The last nightly build (s41731) breaks analysis, s41692 works fine.

Internal error evaluating editor-analyze (InterpreterException; see error log)
rewriting failed, trace:
editor_analyze_0_0
editor_analyze_0_0
analysis_default_editor_0_0
analysis_single_default_interface_0_0
analysis_single_default_3_1
analysis_single_default_4_1
analysis_files_spoofax_5_2
analysis_files_4_2
analysis_files_no_builtins_4_2
measure_time_2_0
map_1_0
analysis_collect_1_2
analysis_collect_2_2

Java trace:

org.spoofax.interpreter.core.InterpreterException: Exception during evaluation
	at org.spoofax.interpreter.core.Interpreter.evaluate(Interpreter.java:120)
	at org.spoofax.interpreter.core.Interpreter.invoke(Interpreter.java:82)
	at org.strategoxt.HybridInterpreter.invoke(HybridInterpreter.java:442)
	at org.strategoxt.imp.debug.core.str.launching.DebuggableHybridInterpreter.invoke(DebuggableHybridInterpreter.java:150)
	at org.strategoxt.imp.runtime.services.StrategoObserver.invoke(StrategoObserver.java:637)
	at org.strategoxt.imp.runtime.services.StrategoObserver.invokeSilent(StrategoObserver.java:695)
	at org.strategoxt.imp.runtime.services.StrategoObserver.update(StrategoObserver.java:399)
	at org.strategoxt.imp.runtime.services.StrategoObserverBackgroundUpdateJob.analyzeFile(StrategoObserverBackgroundUpdateJob.java:118)
	at org.strategoxt.imp.runtime.services.StrategoObserverBackgroundUpdateJob.analyze(StrategoObserverBackgroundUpdateJob.java:64)
	at org.strategoxt.imp.runtime.services.StrategoAnalysisQueue$UpdateJob.run(StrategoAnalysisQueue.java:82)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53)
Caused by: org.strategoxt.lang.StrategoException: Exception in execution of primitive 'LANG_index_stop_collection'
	at org.strategoxt.lang.Context.invokePrimitive(Context.java:240)
	at org.strategoxt.lang.Context.invokePrimitive(Context.java:216)
	at trans.index_stop_collection_0_0.invoke(index_stop_collection_0_0.java:27)
	at trans.analysis_collect_2_2.invoke(analysis_collect_2_2.java:110)
	at trans.analysis_collect_1_2.invoke(analysis_collect_1_2.java:28)
	at trans.lifted917.invoke(lifted917.java:33)
	at org.strategoxt.lang.SRTS_all.map(SRTS_all.java:60)
	at org.strategoxt.lang.SRTS_all.invoke(SRTS_all.java:21)
	at org.strategoxt.lang.parallel.stratego_parallel.ParallelAll.invoke(ParallelAll.java:67)
	at org.strategoxt.lang.compat.override.performance_tweaks.map_1_0_override.invoke(map_1_0_override.java:29)
	at trans.lifted916.invoke(lifted916.java:45)
	at trans.measure_time_2_0.invoke(measure_time_2_0.java:43)
	at trans.analysis_files_no_builtins_4_2.invoke(analysis_files_no_builtins_4_2.java:128)
	at trans.analysis_files_4_2.invoke(analysis_files_4_2.java:33)
	at trans.analysis_files_spoofax_5_2.invoke(analysis_files_spoofax_5_2.java:41)
	at trans.analysis_single_default_4_1.invoke(analysis_single_default_4_1.java:41)
	at trans.analysis_single_default_3_1.invoke(analysis_single_default_3_1.java:28)
	at trans.analysis_single_default_interface_0_0.invoke(analysis_single_default_interface_0_0.java:33)
	at trans.analysis_default_editor_0_0.invoke(analysis_default_editor_0_0.java:38)
	at trans.editor_analyze_0_0.invoke(editor_analyze_0_0.java:28)
	at org.strategoxt.lang.Strategy.invokeDynamic(Strategy.java:30)
	at org.strategoxt.lang.InteropSDefT.evaluate(InteropSDefT.java:192)
	at org.strategoxt.lang.InteropSDefT.evaluate(InteropSDefT.java:183)
	at org.strategoxt.lang.InteropSDefT$StrategyBody.evaluate(InteropSDefT.java:245)
	at org.spoofax.interpreter.core.Interpreter.evaluate(Interpreter.java:109)
	... 10 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
	at org.spoofax.interpreter.library.index.primitives.LANG_index_stop_collection.call(LANG_index_stop_collection.java:21)
	at org.strategoxt.lang.Context.invokePrimitive(Context.java:227)
	... 34 more

Submitted by Daco Harkes on 24 June 2014 at 23:50

This indicates that you are somehow using an old version of the runtime libraries. Are you running custom runtime libraries? If so, update them. If not, try deleting the lib/runtime folder.

I was still running custom, not updated, runtime libraries.
Using just the build in runtime libraries fixed the problem.