Empty project, 1 DSL file, and a Spoofax nature (same without a Spoofax nature):

14:42 | INFO  | c.v.i.DefaultFileSystemManager - Using "/var/folders/c1/zhg5ddcn1rld0gvvtdbxfb700000gn/T/vfs_cache6650732873476554334" as temporary files store.
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | ERROR | o.m.s.e.e.EditorUpdateJob      - Failed to update editor for eclipse:///debug/debug.ice
org.metaborg.core.MetaborgException: Language could not be identified
	at org.metaborg.spoofax.eclipse.editor.EditorUpdateJob.update(EditorUpdateJob.java:201) ~[org.metaborg.spoofax.eclipse_2.0.0.jar:na]
	at org.metaborg.spoofax.eclipse.editor.EditorUpdateJob.run(EditorUpdateJob.java:130) ~[org.metaborg.spoofax.eclipse_2.0.0.jar:na]
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55) [org.eclipse.core.jobs_3.8.0.v20160509-0411.jar:na]
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, content assist is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, reference resolution is disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, hover tooltips are disabled until language is identified
14:42 | WARN  | .t.s.SourceViewerConfiguration - Identified language for eclipse:///debug/debug.ice is null, toggle comment is disabled until language is identified

Eclipse: org.eclipse.platform.ide 4.6.0.I20160606-1100
Spoofax: org.metaborg.spoofax.eclipse 2.0.0
System: Mac OS X x86_64 10.11.6

Submitted by Daco Harkes on 22 August 2016 at 14:47

Issue also on Windows.

Eclipse: org.eclipse.platform.ide 4.6.0.I20160606-1100
Spoofax: org.metaborg.spoofax.eclipse 2.0.0
System: Windows 10 amd64 10.0