diff --git a/build.gradle b/build.gradle
index 3928cb7ee1dc..56afa5e4a9a1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -118,12 +118,19 @@ switch (JavaVersion.current()) {
         break;
 }
 
-task setLocalRepo(type:Exec) {
-    commandLine 'git', 'worktree', 'list'
-    standardOutput = new ByteArrayOutputStream()
+task setLocalRepo(type: Exec) {
+    def outputFile = layout.buildDirectory.file("setLocalRepo-output.txt")
+    outputs.file(outputFile)
+
+    commandLine = [
+        'bash',
+        '-c',
+        "git worktree list > ${outputFile.get().asFile.absolutePath}"
+    ]
+
     doLast {
-        String worktreeList = standardOutput.toString()
-        localRepo = worktreeList.substring(0, worktreeList.indexOf(' ')) + '/.git'
+        String worktreeList = outputFile.get().asFile.text
+        ext.localRepo = worktreeList.substring(0, worktreeList.indexOf(' ')) + '/.git'
     }
 }
 
@@ -146,7 +153,7 @@ spotless {
     //     > Could not create task ':checker-qual:spotlessJava'.
     //        > File signature can only be created for existing regular files, given:
     //          .../checker-framework/checker-qual/build/libs/checker-qual-3.25.1-SNAPSHOT.jar
-    predeclareDepsFromBuildscript()
+    predeclareDeps()
 }
 
 spotlessPredeclare {
@@ -1004,31 +1011,40 @@ subprojects {
         withSourcesJar()
     }
 
+    // Capture project references early.
+    def projectVersion = project.version
+    def projectName = project.name.replaceAll('-', '.')
+
     // Things in this block reference definitions in the subproject that do not exist,
     // until the project is evaluated.
     afterEvaluate {
         // Adds manifest to all Jar files
         tasks.withType(Jar) {
             includeEmptyDirs = false
-            if (archiveFileName.get().startsWith('checker-qual') || archiveFileName.get().startsWith('checker-util')) {
-                metaInf {
-                    from './LICENSE.txt'
-                }
-            } else {
-                metaInf {
-                    from "${rootDir}/LICENSE.txt"
+
+            archiveFileName.map { fileName ->
+                if (fileName.startsWith('checker-qual') || fileName.startsWith('checker-util')) {
+                    metaInf {
+                        from './LICENSE.txt'
+                    }
+                } else {
+                    metaInf {
+                        from "${rootDir}/LICENSE.txt"
+                    }
                 }
             }
             manifest {
-                attributes('Implementation-Version': "${project.version}")
+                attributes('Implementation-Version': "${projectVersion}")
                 attributes('Implementation-URL': 'https://eisop.github.io/')
-                if (! archiveFileName.get().endsWith('source.jar') && ! archiveFileName.get().startsWith('checker-qual')) {
-                    attributes('Automatic-Module-Name': 'org.checkerframework.' + project.name.replaceAll('-', '.'))
-                }
-                if (archiveFileName.get().startsWith('checker-qual') || archiveFileName.get().startsWith('checker-util')) {
-                    attributes('Bundle-License': 'MIT')
-                } else {
-                    attributes('Bundle-License': '(GPL-2.0-only WITH Classpath-exception-2.0)')
+                archiveFileName.map { fileName ->
+                    if (! fileName.endsWith('source.jar') && ! fileName.startsWith('checker-qual')) {
+                        attributes('Automatic-Module-Name': 'org.checkerframework.' + projectName)
+                    }
+                    if (fileName.startsWith('checker-qual') || fileName.startsWith('checker-util')) {
+                        attributes('Bundle-License': 'MIT')
+                    } else {
+                        attributes('Bundle-License': '(GPL-2.0-only WITH Classpath-exception-2.0)')
+                    }
                 }
             }
         }
diff --git a/checker-qual-android/build.gradle b/checker-qual-android/build.gradle
index 1f1b4b58c169..22972f2fbc8a 100644
--- a/checker-qual-android/build.gradle
+++ b/checker-qual-android/build.gradle
@@ -1,12 +1,14 @@
 evaluationDependsOn(':checker-qual')
 
+tasks.register('deletePreviousSources') {
+    // Delete the directory in case a previously copied file should no longer be in checker-qual.
+    delete file(layout.buildDirectory.dir("generated/sources/main/java"))
+}
+
 task copySources(type: Copy) {
     description = 'Copy checker-qual source to checker-qual-android'
+    dependsOn 'deletePreviousSources'
     includeEmptyDirs = false
-    doFirst {
-        // Delete the directory in case a previously copied file should no longer be in checker-qual
-        delete file(layout.buildDirectory.dir("generated/sources/main/java"))
-    }
     from files(project(':checker-qual').sourceSets.main.java)
     include '**/*.java'
     exclude '**/SignednessUtilExtra.java'
diff --git a/checker-qual/build.gradle b/checker-qual/build.gradle
index ba026310f1cd..527aaefaf1b9 100644
--- a/checker-qual/build.gradle
+++ b/checker-qual/build.gradle
@@ -39,6 +39,10 @@ jar {
     manifest {
         attributes('Export-Package': '*')
     }
+    // Work around http://github.com/bndtools/bnd/issues/6346
+    bundle {
+        properties.put("project.group", provider({project.group}))
+    }
 }
 
 apply from: rootProject.file('gradle-mvn-push.gradle')
diff --git a/checker/build.gradle b/checker/build.gradle
index 0d6ddc8d42f6..54932a093544 100644
--- a/checker/build.gradle
+++ b/checker/build.gradle
@@ -133,45 +133,43 @@ jar {
 // This task differs from the `assemble` task in that it does not build Javadoc.
 // It is useful for those who only want to run `javac`.
 // checker.jar is copied to checker/dist/ when it is built by the shadowJar task.
-task assembleForJavac(dependsOn: shadowJar, group: 'Build') {
+task assembleForJavac(group: 'Build') {
     description = 'Builds or downloads jars required by CheckerMain and puts them in checker/dist/.'
+    dependsOn 'copyCheckerQualJar'
+    dependsOn 'copyCheckerUtilJar'
+    dependsOn 'copyJavacJar'
+}
+
+tasks.register('copyCheckerQualJar', Copy) {
+    dependsOn ':checker-qual:jar'
     dependsOn project(':checker-qual').tasks.jar
-    def checkerQualJarFile = file(project(':checker-qual').tasks.getByName('jar').archiveFile)
-    def checkerUtilJarFile = file(project(':checker-util').tasks.getByName('jar').archiveFile)
 
-    doLast {
-        if (!checkerQualJarFile.exists()) {
-            throw new GradleException('File not found: ' + checkerQualJarFile)
-        }
-        copy {
-            from checkerQualJarFile
-            into "${projectDir}/dist"
-            rename { String fileName ->
-                // remove version number on checker-qual.jar
-                fileName.replace(fileName, 'checker-qual.jar')
-            }
-        }
+    from project(':checker-qual').tasks.jar.archiveFile
+    into "${projectDir}/dist"
+    rename { String fileName ->
+        // remove version number on checker-qual.jar
+        fileName.replace(fileName, 'checker-qual.jar')
+    }
+}
 
-        if (!checkerUtilJarFile.exists()) {
-            throw new GradleException('File not found: ' + checkerUtilJarFile)
-        }
-        copy {
-            from checkerUtilJarFile
-            into "${projectDir}/dist"
-            rename { String fileName ->
-                // remove version number on checker-util.jar
-                fileName.replace(fileName, 'checker-util.jar')
-            }
-        }
+tasks.register('copyCheckerUtilJar', Copy) {
+    dependsOn 'shadowJar'
+    dependsOn project(':checker-util').tasks.jar
 
-        copy {
-            // This is required to *run* the Checker Framework on JDK 8.
-            from configurations.javacJar
-            into "${projectDir}/dist"
-            rename { String fileName ->
-                fileName.replace(fileName, 'javac.jar')
-            }
-        }
+    from project(':checker-util').tasks.jar.archiveFile
+    into "${projectDir}/dist"
+    rename { String fileName ->
+        // remove version number on checker-util.jar
+        fileName.replace(fileName, 'checker-util.jar')
+    }
+}
+
+tasks.register('copyJavacJar', Copy) {
+    // This is required to *run* the Checker Framework on JDK 8.
+    from configurations.javacJar
+    into "${projectDir}/dist"
+    rename { String fileName ->
+        fileName.replace(fileName, 'javac.jar')
     }
 }
 
@@ -234,17 +232,22 @@ shadowJar {
     // To see what files are incorporated into the shadow jar file:
     // doFirst { println sourceSets.main.runtimeClasspath.asPath }
     archiveClassifier = 'all'
-    doLast{
-        copy {
-            from archiveFile.get()
-            into file("${projectDir}/dist")
-            rename 'checker.*', 'checker.jar'
-        }
-    }
 
     minimize()
 }
 
+shadowJar.finalizedBy('copyCheckerJar')
+
+tasks.register('copyCheckerJar', Copy) {
+    dependsOn ':checker:shadowJar'
+
+    // This used `from archiveFile.get()` when it was part of shadowJar.
+    // Look at e.g. copyCheckerQualJar whether there is a better way to do this.
+    from file("${projectDir}/build/libs/checker-${project.version}-all.jar")
+    into file("${projectDir}/dist")
+    rename 'checker.*', 'checker.jar'
+}
+
 artifacts {
     // Don't add this here or else the Javadoc and the sources jar is built during the assemble task.
     // archives allJavadocJar
@@ -257,8 +260,12 @@ artifacts {
 
 clean {
     def injected = project.objects.newInstance(InjectedExecOps)
+    def bldDir = buildDir
+    def distDir = "${projectDir}/dist"
+    def cmdlineDir = file('tests/command-line')
+    def nullnessextraDir = file('tests/nullness-extra')
 
-    delete("${projectDir}/dist")
+    delete(distDir)
     delete('tests/calledmethods-delomboked')
     delete('tests/ainfer-testchecker/annotated')
     delete('tests/ainfer-testchecker/inference-output')
@@ -271,20 +278,18 @@ clean {
     delete('tests/build')
     doLast {
         injected.execOps.exec {
-            workingDir = file('tests/command-line')
+            workingDir = cmdlineDir
             commandLine 'make', 'clean'
         }
         injected.execOps.exec {
-            workingDir = file('tests/nullness-extra')
+            workingDir = nullnessextraDir
             commandLine 'make', 'clean'
         }
-    }
-}
 
-clean.doLast {
-    while (buildDir.exists()) {
-        sleep(10000)                // wait 10 seconds
-        buildDir.deleteDir()
+        while(bldDir.exists()) {
+            sleep(10000)                // wait 10 seconds
+            bldDir.deleteDir()
+        }
     }
 }
 
@@ -1090,7 +1095,7 @@ final checkerPom(publication) {
 publishing {
     publications {
         checker(MavenPublication) {
-            project.shadow.component it
+            from components.shadow
             checkerPom it
             artifact checkerJar
             artifact allSourcesJar
diff --git a/docs/build.gradle b/docs/build.gradle
index ecb64aac695e..a5d2858d7ddc 100644
--- a/docs/build.gradle
+++ b/docs/build.gradle
@@ -6,11 +6,12 @@ interface InjectedExecOps {
 
 clean {
     def injected = project.objects.newInstance(InjectedExecOps)
+    def examples = file('examples')
 
     delete('api/')
     doLast {
         injected.execOps.exec {
-            workingDir = file('examples')
+            workingDir = examples
             commandLine 'make', 'clean'
         }
     }
diff --git a/docs/examples/errorprone/gradle.properties b/docs/examples/errorprone/gradle.properties
new file mode 120000
index 000000000000..591a8b3f8db6
--- /dev/null
+++ b/docs/examples/errorprone/gradle.properties
@@ -0,0 +1 @@
+../../../gradle.properties
\ No newline at end of file
diff --git a/docs/examples/jspecify/gradle.properties b/docs/examples/jspecify/gradle.properties
new file mode 120000
index 000000000000..591a8b3f8db6
--- /dev/null
+++ b/docs/examples/jspecify/gradle.properties
@@ -0,0 +1 @@
+../../../gradle.properties
\ No newline at end of file
diff --git a/docs/examples/lombok/gradle.properties b/docs/examples/lombok/gradle.properties
new file mode 120000
index 000000000000..591a8b3f8db6
--- /dev/null
+++ b/docs/examples/lombok/gradle.properties
@@ -0,0 +1 @@
+../../../gradle.properties
\ No newline at end of file
diff --git a/docs/examples/nullaway/gradle.properties b/docs/examples/nullaway/gradle.properties
new file mode 120000
index 000000000000..591a8b3f8db6
--- /dev/null
+++ b/docs/examples/nullaway/gradle.properties
@@ -0,0 +1 @@
+../../../gradle.properties
\ No newline at end of file
diff --git a/framework/build.gradle b/framework/build.gradle
index f6327d3c32d4..fb1d9817d50f 100644
--- a/framework/build.gradle
+++ b/framework/build.gradle
@@ -97,18 +97,52 @@ tasks.register('cloneAnnotatedJdk', CloneTask) {
     outputs.upToDateWhen { false }
 }
 
-task copyAndMinimizeAnnotatedJdkFiles(type: JavaExec, dependsOn: cloneAnnotatedJdk, group: 'Build') {
+tasks.register('copyAnnotatedJdkFiles', Copy) {
+    dependsOn ':framework:cloneAnnotatedJdk'
+
+    def inputDir = "${annotatedJdkHome}/src"
+    def outputDir = "${buildDir}/generated/resources/annotated-jdk/"
+
+    inputs.dir file(inputDir)
+    outputs.dir file(outputDir)
+
+    FileTree tree = fileTree(dir: inputDir)
+    String absolutejdkHome = file(annotatedJdkHome).absolutePath
+    int jdkDirStringSize = absolutejdkHome.size()
+
+    NavigableSet<String> annotatedForFiles = new TreeSet<>();
+    // Populate `annotatedForFiles`.
+    tree.visit { FileVisitDetails fvd ->
+        if (!fvd.file.isDirectory() && fvd.file.name.matches('.*\\.java')
+                && !fvd.file.path.contains('org/checkerframework')) {
+            fvd.getFile().readLines().any { line ->
+                if (line.contains('@AnnotatedFor') || line.contains('org.checkerframework') || line.contains('org.jspecify')) {
+                    annotatedForFiles.add(fvd.file.absolutePath)
+                    return true;
+                }
+            }
+        }
+    }
+
+    from(annotatedJdkHome)
+    into(outputDir)
+    for (String filename : annotatedForFiles) {
+        include filename.substring(jdkDirStringSize)
+    }
+}
+
+task copyAndMinimizeAnnotatedJdkFiles(type: JavaExec, dependsOn: copyAnnotatedJdkFiles, group: 'Build') {
+    def outputDir = "${buildDir}/generated/resources/annotated-jdk/"
+
+    description = "Copy annotated JDK files to ${outputDir}. Removes private and package-private methods, method bodies, comments, etc. from the annotated JDK"
+
     dependsOn ':framework:compileStubifierJava'
     // we need the next two dependencies because we run JavaStubifier using this project's runtimeClasspath,
     // which refers to the jars for these other projects
     dependsOn ':javacutil:jar'
     dependsOn ':dataflow:jar'
-    def inputDir = "${annotatedJdkHome}/src"
-    def outputDir = "${buildDir}/generated/resources/annotated-jdk/"
-
-    description = "Copy annotated JDK files to ${outputDir}. Removes private and package-private methods, method bodies, comments, etc. from the annotated JDK"
 
-    inputs.dir file(inputDir)
+    inputs.dir file(outputDir)
     outputs.dir file(outputDir)
 
     classpath = sourceSets.stubifier.runtimeClasspath
@@ -117,32 +151,6 @@ task copyAndMinimizeAnnotatedJdkFiles(type: JavaExec, dependsOn: cloneAnnotatedJ
 
     mainClass = 'org.checkerframework.framework.stubifier.JavaStubifier'
     args outputDir
-
-    doFirst {
-        FileTree tree = fileTree(dir: inputDir)
-        NavigableSet<String> annotatedForFiles = new TreeSet<>();
-        // Populate `annotatedForFiles`.
-        tree.visit { FileVisitDetails fvd ->
-            if (!fvd.file.isDirectory() && fvd.file.name.matches('.*\\.java')
-                    && !fvd.file.path.contains('org/checkerframework')) {
-                fvd.getFile().readLines().any { line ->
-                    if (line.contains('@AnnotatedFor') || line.contains('org.checkerframework') || line.contains('org.jspecify')) {
-                        annotatedForFiles.add(fvd.file.absolutePath)
-                        return true;
-                    }
-                }
-            }
-        }
-        String absolutejdkHome = file(annotatedJdkHome).absolutePath
-        int jdkDirStringSize = absolutejdkHome.size()
-        copy {
-            from(annotatedJdkHome)
-            into(outputDir)
-            for (String filename : annotatedForFiles) {
-                include filename.substring(jdkDirStringSize)
-            }
-        }
-    }
 }
 
 sourcesJar.dependsOn(copyAndMinimizeAnnotatedJdkFiles)
diff --git a/gradle-mvn-push.gradle b/gradle-mvn-push.gradle
index c011c59dc233..6b335b10571c 100644
--- a/gradle-mvn-push.gradle
+++ b/gradle-mvn-push.gradle
@@ -2,10 +2,13 @@ apply plugin: 'maven-publish'
 apply plugin: 'signing'
 
 final isSnapshot = version.contains('SNAPSHOT')
-// https://github.com/johnrengelman/shadow/issues/586#issuecomment-708375599
-components.java.withVariantsFromConfiguration(configurations.shadowRuntimeElements) {
-    skip()
-}
+/* TODO: this work-around isn't working anymore. Is it still needed?
+ // https://github.com/johnrengelman/shadow/issues/586#issuecomment-708375599
+ components.java.withVariantsFromConfiguration(configurations.shadowRuntimeElements) {
+ skip()
+ }
+ */
+
 publishing {
     repositories {
         maven {
@@ -22,7 +25,6 @@ publishing {
 }
 
 signing {
-
     // Use external gpg cmd.  This makes it easy to use gpg-agent,
     // to avoid being prompted for a password once per artifact.
     useGpgCmd()
diff --git a/gradle.properties b/gradle.properties
index b854190ae91c..a7dc7b9fb887 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -4,3 +4,4 @@ org.gradle.parallel=true
 
 org.gradle.jvmargs=-Xmx2g -Dfile.encoding=UTF-8
 org.gradle.caching=true
+org.gradle.configuration-cache=true
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index 1b33c55baabb..8bdaf60c75ab 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index aaaabb3cb9fe..37f78a6af837 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.4-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.3.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
diff --git a/gradlew b/gradlew
index 23d15a936707..ef07e0162b18 100755
--- a/gradlew
+++ b/gradlew
@@ -1,7 +1,7 @@
 #!/bin/sh
 
 #
-# Copyright © 2015-2021 the original authors.
+# Copyright © 2015 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.