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I think it would be nice if the org.eclipse.xtext.util.MergeableManifest class used by org.eclipse.xtext.generator.Generator would respect the org.eclipse.xtext.generator.Naming#lineDelimiter setting for the generation. Currently it insists on CRLF line feeds. AFAICT there is no requirement that CRLF must be used in manifests. It's rather the opposite (any of CRLF, CR, or LF are accepted): https://docs.oracle.com/javase/8/docs/technotes/guides/jar/jar.html#JARManifest.
The spec doesn't demand CRLF but from looking at the code in java.util.jar.Manifest.write(OutputStream) CRLF is always used to write a manifest file. We need to decide if we want to use that default as the only supported line delimiter or if we want to make it customizable.
OK. AFAIK the PDE tooling will use the platform default, but I am not 100% sure about that.
After a brief offline discussion, there's a tendency towards configurable line endings also for the manifests. While we're at it, we have to make sure that manifests are always UTF-8 encoded.
*** This bug has been marked as a duplicate of bug 378980 ***