+    public ConjureExtension(Project project) {
         // Projects using sufficiently new gradle-conjure have jetbrains-annotations
         // added by default. Conjure generators ignore unknown flags and will not be
         // impacted if generators have not been updated.
         // See https://github.com/palantir/conjure-java/pull/1884
         javaOptions.addFlag("jetbrainsContractAnnotations");
+
+        if (Boolean.parseBoolean((String) project.findProperty("conjure.java.jakartaPackages"))) {
+            javaOptions.addFlag("jakartaPackages");
+        }
     }
 
     public final void typescript(

gradle-conjure/src/main/java/com/palantir/gradle/conjure/ConjureBasePlugin.java

@@ -59,7 +59,8 @@ public void apply(Project project) {
                         ConjureProductDependenciesExtension.EXTENSION_NAME,
                         ConjureProductDependenciesExtension.class,
                         project);
-        conjureExtension = project.getExtensions().create(ConjureExtension.EXTENSION_NAME, ConjureExtension.class);
+        conjureExtension =
+                project.getExtensions().create(ConjureExtension.EXTENSION_NAME, ConjureExtension.class, project);
         SourceDirectorySet conjureSourceSet = createConjureSourceSet(project);
         TaskProvider<Copy> copyConjureSourcesTask = createCopyConjureSourceTask(project, conjureSourceSet);
         compileIrProvider =

gradle-conjure/src/main/java/com/palantir/gradle/conjure/ConjureJavaLocalCodegenPlugin.java

@@ -53,7 +53,7 @@ public void apply(Project project) {
         project.getPlugins().apply(JavaBasePlugin.class);
 
         ConjureExtension extension =
-                project.getExtensions().create(ConjureExtension.EXTENSION_NAME, ConjureExtension.class);
+                project.getExtensions().create(ConjureExtension.EXTENSION_NAME, ConjureExtension.class, project);
 
         Configuration conjureIrConfiguration = project.getConfigurations().create(CONJURE_CONFIGURATION);
         TaskProvider<Copy> extractConjureIr = project.getTasks().register("extractConjureIr", Copy.class, task -> {
@@ -79,12 +79,11 @@ private static void setupSubprojects(
             createGenerateTask(subproject, extension, extractJavaTask, extractConjureIr);
         });
 
+        project.getChildProjects().forEach((_name, subproject) -> {
+            configureDependencies(subproject, extension);
+        });
+
         project.afterEvaluate(_p -> {
-            project.getChildProjects().forEach((_name, subproject) -> {
-                // Configure subproject dependencies in after-evaluate to ensure
-                // extension the has been evaluated.
-                configureDependencies(subproject, extension);
-            });
             // Validating that each subproject has a corresponding definition and vice versa.
             // We do this in afterEvaluate to ensure the configuration is populated.
             Set<String> apis = conjureIrConfiguration.getAllDependencies().stream()

gradle-conjure/src/main/java/com/palantir/gradle/conjure/ConjureLocalPlugin.java

@@ -57,7 +57,7 @@ public void apply(Project project) {
                 project.getConfigurations().maybeCreate(ConjurePlugin.CONJURE_GENERATORS_CONFIGURATION_NAME);
 
         ConjureExtension extension =
-                project.getExtensions().create(ConjureExtension.EXTENSION_NAME, ConjureExtension.class);
+                project.getExtensions().create(ConjureExtension.EXTENSION_NAME, ConjureExtension.class, project);
 
         TaskProvider<Task> generateConjure = project.getTasks().register("generateConjure", task -> {
             task.setDescription("Generates code for all requested languages (for which there is a subproject) "

gradle-conjure/src/main/java/com/palantir/gradle/conjure/ConjurePlugin.java

@@ -173,15 +173,15 @@ private void setupConjureJavaProjects(
                             + difference);
         }
 
-        project.afterEvaluate(_p -> configs.forEach((suffix, config) -> setupDerivedJavaProject(
+        configs.forEach((suffix, config) -> setupDerivedJavaProject(
                 suffix,
                 project,
                 optionsSupplier,
                 compileConjure,
                 compileIrTask,
                 productDependencyExt,
                 extractJavaTask,
-                config)));
+                config));
     }
 
     private static Project setupDerivedJavaProject(

gradle-conjure/src/test/groovy/com/palantir/gradle/conjure/ConjurePluginTest.groovy

@@ -523,13 +523,9 @@ class ConjurePluginTest extends IntegrationSpec {
             }
         }
         """.stripIndent()
-        file('api/build.gradle') << '''
-        conjure {
-            java {
-                jakartaPackages = true
-            }
-        }
-        '''.stripIndent()
+        createFile('gradle.properties') << """
+        conjure.java.jakartaPackages=true
+        """.stripIndent()
         updateSettings(prefix)
 
         when: