works so...

build.gradle

@@ -71,8 +71,8 @@ if (!getFile(targetPackageJava).exists() && !getFile(targetPackageScala).exists(
 }
 
 if (apiPackage) {
-    targetPackageJava = 'src/api/java/' + modGroupPath
+    targetPackageJava = 'src/api/java/' + modGroupPath + '/api'
-    targetPackageScala = 'src/api/java/' + modGroupPath
+    targetPackageScala = 'src/api/java/' + modGroupPath + '/api'
     if (!getFile(targetPackageJava).exists() && !getFile(targetPackageScala).exists()) {
         throw new GradleException("Could not resolve \"apiPackage\"! Could not find ${targetPackageJava} or ${targetPackageScala}")
     }
@@ -439,9 +439,6 @@ processResources {
             rename "(${at})", 'META-INF/$1'
         }
     }
-
-    from sourceSets.api.output
-    dependsOn apiClasses
 }
 
 // Automatically generate a mixin json file if it does not already exist
@@ -516,16 +513,26 @@ jar {
             it.isDirectory() ? it : zipTree(it)
         }
     }
+
+    from sourceSets.api.output
+    dependsOn apiClasses
+
+    // specify which files are really included, can control which APIs should be in
+    include "appeng/**"
+    include "assets/**"
+    include "mcmod.info"
+    include "pack.mcmeta"
+    include "META-INF/appeng_at.cfg"
 }
 
 // Create API library jar
 tasks.register('apiJar', Jar) {
     archiveClassifier.set 'api'
-    from(sourceSets.main.java) {
+    from(sourceSets.api.java) {
         include "${modGroupPath}/${apiPackagePath}/**"
     }
 
-    from(sourceSets.main.output) {
+    from(sourceSets.api.output) {
         include "${modGroupPath}/${apiPackagePath}/**"
     }
 }

gradle.properties

@@ -44,7 +44,7 @@ modGroup=appeng
 # This field can be left empty if you want your mod's version to be determined by the latest git tag instead.
 modVersion=rv6-stable-7-extended_life-v0.55.16
 # Whether to use the old jar naming structure (modid-mcversion-version) instead of the new version (modid-version)
-includeMCVersionJar=true
+includeMCVersionJar=false
 # The name of your jar when you produce builds, not including any versioning info
 modArchivesBaseName=appliedenergistics2
 # Will update your build.gradle automatically whenever an update is available
@@ -68,7 +68,7 @@ gradleTokenVersion=VERSION
 # In case your mod provides an API for other mods to implement you may declare its package here. Otherwise, you can
 # leave this property empty.
 # Example value: apiPackage = api + modGroup = com.myname.mymodid -> com.myname.mymodid.api
-apiPackage=true
+apiPackage=api
 # Specify the configuration file for Forge's access transformers here. It must be placed into /src/main/resources/
 # There can be multiple files in a comma-separated list.
 # Example value: mymodid_at.cfg,jei_at.cfg

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.2-all.zip
 networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists