The "jmod" tool needs to update .jar files as well as .jmod files when adding hashes to the module-info file. This is handled in the method jdk.tools.jmod.JmodTask.updateModularJar() for modular jar files and in the methods jdk.tools.jmod.JmodTask.updateJmodFile() and jdk.tools.jmod.JmodOutputStream.writeEntry() for .jmod files.

Unfortunately, both implementations are incorrect because they are writing the JarEntry/ZipEntry entries which they reading from the ZipInputStream verbatim to the ZipOutputStream. This approach is not correct, because Zip/Entry/JarEntry contains both, the compressed and uncompressed size of the corresponding entry. But the original Deflater which initially compressed that entry can be either different from the current one or it might have used a different compression level compared to the current Deflater which re-deflates the entry data.

When the newly created entry is closed, the new compressed size will be checked against the original compressed size if that was recorded in the ZipEntry/JarEntry entry and an exception will be thrown, when they differ. For modular jar files it looks as follows:

$ jmod hash --module-path . --hash-modules .*
Error: java.util.zip.ZipException: invalid entry compressed size (expected 58 but got 57 bytes)
java.io.UncheckedIOException: java.util.zip.ZipException: invalid entry compressed size (expected 58 but got 57 bytes)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.lambda$updateModularJar$3(JmodTask.java:995)
	at java.base/java.util.zip.ZipFile$EntrySpliterator.tryAdvance(ZipFile.java:571)
	at java.base/java.util.Spliterator.forEachRemaining(Spliterator.java:326)
	at java.base/java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:658)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.updateModularJar(JmodTask.java:980)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.updateModuleInfo(JmodTask.java:957)
	at jdk.jlink/jdk.tools.jmod.JmodTask.lambda$hashModules$3(JmodTask.java:300)
	at java.base/java.util.HashMap.forEach(HashMap.java:1425)
	at jdk.jlink/jdk.tools.jmod.JmodTask.hashModules(JmodTask.java:291)
	at jdk.jlink/jdk.tools.jmod.JmodTask.run(JmodTask.java:220)
	at jdk.jlink/jdk.tools.jmod.Main.main(Main.java:34)
	Suppressed: java.util.zip.ZipException: invalid entry compressed size (expected 58 but got 57 bytes)
		at java.base/java.util.zip.ZipOutputStream.closeEntry(ZipOutputStream.java:267)
		at java.base/java.util.zip.ZipOutputStream.finish(ZipOutputStream.java:360)
		at java.base/java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:237)
		at java.base/java.util.zip.ZipOutputStream.close(ZipOutputStream.java:377)
		at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.updateModularJar(JmodTask.java:976)
		... 6 more
Caused by: java.util.zip.ZipException: invalid entry compressed size (expected 58 but got 57 bytes)
	at java.base/java.util.zip.ZipOutputStream.closeEntry(ZipOutputStream.java:267)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.lambda$updateModularJar$3(JmodTask.java:992)
	... 10 more

For jmod files it looks like this:

$ jmod hash --module-path . --hash-modules .*
Error: java.util.zip.ZipException: invalid entry compressed size (expected 383 but got 377 bytes)
java.io.UncheckedIOException: java.util.zip.ZipException: invalid entry compressed size (expected 383 but got 377 bytes)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.lambda$updateJmodFile$4(JmodTask.java:1021)
	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
	at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
	at java.base/java.util.zip.ZipFile$EntrySpliterator.tryAdvance(ZipFile.java:571)
	at java.base/java.util.Spliterator.forEachRemaining(Spliterator.java:326)
	at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
	at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.updateJmodFile(JmodTask.java:1009)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.updateModuleInfo(JmodTask.java:955)
	at jdk.jlink/jdk.tools.jmod.JmodTask.lambda$hashModules$3(JmodTask.java:300)
	at java.base/java.util.HashMap.forEach(HashMap.java:1425)
	at jdk.jlink/jdk.tools.jmod.JmodTask.hashModules(JmodTask.java:291)
	at jdk.jlink/jdk.tools.jmod.JmodTask.run(JmodTask.java:220)
	at jdk.jlink/jdk.tools.jmod.Main.main(Main.java:34)
	Suppressed: java.util.zip.ZipException: invalid entry compressed size (expected 383 but got 377 bytes)
		at java.base/java.util.zip.ZipOutputStream.closeEntry(ZipOutputStream.java:267)
		at java.base/java.util.zip.ZipOutputStream.finish(ZipOutputStream.java:360)
		at java.base/java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:237)
		at java.base/java.util.zip.ZipOutputStream.close(ZipOutputStream.java:377)
		at jdk.jlink/jdk.tools.jmod.JmodOutputStream.close(JmodOutputStream.java:114)
		at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.updateJmodFile(JmodTask.java:1006)
		... 6 more
Caused by: java.util.zip.ZipException: invalid entry compressed size (expected 383 but got 377 bytes)
	at java.base/java.util.zip.ZipOutputStream.closeEntry(ZipOutputStream.java:267)
	at jdk.jlink/jdk.tools.jmod.JmodOutputStream.writeEntry(JmodOutputStream.java:97)
	at jdk.jlink/jdk.tools.jmod.JmodTask$Hasher.lambda$updateJmodFile$4(JmodTask.java:1018)
	... 17 more

The errors can be provoked by creating the initial jar or jmod files with a different zlib implementation (e.g. LD_LIBRARY_PATH=/ziptests/build/zlib-cloudflare jar -cf ../mb_cf.jar *)

The fix is simple. Instead of copying the ZipEntry/JarEntry entries verbatim to the output stream, simply write newly created ZipEntry/JarEntry entries to the output stream which only contain the required attributes. This is also the way how this is done by the jar tool, when it updates jar files.