Move source sets

.gitignore

@@ -132,3 +132,4 @@ target/
 *.ipr
 *.iws
 *.iml
+/.gradle/

build.gradle

@@ -82,15 +82,13 @@ allprojects {
         // Also, build and use ManualTaglet as a taglet.
         tasks.withType(Javadoc) {
             dependsOn(':checker:shadowJar')
-            dependsOn(':javacutil:tagletClasses')
+            dependsOn(':util:tagletClasses')
             doFirst {
                 options.encoding = 'UTF-8'
                 options.memberLevel = javadocMemberLevel
                 classpath += files(project(':checker').tasks.getByName('shadowJar').archivePath)
-                if (!project.name.toString().equals("javacutil")) {
-                    options.taglets 'org.checkerframework.javacutil.dist.ManualTaglet'
-                    options.tagletPath(project(':javacutil').sourceSets.taglet.output as File[])
-                }
+                options.taglets 'org.checkerframework.taglet.ManualTaglet'
+                options.tagletPath(project(':util').sourceSets.taglet.output as File[])
                 options.links = ['http://docs.oracle.com/javase/8/docs/api/', 'https://docs.oracle.com/javase/8/docs/jdk/api/javac/tree/']
                 // This file is looked for by Javadoc.
                 file("${destinationDir}/resources/fonts/").mkdirs()
@@ -139,12 +137,13 @@ def createCheckTypeTask(projectName, checker, shortName) {
     project("${projectName}").tasks.create(name: "check${shortName}", type: JavaCompile, dependsOn: ':checker:shadowJar') {
         description "Run the ${shortName} Checker on the main sources."
         group 'Verification'
+        dependsOn ':jdk8:downloadJdk'
         // Always run the task.
         outputs.upToDateWhen { false }
         source = project("${projectName}").sourceSets.main.java
-        classpath = project("${projectName}").compileJava.classpath
+        classpath = files(project("${projectName}").compileJava.classpath,project(':checker-qual').sourceSets.main.output)
         destinationDir = file("${buildDir}")
-        dependsOn project(':checker-qual').tasks.jar
+
         options.annotationProcessorPath = files(project(':checker').tasks.shadowJar.archivePath)
         options.compilerArgs += [
                 '-processor', "${checker}",
@@ -166,8 +165,9 @@ def createCheckTypeTask(projectName, checker, shortName) {
  */
 List<String> getJavaFilesToFormat(projectName) {
     List<File> javaFiles = new ArrayList<>();
-    javaFiles.addAll(project(':' + projectName).sourceSets.main.java.files)
-    javaFiles.addAll(project(':' + projectName).sourceSets.test.java.files)
+    project(':' + projectName).sourceSets.forEach { set ->
+        javaFiles.addAll(set.java.files)
+    }
     // Collect all java files in tests directory
     fileTree("${project(projectName).projectDir}/tests").visit { details ->
         if (!details.path.contains("nullness-javac-errors") && details.name.endsWith('java')) {
@@ -196,7 +196,7 @@ task htmlValidate(type: Exec) {
 task allJavadoc(type: Javadoc, group: "Documentation") {
     description = 'Generates a global API documentation for all the modules'
     dependsOn(':checker:shadowJar')
-    dependsOn(':javacutil:tagletClasses')
+    dependsOn(':util:tagletClasses')
     source(project(':checker').sourceSets.main.allJava, project(':framework').sourceSets.main.allJava,
             project(':dataflow').sourceSets.main.allJava, project(':javacutil').sourceSets.main.allJava)
 
@@ -384,7 +384,7 @@ subprojects {
         }
 
         // Create a task for each JUnit test class whose name is the same as the JUnit class name.
-        sourceSets.test.allJava.filter { it.path.contains('s/src/tests') }.forEach { file ->
+        sourceSets.test.allJava.filter { it.path.contains('src/test/java/tests') }.forEach { file ->
             String junitClassName = file.name.replaceAll(".java", "")
             tasks.create(name: "${junitClassName}", type: Test) {
                 description "Run ${junitClassName} tests."

checker-qual/.classpath

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="bin/main" path="generated-src/main">
+	<classpathentry kind="src" output="bin/main" path="src/main/java">
 		<attributes>
 			<attribute name="gradle_scope" value="main"/>
 			<attribute name="gradle_used_by_scope" value="main,test"/>
@@ -24,7 +24,7 @@
 			<attribute name="gradle_used_by_scope" value="test"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="bin/compatQual" path="generated-src/compat">
+	<classpathentry kind="src" output="bin/compatQual" path="src/compatQual/java">
 		<attributes>
 			<attribute name="gradle_scope" value="compatQual"/>
 			<attribute name="gradle_used_by_scope" value="compatQual"/>

checker-qual/.project

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
 	<name>checker-qual</name>
-	<comment>Project checker-qual created by Buildship.</comment>
+	<comment></comment>
 	<projects>
 	</projects>
 	<buildSpec>

checker-qual/build.gradle

@@ -1,26 +1,16 @@
 sourceSets {
-    main {
-        java {
-            srcDirs = ['generated-src/main']
-        }
-    }
-
-    compatQual {
-        java {
-            srcDirs = ['generated-src/compat']
-        }
-    }
+    compatQual
 }
 
 task copySources(type: Copy) {
     description 'Copy checker-qual source from other projects.'
     includeEmptyDirs = false
     doFirst {
         // Delete the directory in case a previously copied file should no longer be in checker-qual
-        delete file('generated-src/main/')
+        delete file('src/main/java')
     }
 
-    from files('../checker/src', '../dataflow/src', '../framework/src')
+    from files('../checker/src/main/java', '../dataflow/src/main/java', '../framework/src/main/java')
     include "**/FormatUtil.java"
     include "**/NullnessUtil.java"
     include "**/RegexUtil.java"
@@ -35,7 +25,7 @@ task copySources(type: Copy) {
     // Make files read only.
     fileMode(0444)
 
-    into file('generated-src/main/')
+    into file('src/main/java')
 }
 
 compileJava {
@@ -47,15 +37,15 @@ task copyCompatQual(type: Copy) {
     includeEmptyDirs = false
     doFirst {
         // Delete the directory in case a previously copied file should no longer be in checker-qual
-        delete file('generated-src/compat/')
+        delete file('src/compat/java')
     }
 
-    from files('../checker/src', '../framework/src')
+    from files('../checker/src/main/java', '../framework/src/main/java')
     include "**/compatqual/*.java"
     // Make files read only.
     fileMode(0444)
 
-    into file('generated-src/compat')
+    into file('src/compat/java')
 }
 
 compileCompatQualJava {

checker/.classpath

@@ -1,10 +1,41 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry combineaccessrules="false" kind="src" path="/framework"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry excluding="testannotations/" kind="src" path="tests/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="/framework/tests/junit-4.12.jar"/>
-	<classpathentry kind="lib" path="/framework/tests/hamcrest-core-1.3.jar"/>
-	<classpathentry kind="output" path="build"/>
+	<classpathentry kind="src" output="bin/main" path="src/main/java">
+		<attributes>
+			<attribute name="gradle_scope" value="main"/>
+			<attribute name="gradle_used_by_scope" value="main,test"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/test" path="src/test/java">
+		<attributes>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value="test"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/test" path="src/test/resources">
+		<attributes>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value="test"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/testannotations" path="src/testannotations/java">
+		<attributes>
+			<attribute name="gradle_scope" value="testannotations"/>
+			<attribute name="gradle_used_by_scope" value="test,testannotations"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/testannotations" path="src/testannotations/resources">
+		<attributes>
+			<attribute name="gradle_scope" value="testannotations"/>
+			<attribute name="gradle_used_by_scope" value="test,testannotations"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
+	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
+	<classpathentry kind="src" path="/framework"/>
+	<classpathentry kind="src" path="/dataflow"/>
+	<classpathentry kind="src" path="/javacutil"/>
+	<classpathentry kind="src" path="/checker-qual"/>
+	<classpathentry kind="src" path="/util"/>
+	<classpathentry kind="output" path="bin/default"/>
 </classpath>

checker/.project

@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
 </projectDescription>

checker/build.gradle

@@ -1,28 +1,25 @@
+sourceSets {
+    main {
+        resources {
+            // Stub files, message.properties, etc.
+            srcDirs = ['src/main/java']
+            exclude '**/*.java'
+        }
+    }
+    testannotations
+}
+
 dependencies {
     compile project(':framework')
     compile project(':dataflow')
     compile project(':javacutil')
     compile project(':checker-qual')
 
     testCompile group: 'junit', name: 'junit', version: '4.12'
-}
+    testCompile project(':util')
+    testCompile sourceSets.testannotations.output
 
-sourceSets {
-    main {
-        java {
-            srcDirs = ['src']
-        }
-        resources {
-            // Stub files, message.properties, etc.
-            srcDirs = ['src']
-            exclude '**/*.java'
-        }
-    }
-    test {
-        java {
-            srcDirs = ['tests/src', '../framework/src/org/checkerframework/framework/test']
-        }
-    }
+    testannotationsCompile project(':checker-qual')
 }
 
 jar {

checker/src/org/checkerframework/checker/index/upperbound/OffsetEquation.java → checker/src/main/java/org/checkerframework/checker/index/upperbound/OffsetEquation.java

@@ -17,9 +17,9 @@
 import org.checkerframework.framework.util.FlowExpressionParseUtil;
 import org.checkerframework.framework.util.FlowExpressionParseUtil.FlowExpressionContext;
 import org.checkerframework.framework.util.FlowExpressionParseUtil.FlowExpressionParseException;
-import org.checkerframework.framework.util.PluginUtil;
 import org.checkerframework.framework.util.dependenttypes.DependentTypesError;
 import org.checkerframework.javacutil.AnnotationProvider;
+import org.checkerframework.javacutil.PluginUtil;
 import org.checkerframework.javacutil.TreeUtils;
 
 /**