2023-06->2023-09 Seems to have broke dependency graph management in our project (#1698)

* Add test for reproducing #1654
* Fix to make that test pass

---------

Co-authored-by: Stephan Herrmann <[email protected]>

Author: haubi

org.eclipse.jdt.apt.tests/src/org/eclipse/jdt/apt/tests/AnnotationProcessingCompilerToolTest.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2000, 2022 IBM Corporation and others.
+ * Copyright (c) 2000, 2022-2023 IBM Corporation and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -10,6 +10,7 @@
  *
  * Contributors:
  *     Salesforce - copied and adapted from org.eclipse.jdt.core.tests.compiler.regression.BatchCompilerTest
+ *     SSI Schaefer IT Solutions GmbH - add test_github1654()
  *******************************************************************************/
 package org.eclipse.jdt.apt.tests;
 
@@ -109,6 +110,84 @@ public void test_github844() throws IOException {
 		// @formatter:on
 	}
 
+	public void test_github1654() throws IOException {
+		// @formatter:off
+		runTest(
+			true /* shouldCompileOK */,
+			new String [] { /* sourceFiles */
+				"X.java", """
+					package p1;
+					import org.eclipse.jdt.apt.tests.external.annotations.batch.BatchGen;
+					@BatchGen
+					public class X {
+					}
+					""",
+				"Anno.java", """
+					package p1;
+					public @interface Anno {
+						public static final String V = "V";
+						String v() default "";
+					}
+					""",
+				"Breaks.java", """
+					package p2;
+					import p1.Anno;
+					import p1.gen.Class1;
+					@Anno (v = Anno.V)
+					public class Breaks {
+						public Class1 c1;
+					};
+					""",
+				"Works1.java", """
+					package p2;
+					import p1.Anno;
+					import p1.gen.Class1;
+					@Anno // (v = Anno.V)
+					public class Works1 {
+						public Class1 c1;
+					};
+					""",
+				"Works2.java", """
+					package p2;
+					import p1.Anno;
+					// import p1.gen.Class1;
+					@Anno(v = Anno.V)
+					public class Works2 {
+						// public Class1 c1;
+						public p1.gen.Class1 c1;
+					};
+					""",
+			},
+			null /* standardJavaFileManager */,
+			Arrays.asList(
+					"-d", OUTPUT_DIR,
+			        "-source", "1.6",
+			        "-g", "-preserveAllLocals",
+			        "-cp",  OUTPUT_DIR  + File.pathSeparator + _extJar.getAbsolutePath() ,
+			        "-s", OUTPUT_DIR  +  File.separator + "src-gen",
+			        "-processorpath", _extJar.getAbsolutePath(),
+			        "-XprintProcessorInfo",
+			        // TODO: after fixing the issue, enable and update expected output of:
+			        // "-XprintRounds",
+			        "-proceedOnError"
+					) /* options */,
+			new String[] { /* compileFileNames */
+				"X.java",
+				"Anno.java",
+				"Breaks.java",
+				"Works1.java",
+				"Works2.java"
+			},
+			"Discovered processor service org.eclipse.jdt.apt.tests.external.annotations.batch.BatchGenProcessor\n" +
+			"  supporting [org.eclipse.jdt.apt.tests.external.annotations.batch.BatchGen]\n" + 
+			"  in jar:"  + Path.of(_extJar.getCanonicalPath()).toUri().toURL().toString() + "!/\n" + 
+			"Processor org.eclipse.jdt.apt.tests.external.annotations.batch.BatchGenProcessor matches [org.eclipse.jdt.apt.tests.external.annotations.batch.BatchGen] and returns true\n" + 
+			"Processor org.eclipse.jdt.apt.tests.external.annotations.batch.BatchGenProcessor matches [] and returns false\n",
+			"" /* expectedErrOutputString */,
+			true /* shouldFlushOutputDirectory */ );
+		// @formatter:on
+	}
+	
 	protected static class CompilerInvocationTestsArguments {
 		StandardJavaFileManager standardJavaFileManager;
 		List<String> options;

org.eclipse.jdt.core.compiler.batch/src/org/eclipse/jdt/internal/compiler/lookup/CompilationUnitScope.java

@@ -412,8 +412,13 @@ void connectTypeHierarchy() {
 void integrateAnnotationsInHierarchy() {
 	// Only now that all hierarchy information is built we're ready for ...
 	// ... integrating annotations
-	for (int i = 0, length = this.topLevelTypes.length; i < length; i++)
-		this.topLevelTypes[i].scope.referenceType().updateSupertypesWithAnnotations(Collections.emptyMap());
+	try {
+		this.environment.suppressImportErrors = true;
+		for (int i = 0, length = this.topLevelTypes.length; i < length; i++)
+			this.topLevelTypes[i].scope.referenceType().updateSupertypesWithAnnotations(Collections.emptyMap());
+	} finally {
+		this.environment.suppressImportErrors = false;
+	}
 	// ... checking on permitted types
 	connectPermittedTypes();
 	for (int i = 0, length = this.topLevelTypes.length; i < length; i++)