Properly fix issue with checkerframework Gradle plugin.

Previously, `lsif-java index` had custom logic to disable the
checkerframework Gradle plugin in order to prevent the error
"plug-in not found: semanticdb". This commit replaces that custom logic
with a proper fix to this bug, which is to automatically inject the
SemanticDB compiler plugin jar to the annotation processor path
as well as the compile classpath.

Author: olafurpg

lsif-java/src/main/scala/com/sourcegraph/lsif_java/buildtools/GradleBuildTool.scala

@@ -78,17 +78,7 @@ class GradleBuildTool(index: IndexCommand) extends BuildTool("Gradle", index) {
       buildCommand +=
         s"-Porg.gradle.java.installations.paths=${toolchains.paths()}"
     }
-    buildCommand ++=
-      index.finalBuildCommand(
-        List(
-          // Disable the checkerframework plugin because it updates the processorpath
-          // in a way that causes the error "plug-in not found: semanticdb".
-          // Details: https://github.com/kelloggm/checkerframework-gradle-plugin/blob/76d1926ae22144b082dfcfde1abe625750469398/src/main/groovy/org/checkerframework/gradle/plugin/CheckerFrameworkPlugin.groovy#L374-L376
-          "-PskipCheckerFramework",
-          "clean",
-          "compileTestJava"
-        )
-      )
+    buildCommand ++= index.finalBuildCommand(List("clean", "compileTestJava"))
     buildCommand += lsifJavaDependencies
 
     val result = index.process(buildCommand, env = Map("TERM" -> "dumb"))

semanticdb-agent/src/main/java/com/sourcegraph/semanticdb_javac/SemanticdbAgent.java

@@ -49,6 +49,17 @@ public static void premain(String agentArgs, Instrumentation inst) {
                     named("getCompileClasspath"),
                     DefaultJvmLanguageCompileSpecAdvice.class.getName()))
         .installOn(inst);
+    new AgentBuilder.Default()
+        .disableClassFormatChanges()
+        .type(
+            named("org.gradle.api.internal.tasks.compile.DefaultJavaCompileSpec")
+                .or(named("tests.GradleDefaultJavaCompileSpec")))
+        .transform(
+            new AgentBuilder.Transformer.ForAdvice()
+                .advice(
+                    named("getAnnotationProcessorPath"),
+                    DefaultJavaCompileSpecAdvice.class.getName()))
+        .installOn(inst);
     new AgentBuilder.Default()
         .type(
             named("org.gradle.api.internal.tasks.compile.JavaCompilerArgumentsBuilder")
@@ -92,6 +103,23 @@ public static void getClasspath(
     }
   }
 
+  @SuppressWarnings("all")
+  public static class DefaultJavaCompileSpecAdvice {
+    @Advice.OnMethodExit
+    public static void getAnnotationProcessorPath(
+        @Advice.Return(readOnly = false, typing = DYNAMIC) List<File> classpath) {
+      if (classpath == null) return;
+      String PLUGINPATH = System.getProperty("semanticdb.pluginpath");
+      if (PLUGINPATH == null) throw new NoSuchElementException("-Dsemanticdb.pluginpath");
+      File semanticdbJar = new File(PLUGINPATH);
+      if (!classpath.contains(semanticdbJar)) {
+        List<File> newClasspath = new ArrayList<>(classpath);
+        newClasspath.add(semanticdbJar);
+        classpath = newClasspath;
+      }
+    }
+  }
+
   @SuppressWarnings("all")
   public static class JavaCompilerArgumentsBuilderAdvice {