1. Use AtomicFileWriter on the hypothesis that an exception during save() caused truncation.
2. Improve logging from the cleanup thread since that may be related to the root cause.
3. Regardless of the cause, recover more gracefully by deleting any truncated file rather than throwing the error up.

Instead it was being thrown in a Future that the master did not wait for:
the writing side failed with a closed pipe exception, and this meaningless error was thrown up.
Fixing by waiting for the reading side first, so any error there will be thrown up.
(If there was _also_ an error on the writing side, we would miss it, but typically this will just be the closed stream.)

[GROOVY-4292] Update Groovy to 1.8.9 to avoid random livelock during startup when init.groovy specified.
"GroovyInitScript.init" daemon prio=10 tid=0x00007f28d0001800 nid=0x48 runnable [0x00007f28cb79e000]
   java.lang.Thread.State: RUNNABLE
	at java.util.WeakHashMap.get(Unknown Source)
	at org.codehaus.groovy.ast.ClassHelper.makeCached(ClassHelper.java:121)
	at org.codehaus.groovy.ast.ClassHelper.makeWithoutCaching(ClassHelper.java:183)
	at org.codehaus.groovy.ast.ClassHelper.make(ClassHelper.java:170)
	at org.codehaus.groovy.ast.ClassHelper.make(ClassHelper.java:159)
	at org.codehaus.groovy.vmplugin.v5.Java5.makeClassNode(Java5.java:382)
	at org.codehaus.groovy.vmplugin.v5.Java5.makeParameter(Java5.java:403)
	at org.codehaus.groovy.vmplugin.v5.Java5.makeParameters(Java5.java:396)
	at org.codehaus.groovy.vmplugin.v5.Java5.configureClassNode(Java5.java:331)
	at org.codehaus.groovy.ast.ClassNode.lazyClassInit(ClassNode.java:262)
	- locked <0x00000000f4bfe2b0> (a java.lang.Object)
	at org.codehaus.groovy.ast.ClassNode.getInterfaces(ClassNode.java:356)
	at org.codehaus.groovy.ast.ClassNode.declaresInterface(ClassNode.java:946)
	at org.codehaus.groovy.ast.ClassNode.implementsInterface(ClassNode.java:926)
	at org.codehaus.groovy.ast.ClassNode.isDerivedFromGroovyObject(ClassNode.java:916)
	at org.codehaus.groovy.classgen.AsmClassGenerator.isGroovyObject(AsmClassGenerator.java:1070)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitPropertyExpression(AsmClassGenerator.java:1027)
	at org.codehaus.groovy.ast.expr.PropertyExpression.visit(PropertyExpression.java:55)
	at org.codehaus.groovy.classgen.asm.BinaryExpressionHelper.evaluateEqual(BinaryExpressionHelper.java:287)
	at org.codehaus.groovy.classgen.asm.BinaryExpressionHelper.eval(BinaryExpressionHelper.java:76)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitBinaryExpression(AsmClassGenerator.java:519)
	at org.codehaus.groovy.ast.expr.BinaryExpression.visit(BinaryExpression.java:49)
	at org.codehaus.groovy.classgen.asm.StatementWriter.writeExpressionStatement(StatementWriter.java:599)
	at org.codehaus.groovy.classgen.asm.OptimizingStatementWriter.writeExpressionStatement(OptimizingStatementWriter.java:354)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitExpressionStatement(AsmClassGenerator.java:501)
	at org.codehaus.groovy.ast.stmt.ExpressionStatement.visit(ExpressionStatement.java:40)
	at org.codehaus.groovy.classgen.asm.StatementWriter.writeBlockStatement(StatementWriter.java:80)
	at org.codehaus.groovy.classgen.asm.OptimizingStatementWriter.writeBlockStatement(OptimizingStatementWriter.java:155)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitBlockStatement(AsmClassGenerator.java:447)
	at org.codehaus.groovy.ast.stmt.BlockStatement.visit(BlockStatement.java:69)
	at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClassCodeContainer(ClassCodeVisitorSupport.java:101)
	at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitConstructorOrMethod(ClassCodeVisitorSupport.java:112)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitStdMethod(AsmClassGenerator.java:312)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitConstructorOrMethod(AsmClassGenerator.java:269)
	at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitMethod(ClassCodeVisitorSupport.java:123)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitMethod(AsmClassGenerator.java:389)
	at org.codehaus.groovy.ast.ClassNode.visitContents(ClassNode.java:1056)
	at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClass(ClassCodeVisitorSupport.java:50)
	at org.codehaus.groovy.classgen.AsmClassGenerator.visitClass(AsmClassGenerator.java:173)
	at org.codehaus.groovy.control.CompilationUnit$14.call(CompilationUnit.java:767)
	at org.codehaus.groovy.control.CompilationUnit.applyToPrimaryClassNodes(CompilationUnit.java:967)
	at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:546)
	at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:524)
	at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:501)
	at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:306)
	at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:287)
	at groovy.lang.GroovyShell.parseClass(GroovyShell.java:731)
	at groovy.lang.GroovyShell.parse(GroovyShell.java:743)
	at groovy.lang.GroovyShell.evaluate(GroovyShell.java:578)
	at hudson.init.impl.GroovyInitScript.execute(GroovyInitScript.java:83)
	at hudson.init.impl.GroovyInitScript.execute(GroovyInitScript.java:78)
	at hudson.init.impl.GroovyInitScript.init(GroovyInitScript.java:57)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at hudson.init.InitializerFinder.invoke(InitializerFinder.java:120)
	at hudson.init.InitializerFinder$TaskImpl.run(InitializerFinder.java:184)
	at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:259)
	at jenkins.model.Jenkins$7.runTask(Jenkins.java:889)
	at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:187)
	at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:94)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)

Root cause of class loading error (on jnr.ffi.util.ref.internal.Finalizer$ShutDown) still unclear,
but easy fix is to simplify ClientAuthenticationCache.save to use FilePath.chmod,
which at least for now relies on hudson.util.jna.GNUCLibrary rather than JNR.

[FIXED JENKINS-19135] Permit a user to configure an axis with no values without throwing exceptions.
The project cannot be usefully built in this case but at least they can go back and reconfigure it.
Also fixing Layouter.Column to not throw NoSuchElementException (in violation of Iterator contract)
and thus break project overview when there is an empty Axis in the trivial list (due to an unintentional IndexOutOfBoundsException).

Added another attribute 'checkDependsOn' on <input> elements (akin to
'fillDependsOn', etc) to list up the other dependency controls, and
insert appropriate onchange events.

'checkUrl' is now just the stem portion of the URL to invoke, and
the client script builds up the query parameters.

Also [JENKINS-19042] does not seem to have made it into 1.526; seems to have been towards 1.527.

Integrated bytecode-compatibility-transformer that allows core to
do signature changes on properties that plugins might depend on.

The library performs necessary bytecode transformation to achieve this.

The first use of this is to fix plugins that looks for List
AbstractProject.triggers, thereby resolving JENKINS-18677.

For the time being, I'm not loading such compatibility annotations from
plugins, but I did code that in PluginManager. Let's see how this
feature work out for a while in the core, and if it looks stable and
solid, we'll open it up to plugins at that point.