Indexer: improve logging for empty .class/.jar files

[jukzi]

As happening with empty dummy ".class" / empty.jar files in tests for example during:
JavaElementDeltaTests.testChangeExternalLibFolder3(),
CompletionTests2.testBug281598b().
Empty files are no real problem they just do not need to be indexed.

was ArrayIndexOutOfBoundsException / "java.util.zip.ZipException: zip file is empty" with long stacktraces flooding the logfile

[jukzi]

was for example

!ENTRY org.eclipse.jdt.core 4 4 2024-12-20 05:06:49.342
!MESSAGE Failed to index /P/empty.jar
!STACK 0
java.util.zip.ZipException: zip file is empty
	at java.base/java.util.zip.ZipFile$Source.zerror(ZipFile.java:1781)
	at java.base/java.util.zip.ZipFile$Source.findEND(ZipFile.java:1562)
	at java.base/java.util.zip.ZipFile$Source.initCEN(ZipFile.java:1657)
	at java.base/java.util.zip.ZipFile$Source.<init>(ZipFile.java:1495)
	at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1458)
	at java.base/java.util.zip.ZipFile$CleanableResource.<init>(ZipFile.java:724)
	at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:251)
	at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:180)
	at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:194)
	at org.eclipse.jdt.internal.core.search.indexing.AddJarFileToIndex.execute(AddJarFileToIndex.java:154)
	at org.eclipse.jdt.internal.core.search.processing.JobManager.indexerLoop(JobManager.java:541)
	at java.base/java.lang.Thread.run(Thread.java:1583)

!ENTRY org.eclipse.jdt.core 4 4 2024-12-20 05:06:49.342

!ENTRY org.eclipse.jdt.core 2 0 2024-12-20 04:59:55.951
!MESSAGE The Java indexing could not index /.org.eclipse.jdt.core.external.folders/.link12/p/X.class. This .class file doesn't follow the class file format specification. Please report this issue against the .class file vendor
!STACK 0
org.eclipse.jdt.internal.compiler.classfmt.ClassFormatException
	at org.eclipse.jdt.internal.compiler.classfmt.ClassFileReader.<init>(ClassFileReader.java:554)
	at org.eclipse.jdt.internal.compiler.classfmt.ClassFileReader.<init>(ClassFileReader.java:218)
	at org.eclipse.jdt.internal.core.search.indexing.BinaryIndexer.indexDocument(BinaryIndexer.java:684)
	at org.eclipse.jdt.internal.core.search.JavaSearchParticipant.indexDocument(JavaSearchParticipant.java:99)
	at org.eclipse.jdt.internal.core.search.indexing.IndexManager.indexDocument(IndexManager.java:662)
	at org.eclipse.jdt.internal.core.search.indexing.IndexManager$2.execute(IndexManager.java:1267)
	at org.eclipse.jdt.internal.core.search.processing.JobManager.indexerLoop(JobManager.java:541)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused in /.org.eclipse.jdt.core.external.folders/.link12/p/X.class by: java.lang.ArrayIndexOutOfBoundsException: Index 6 out of bounds for length 0
	at org.eclipse.jdt.internal.compiler.classfmt.ClassFileStruct.u2At(ClassFileStruct.java:55)
	at org.eclipse.jdt.internal.compiler.classfmt.ClassFileReader.<init>(ClassFileReader.java:246)
	at org.eclipse.jdt.internal.compiler.classfmt.ClassFileReader.<init>(ClassFileReader.java:218)
	at org.eclipse.jdt.internal.core.search.indexing.BinaryIndexer.indexDocument(BinaryIndexer.java:684)
	at org.eclipse.jdt.internal.core.search.JavaSearchParticipant.indexDocument(JavaSearchParticipant.java:99)
	at org.eclipse.jdt.internal.core.search.indexing.IndexManager.indexDocument(IndexManager.java:662)
	at org.eclipse.jdt.internal.core.search.indexing.IndexManager$2.execute(IndexManager.java:1267)
	at org.eclipse.jdt.internal.core.search.processing.JobManager.indexerLoop(JobManager.java:541)
	at java.base/java.lang.Thread.run(Thread.java:1583)

!MESSAGE File no longer exists: /TypeHierarchy/linked.jar
!STACK 0
java.nio.file.NoSuchFileException: C:\Users\genie.releng\workspace\AutomatedTests\ep435I-unit-win32-x86_64-java21\workarea\I20241219-1920\eclipse-testing\test-eclipse\eclipse\jdt_model_folder\unknown.jar
	at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85)
	at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103)
	at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108)
	at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53)
	at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38)
	at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:197)
	at java.base/java.nio.file.Files.readAttributes(Files.java:1853)
	at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1445)
	at java.base/java.util.zip.ZipFile$CleanableResource.<init>(ZipFile.java:724)
	at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:251)
	at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:180)
	at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:194)
	at org.eclipse.jdt.internal.core.search.indexing.AddJarFileToIndex.execute(AddJarFileToIndex.java:154)
	at org.eclipse.jdt.internal.core.search.processing.JobManager.indexerLoop(JobManager.java:541)
	at java.base/java.lang.Thread.run(Thread.java:1583)

https://download.eclipse.org/eclipse/downloads/drops4/R-4.32-202406010610/testresults/ep432I-unit-win32-java17_win32.win32.x86_64_17/org.eclipse.jdt.core.tests.model.AllJavaModelTests.txt