--- a/mx/commands.py	Thu Jun 28 14:15:00 2012 +0200
+++ b/mx/commands.py	Thu Jun 28 15:36:28 2012 +0200
@@ -37,7 +37,7 @@
 _graal_home = dirname(dirname(__file__))
 
 """ Used to distinguish an exported GraalVM (see 'mx export'). """
-_vmSourcesAvailable = exists(join(_graal_home, 'make')) and exists(join(_graal_home, 'src')) 
+_vmSourcesAvailable = exists(join(_graal_home, 'make')) and exists(join(_graal_home, 'src'))
 
 """ The VM that will be run by the 'vm' command: graal(default), client or server.
     This can be set via the global '--vm' option. """
@@ -73,7 +73,7 @@
  * or visit www.oracle.com if you need additional information or have any
  * questions.
  */
- 
+
 """
 
 def clean(args):
@@ -88,22 +88,22 @@
 
 def export(args):
     """create a GraalVM zip file for distribution"""
-    
+
     parser = ArgumentParser(prog='mx export');
     parser.add_argument('--omit-vm-build', action='store_false', dest='vmbuild', help='omit VM build step')
     parser.add_argument('--omit-dist-init', action='store_false', dest='distInit', help='omit class files and IDE configurations from distribution')
     parser.add_argument('zipfile', nargs=REMAINDER, metavar='zipfile')
 
     args = parser.parse_args(args)
-    
+
     tmp = tempfile.mkdtemp(prefix='tmp', dir=_graal_home)
     if args.vmbuild:
         # Make sure the product VM binary is up to date
         build(['product'])
-        
+
     mx.log('Copying Java sources and mx files...')
     mx.run(('hg archive -I graal -I mx -I mxtool -I mx.sh ' + tmp).split())
-    
+
     # Copy the GraalVM JDK
     mx.log('Copying GraalVM JDK...')
     src = _jdk()
@@ -123,11 +123,11 @@
         mx.run('mx build'.split(), cwd=tmp)
         mx.log('Creating IDE configurations...')
         mx.run('mx ideinit'.split(), cwd=tmp)
-        
+
     # clean up temp directory
     mx.log('Cleaning up...')
     shutil.rmtree(tmp)
-    
+
     mx.log('Created distribution in ' + zfName)
 
 def example(args):
@@ -140,7 +140,7 @@
     def run_example(verbose, project, mainClass):
         cp = mx.classpath(project)
         sharedArgs = ['-Xcomp', '-XX:CompileOnly=Main', mainClass]
-        
+
         res = []
         mx.log("=== Server VM ===")
         printArg = '-XX:+PrintCompilation' if verbose else '-XX:-PrintCompilation'
@@ -150,7 +150,7 @@
         res.append(vm(['-cp', cp, printArg, '-G:-Extend', '-G:-Inline'] + sharedArgs))
         mx.log("=== Graal VM with extensions ===")
         res.append(vm(['-cp', cp, printArg, '-G:+Extend', '-G:-Inline'] + sharedArgs))
-        
+
         if len([x for x in res if x != 0]) != 0:
             return 1
         return 0
@@ -173,7 +173,7 @@
 
 def dacapo(args):
     """run one or all DaCapo benchmarks
-    
+
     DaCapo options are distinguished from VM options by a '@' prefix.
     For example, '@-n @5' will pass '-n 5' to the
     DaCapo harness."""
@@ -196,52 +196,52 @@
                     del args[0]
                 else:
                     bm = args[0]
-                
+
                 del args[0]
                 if bm not in sanitycheck.dacapoSanityWarmup.keys():
                     mx.abort('unknown benchmark: ' + bm + '\nselect one of: ' + str(sanitycheck.dacapoSanityWarmup.keys()))
                 numTests[bm] = n
-    
-    if len(numTests) is 0:    
+
+    if len(numTests) is 0:
         for bench in sanitycheck.dacapoSanityWarmup.keys():
             numTests[bench] = 1
-    
+
     # Extract DaCapo options
     dacapoArgs = [(arg[1:]) for arg in args if arg.startswith('@')]
-    
-    # The remainder are VM options 
+
+    # The remainder are VM options
     vmOpts = [arg for arg in args if not arg.startswith('@')]
     vm = _vm
-    
+
     failed = []
     for (test, n) in numTests.items():
         if not sanitycheck.getDacapo(test, n, dacapoArgs).test(vm, opts=vmOpts):
             failed.append(test)
-    
+
     if len(failed) != 0:
         mx.abort('DaCapo failures: ' + str(failed))
-    
+
 def intro(args):
     """run a simple program and visualize its compilation in the Graal Visualizer"""
     # Start the visualizer in a separate thread
     t = Thread(target=gv, args=([[]]))
     t.start()
-    
+
     # Give visualizer time to start
     mx.log('Waiting 5 seconds for visualizer to start')
     time.sleep(5)
-    
+
     vm(['-G:Dump=', '-G:MethodFilter=greet', '-Xcomp', '-XX:CompileOnly=HelloWorld::greet', '-cp', mx.classpath('com.oracle.graal.examples')] + args + ['examples.HelloWorld'])
 
 def scaladacapo(args):
     """run one or all Scala DaCapo benchmarks
-    
+
     Scala DaCapo options are distinguished from VM options by a '@' prefix.
     For example, '@--iterations @5' will pass '--iterations 5' to the
     DaCapo harness."""
 
     numTests = {}
-    
+
     if len(args) > 0:
         level = getattr(sanitycheck.SanityCheckLevel, args[0], None)
         if level is not None:
@@ -259,34 +259,34 @@
                     del args[0]
                 else:
                     bm = args[0]
-                
+
                 del args[0]
                 if bm not in sanitycheck.dacapoScalaSanityWarmup.keys():
                     mx.abort('unknown benchmark: ' + bm + '\nselect one of: ' + str(sanitycheck.dacapoScalaSanityWarmup.keys()))
                 numTests[bm] = n
-    
-    if len(numTests) is 0:    
+
+    if len(numTests) is 0:
         for bench in sanitycheck.dacapoScalaSanityWarmup.keys():
             numTests[bench] = 1
-    
+
     # Extract DaCapo options
     dacapoArgs = [(arg[1:]) for arg in args if arg.startswith('@')]
-    
-    # The remainder are VM options 
+
+    # The remainder are VM options
     vmOpts = [arg for arg in args if not arg.startswith('@')]
     vm = _vm;
-    
+
     failed = []
     for (test, n) in numTests.items():
         if not sanitycheck.getScalaDacapo(test, n, dacapoArgs).test(vm, opts=vmOpts):
             failed.append(test)
-    
+
     if len(failed) != 0:
         mx.abort('Scala DaCapo failures: ' + str(failed))
 
 def _vmLibDirInJdk(jdk):
     """
-    Get the directory within a JDK where the server and client 
+    Get the directory within a JDK where the server and client
     subdirectories are located.
     """
     if platform.system() == 'Darwin':
@@ -322,13 +322,13 @@
                 if not exists(src):
                     mx.abort('Host JDK directory is missing: ' + src)
                 shutil.copytree(src, dst)
-                
+
             # Make a copy of the default VM so that this JDK can be
-            # reliably used as the bootstrap for a HotSpot build.                
+            # reliably used as the bootstrap for a HotSpot build.
             jvmCfg = _vmCfgInJdk(jdk)
             if not exists(jvmCfg):
                 mx.abort(jvmCfg + ' does not exist')
-                
+
             lines = []
             defaultVM = None
             with open(jvmCfg) as f:
@@ -343,11 +343,11 @@
 
             assert defaultVM is not None, 'Could not find default VM in ' + jvmCfg
             shutil.copytree(join(_vmLibDirInJdk(jdk), defaultVM), join(_vmLibDirInJdk(jdk), defaultVM + '0'))
-            
+
             with open(jvmCfg, 'w') as f:
                 for line in lines:
                     f.write(line)
-                    
+
             # Install a copy of the disassembler library
             try:
                 hsdis([], copyToDir=_vmLibDirInJdk(jdk))
@@ -356,14 +356,14 @@
     else:
         if not exists(jdk):
             mx.abort('The ' + build + ' VM has not been created - run \'mx clean; mx build ' + build + '\'')
-    return jdk 
+    return jdk
 
 # run a command in the windows SDK Debug Shell
 def _runInDebugShell(cmd, workingDir, logFile=None, findInOutput=None, respondTo={}):
     newLine = os.linesep
     STARTTOKEN = 'RUNINDEBUGSHELL_STARTSEQUENCE'
     ENDTOKEN = 'RUNINDEBUGSHELL_ENDSEQUENCE'
-    
+
     winSDK = mx.get_env('WIN_SDK', 'C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\')
 
     p = subprocess.Popen('cmd.exe /E:ON /V:ON /K ""' + winSDK + '/Bin/SetEnv.cmd" & echo ' + STARTTOKEN + '"', \
@@ -402,22 +402,22 @@
     if logFile:
         log.close()
     return ret
-    
+
 def jdkhome(args, vm=None):
     """prints the JDK directory selected for the 'vm' command"""
-    
+
     build = _vmbuild if _vmSourcesAvailable else 'product'
     print join(_graal_home, 'jdk' + mx.java().version, build)
 
 def build(args, vm=None):
     """build the VM binary
-    
+
     The global '--vm' option selects which VM to build. This command also
     compiles the Graal classes irrespective of what VM is being built.
     The optional last argument specifies what build level is to be used
     for the VM binary."""
-    
-    # Call mx.build to compile the Java sources        
+
+    # Call mx.build to compile the Java sources
     opts2 = mx.build(['--source', '1.7'] + args, parser=ArgumentParser(prog='mx build'))
 
     if not _vmSourcesAvailable or not opts2.native:
@@ -429,7 +429,7 @@
 
     if vm is None:
         vm = _vm
-        
+
     if vm == 'server':
         buildSuffix = ''
     elif vm == 'client':
@@ -437,7 +437,7 @@
     else:
         assert vm == 'graal', vm
         buildSuffix = 'graal'
-        
+
     for build in builds:
         if build == 'ide-build-target':
             build = os.environ.get('IDE_BUILD_TARGET', 'product')
@@ -446,16 +446,16 @@
                 continue
 
         jdk = _jdk(build, create=True)
-            
+
         vmDir = join(_vmLibDirInJdk(jdk), vm)
         if not exists(vmDir):
             mx.log('Creating VM directory in JDK7: ' + vmDir)
             os.makedirs(vmDir)
-    
+
         def filterXusage(line):
             if not 'Xusage.txt' in line:
                 sys.stderr.write(line + os.linesep)
-                
+
         # Check that the declaration of graal_projects in arguments.cpp is up to date
         argumentsCpp = join(_graal_home, 'src', 'share', 'vm', 'runtime', 'arguments.cpp')
         assert exists(argumentsCpp), 'File does not exist: ' + argumentsCpp
@@ -478,9 +478,9 @@
         # Check if a build really needs to be done
         timestampFile = join(vmDir, '.build-timestamp')
         if opts2.force or not exists(timestampFile):
-            mustBuild = True 
+            mustBuild = True
         else:
-            mustBuild = False 
+            mustBuild = False
             timestamp = os.path.getmtime(timestampFile)
             sources = []
             for d in ['src', 'make']:
@@ -493,7 +493,7 @@
                 if len(f) != 0 and os.path.getmtime(f) > timestamp:
                     mustBuild = True
                     break
-                    
+
         if not mustBuild:
             mx.log('[all files in src and make directories are older than ' + timestampFile[len(_graal_home) + 1:] + ' - skipping native build]')
             continue
@@ -510,11 +510,11 @@
             winCompileSuccess = re.compile(r"^Writing \.vcxproj file:")
             if not _runInDebugShell(winCompileCmd, _graal_home, compilelogfile, winCompileSuccess):
                 mx.log('Error executing create command')
-                return 
+                return
             winBuildCmd = 'msbuild ' + _graal_home + r'\build\vs-amd64\jvm.vcxproj /p:Configuration=' + project_config + ' /p:Platform=x64'
             if not _runInDebugShell(winBuildCmd, _graal_home, compilelogfile):
                 mx.log('Error building project')
-                return 
+                return
         else:
             cpus = multiprocessing.cpu_count()
             if build == 'debug':
@@ -525,18 +525,18 @@
             env.setdefault('HOTSPOT_BUILD_JOBS', str(cpus))
             env['ALT_BOOTDIR'] = jdk
             env.setdefault('INSTALL', 'y')
-            
+
             # Clear these 2 variables as having them set can cause very confusing build problems
             env.pop('LD_LIBRARY_PATH', None)
             env.pop('CLASSPATH', None)
-            
+
             mx.run([mx.gmake_cmd(), build + buildSuffix], cwd=join(_graal_home, 'make'), err=filterXusage)
-        
+
         jvmCfg = _vmCfgInJdk(jdk)
         found = False
         if not exists(jvmCfg):
             mx.abort(jvmCfg + ' does not exist')
-        
+
         prefix = '-' + vm
         vmKnown = prefix + ' KNOWN\n'
         lines = []
@@ -572,7 +572,7 @@
 
     if vm is None:
         vm = _vm
-        
+
     build = vmbuild if vmbuild is not None else _vmbuild if _vmSourcesAvailable else 'product'
     jdk = _jdk(build)
     mx.expand_project_in_args(args)
@@ -650,46 +650,46 @@
             if s in c:
                 return True
         return False
-    
+
     for p in mx.projects():
         if getattr(p, 'testHarness', None) == harnessName:
             classes = []
             _find_classes_with_annotations(classes, p, None, ['@Test'])
-        
+
             if len(pos) != 0:
                 classes = [c for c in classes if containsAny(c, pos)]
             if len(neg) != 0:
                 classes = [c for c in classes if not containsAny(c, neg)]
-            
+
             if len(classes) != 0:
                 mx.log('running tests in ' + p.name)
-                harness(p, vmArgs, classes)                
+                harness(p, vmArgs, classes)
 
 def unittest(args):
     """run the Graal Compiler Unit Tests in the GraalVM
-    
+
     If filters are supplied, only tests whose fully qualified name
     include a filter as a substring are run. Negative filters are
     those with a '-' prefix. VM args should have a @ prefix."""
-    
+
     def harness(p, vmArgs, classes):
         vm(['-XX:-BootstrapGraal', '-esa'] + vmArgs + ['-cp', mx.classpath(p.name), 'org.junit.runner.JUnitCore'] + classes)
     _run_tests(args, 'unittest', harness)
-    
+
 def jtt(args):
     """run the Java Tester Tests in the GraalVM
-    
+
     If filters are supplied, only tests whose fully qualified name
     include a filter as a substring are run. Negative filters are
     those with a '-' prefix. VM args should have a @ prefix."""
-    
+
     def harness(p, vmArgs, classes):
         vm(['-XX:-BootstrapGraal', '-XX:CompileOnly=com/oracle/graal/jtt', '-XX:CompileCommand=compileonly,java/lang/Object::<init>', '-XX:CompileCommand=quiet', '-Xcomp', '-esa'] + vmArgs + ['-cp', mx.classpath(p.name), 'org.junit.runner.JUnitCore'] + classes)
     _run_tests(args, 'jtt', harness)
-    
+
 def buildvms(args):
     """build one or more VMs in various configurations"""
-    
+
     parser = ArgumentParser(prog='mx buildvms');
     parser.add_argument('--vms', help='a comma separated list of VMs to build (default: server,client,graal)', default='server,client,graal')
     parser.add_argument('--builds', help='a comma separated list of build types (default: product,fastdebug,debug)', default='product,fastdebug,debug')
@@ -697,7 +697,7 @@
     args = parser.parse_args(args)
     vms = args.vms.split(',')
     builds = args.builds.split(',')
-    
+
     allStart = time.time()
     for v in vms:
         for vmbuild in builds:
@@ -717,7 +717,7 @@
 
     If this command exits with a 0 exit code, then the source code is in
     a state that would be accepted for integration into the main repository."""
-    
+
     class Task:
         def __init__(self, title):
             self.start = time.time()
@@ -736,7 +736,7 @@
             mx.log(time.strftime('gate: %d %b %Y %H:%M:%S: ABORT: ') + self.title + ' [' + str(self.duration) + ']')
             mx.abort(codeOrMessage)
             return self
-             
+
     parser = ArgumentParser(prog='mx gate');
     parser.add_argument('-j', '--omit-java-clean', action='store_false', dest='cleanJava', help='omit cleaning Java native code')
     parser.add_argument('-n', '--omit-native-build', action='store_false', dest='buildNative', help='omit cleaning and building native code')
@@ -748,11 +748,11 @@
     global _vmbuild
     global _vm
     global _jacoco
-    
-    tasks = []             
+
+    tasks = []
     total = Task('Gate')
     try:
-        
+
         t = Task('Clean')
         cleanArgs = []
         if not args.buildNative:
@@ -761,48 +761,48 @@
             cleanArgs.append('--no-java')
         clean(cleanArgs)
         tasks.append(t.stop())
-        
+
         t = Task('BuildJava')
         build(['--no-native'])
         tasks.append(t.stop())
         for vmbuild in ['fastdebug', 'product']:
             _vmbuild = vmbuild
-            
+
             if args.buildNative:
                 t = Task('BuildHotSpotGraal:' + vmbuild)
                 buildvms(['--vms', 'graal', '--builds', vmbuild])
                 tasks.append(t.stop())
-            
+
             t = Task('BootstrapWithSystemAssertions:' + vmbuild)
             vm(['-esa', '-version'])
             tasks.append(t.stop())
-            
+
             if vmbuild == 'product' and args.jacocout is not None:
                 _jacoco = 'on'
-            
+
             t = Task('UnitTests:' + vmbuild)
             unittest([])
             tasks.append(t.stop())
-            
+
             if vmbuild == 'product' and args.jacocout is not None:
                 _jacoco = 'append'
-            
+
             t = Task('JavaTesterTests:' + vmbuild)
             jtt(['@-XX:CompileCommand=exclude,*::run*'] if vmbuild == 'product'  else [])
             tasks.append(t.stop())
-            
+
             if vmbuild == 'product' and args.jacocout is not None:
                 _jacoco = 'off'
-            
+
             for test in sanitycheck.getDacapos(level=sanitycheck.SanityCheckLevel.Gate, gateBuildLevel=vmbuild):
                 t = Task(str(test) + ':' + vmbuild)
                 if not test.test('graal'):
                     t.abort(test.name + ' Failed')
                 tasks.append(t.stop())
-        
+
         if args.jacocout is not None:
             jacocoreport([args.jacocout])
-        
+
         t = Task('BootstrapWithDeoptALot')
         vm(['-XX:+DeoptimizeALot', '-XX:+VerifyOops', '-version'], vmbuild='fastdebug')
         tasks.append(t.stop())
@@ -811,13 +811,13 @@
         if mx.checkstyle([]) != 0:
             t.abort('Checkstyle warnings were found')
         tasks.append(t.stop())
-    
+
         t = Task('Canonicalization Check')
         mx.log(time.strftime('%d %b %Y %H:%M:%S - Ensuring mx/projects files are canonicalized...'))
         if mx.canonicalizeprojects([]) != 0:
             t.abort('Rerun "mx canonicalizeprojects" and check-in the modified mx/projects files.')
         tasks.append(t.stop())
-    
+
         t = Task('CleanAndBuildGraalVisualizer')
         mx.run(['ant', '-f', join(_graal_home, 'visualizer', 'build.xml'), '-q', 'clean', 'build'])
         tasks.append(t.stop())
@@ -836,17 +836,17 @@
                     t = Task('DaCapo_pmd:' + theVm + ':' + vmbuild)
                     dacapo(['pmd'])
                     tasks.append(t.stop())
-        
+
     except KeyboardInterrupt:
         total.abort(1)
-    
+
     except BaseException as e:
         import traceback
         traceback.print_exc()
         total.abort(str(e))
 
     total.stop()
-    
+
     mx.log('Gate task times:')
     for t in tasks:
         mx.log('  ' + str(t.duration) + '\t' + t.title)
@@ -860,7 +860,7 @@
         if not exists(join(_graal_home, 'visualizer', 'build.xml')):
             mx.log('[This initial execution may take a while as the NetBeans platform needs to be downloaded]')
         mx.run(['ant', '-f', join(_graal_home, 'visualizer', 'build.xml'), '-l', fp.name, 'run'])
-    
+
 def igv(args):
     """run the Ideal Graph Visualizer"""
     with open(join(_graal_home, '.ideal_graph_visualizer.log'), 'w') as fp:
@@ -897,7 +897,7 @@
             if dacapo not in sanitycheck.dacapoSanityWarmup.keys():
                 mx.abort('Unknown dacapo : ' + dacapo)
             benchmarks += [sanitycheck.getDacapo(dacapo, sanitycheck.dacapoSanityWarmup[dacapo][sanitycheck.SanityCheckLevel.Benchmark])]
-    
+
     if ('scaladacapo' in args or 'all' in args):
         benchmarks += sanitycheck.getScalaDacapos(level=sanitycheck.SanityCheckLevel.Benchmark)
     else:
@@ -906,7 +906,7 @@
             if dacapo not in sanitycheck.dacapoScalaSanityWarmup.keys():
                 mx.abort('Unknown dacapo : ' + dacapo)
             benchmarks += [sanitycheck.getScalaDacapo(dacapo, sanitycheck.dacapoScalaSanityWarmup[dacapo][sanitycheck.SanityCheckLevel.Benchmark])]
-        
+
     #Bootstrap
     if ('bootstrap' in args or 'all' in args):
         benchmarks += sanitycheck.getBootstraps()
@@ -917,7 +917,7 @@
         specjvms = [a[12:] for a in args if a.startswith('specjvm2008:')]
         for specjvm in specjvms:
             benchmarks += [sanitycheck.getSPECjvm2008([specjvm], True, 120, 120)]
-    
+
     for test in benchmarks:
         for (group, res) in test.bench(vm).items():
             if not results.has_key(group):
@@ -927,10 +927,10 @@
     if resultFile:
         with open(resultFile, 'w') as f:
             f.write(json.dumps(results))
-    
+
 def specjvm2008(args):
     """run one or all SPECjvm2008 benchmarks
-    
+
     All options begining with - will be passed to the vm except for -ikv -wt and -it.
     Other options are supposed to be benchmark names and will be passed to SPECjvm2008."""
     benchArgs = [a for a in args if a[0] != '-']
@@ -962,7 +962,7 @@
         benchArgs.remove(args[itIdx+1])
     vm = _vm;
     sanitycheck.getSPECjvm2008(benchArgs, skipValid, wt, it).bench(vm, opts=vmArgs)
-    
+
 def hsdis(args, copyToDir=None):
     """downloads the hsdis library
 
@@ -977,7 +977,7 @@
         mx.download(path, ['http://lafo.ssw.uni-linz.ac.at/hsdis/' + flavor + "/" + lib])
     if copyToDir is not None and exists(copyToDir):
         shutil.copy(path, copyToDir)
-    
+
 def hcfdis(args):
     """disassembles HexCodeFiles embedded in text files
 
@@ -1000,24 +1000,17 @@
     elif len(args) > 1:
         mx.abort('jacocoreport takes only one argument : an output directory')
     mx.run_java(['-jar', jacocoreport.get_path(True), '-in', 'jacoco.exec', '-g', join(_graal_home, 'graal'), out])
-    
+
 def _fix_overview_summary(path, topLink):
     """
     Processes an "overview-summary.html" generated by javadoc to put the complete
     summary text above the Packages table.
     """
-    
+
     # This uses scraping and so will break if the relevant content produced by javadoc changes in any way!
-    orig = path + '.orig'
-    if exists(orig):
-        with open(orig) as fp:
-            content = fp.read()
-    else:
-        with open(path) as fp:
-            content = fp.read()
-        with open(orig, 'w') as fp:
-            fp.write(content)
-    
+    with open(path) as fp:
+        content = fp.read()
+
     class Chunk:
         def __init__(self, content, ldelim, rdelim):
             lindex = content.find(ldelim)
@@ -1028,20 +1021,20 @@
                 self.text = content[lindex + len(ldelim):rindex]
             else:
                 self.text = None
-                
+
         def replace(self, content, repl):
             lindex = content.find(self.ldelim)
             rindex = content.find(self.rdelim)
             old = content[lindex:rindex + len(self.rdelim)]
             return content.replace(old, repl)
-                
+
     chunk1 = Chunk(content, """<div class="header">
 <div class="subTitle">
 <div class="block">""", """</div>
 </div>
 <p>See: <a href="#overview_description">Description</a></p>
 </div>""")
-    
+
     chunk2 = Chunk(content, """<div class="footer"><a name="overview_description">
 <!--   -->
 </a>
@@ -1051,106 +1044,100 @@
 </div>
 <!-- ======= START OF BOTTOM NAVBAR ====== -->""")
 
-    if not chunk1.text:
-        mx.log('Could not find header section in ' + path)
-        return
-            
-    if not chunk2.text:
-        mx.log('Could not find footer section in ' + path)
-        return
+    assert chunk1.text, 'Could not find header section in ' + path
+    assert chunk2.text, 'Could not find footer section in ' + path
 
     content = chunk1.replace(content, '<div class="header"><div class="subTitle"><div class="block">' + topLink + chunk2.text +'</div></div></div>')
     content = chunk2.replace(content, '')
-    
+
     with open(path, 'w') as fp:
         fp.write(content)
-    
+
 def site(args):
     """creates a website containing javadoc and the project dependency graph"""
-    
+
     parser = ArgumentParser(prog='site')
     parser.add_argument('-d', '--base', action='store', help='directory for generated site', required=True, metavar='<dir>')
-    parser.add_argument('-c', '--clean', action='store_true', help='remove existing site in <dir>')
-    parser.add_argument('-t', '--test', action='store_true', help='omit the Javadoc execution (useful for testing)')
 
     args = parser.parse_args(args)
-    
+
     args.base = os.path.abspath(args.base)
-    
-    if not exists(args.base):
-        os.mkdir(args.base)
-    elif args.clean:
-        shutil.rmtree(args.base)
-        os.mkdir(args.base)
-    
-    unified = join(args.base, 'all')
+    tmpbase = tempfile.mkdtemp(prefix=basename(args.base) + '.', dir=dirname(args.base))
+    unified = join(tmpbase, 'all')
 
-    if not args.test:
+    try:
         # Create javadoc for each project
-        mx.javadoc(['--base', args.base])
+        mx.javadoc(['--base', tmpbase])
 
         # Create unified javadoc for all projects
-        if exists(unified):
-            shutil.rmtree(unified)
-        mx.javadoc(['--base', args.base,
+        mx.javadoc(['--base', tmpbase,
                     '--unified',
                     '--arg', '@-windowtitle', '--arg', '@Graal OpenJDK Project Documentation',
                     '--arg', '@-doctitle', '--arg', '@Graal OpenJDK Project Documentation',
                     '--arg', '@-overview', '--arg', '@' + join(_graal_home, 'graal', 'overview.html')])
-        os.rename(join(args.base, 'javadoc'), unified)
+        os.rename(join(tmpbase, 'javadoc'), unified)
 
-    # Generate dependency graph with Graphviz
-    _, tmp = tempfile.mkstemp()
-    try:
-        svg = join(args.base, 'all', 'modules.svg')
-        jpg = join(args.base, 'all', 'modules.jpg')
-        with open(tmp, 'w') as fp:
-            print >> fp, 'digraph projects {'
-            print >> fp, 'rankdir=BT;'
-            print >> fp, 'size = "13,13";'
-            print >> fp, 'node [shape=rect, fontcolor="blue"];'
-            #print >> fp, 'edge [color="green"];'
-            for p in mx.projects():
-                print >> fp, '"' + p.name + '" [URL = "../' + p.name + '/javadoc/index.html", target = "_top"]'  
-                for dep in p.canonical_deps():
-                    if mx.project(dep, False):
-                        print >> fp, '"' + p.name + '" -> "' + dep + '"'
-            depths = dict()
-            for p in mx.projects():
-                d = p.max_depth()
-                depths.setdefault(d, list()).append(p.name)
-            for d, names in depths.iteritems():
-                print >> fp, '{ rank = same; "' + '"; "'.join(names) + '"; }' 
-            print >> fp, '}'
+        # Generate dependency graph with Graphviz
+        _, tmp = tempfile.mkstemp()
+        try:
+            svg = join(tmpbase, 'all', 'modules.svg')
+            jpg = join(tmpbase, 'all', 'modules.jpg')
+            with open(tmp, 'w') as fp:
+                print >> fp, 'digraph projects {'
+                print >> fp, 'rankdir=BT;'
+                print >> fp, 'size = "13,13";'
+                print >> fp, 'node [shape=rect, fontcolor="blue"];'
+                #print >> fp, 'edge [color="green"];'
+                for p in mx.projects():
+                    print >> fp, '"' + p.name + '" [URL = "../' + p.name + '/javadoc/index.html", target = "_top"]'
+                    for dep in p.canonical_deps():
+                        if mx.project(dep, False):
+                            print >> fp, '"' + p.name + '" -> "' + dep + '"'
+                depths = dict()
+                for p in mx.projects():
+                    d = p.max_depth()
+                    depths.setdefault(d, list()).append(p.name)
+                for d, names in depths.iteritems():
+                    print >> fp, '{ rank = same; "' + '"; "'.join(names) + '"; }'
+                print >> fp, '}'
+
+            mx.run(['dot', '-Tsvg', '-o' + svg, '-Tjpg', '-o' + jpg, tmp])
+
+        finally:
+            os.remove(tmp)
 
-        mx.run(['dot', '-Tsvg', '-o' + svg, '-Tjpg', '-o' + jpg, tmp])
-        
-    finally:
-        os.remove(tmp)
-
-    # Post-process generated SVG to remove title elements which most browsers
-    # render as redundant (and annoying) tooltips.
-    with open(svg, 'r') as fp:
-        content = fp.read()
-    content = re.sub('<title>.*</title>', '', content)
-    content = re.sub('xlink:title="[^"]*"', '', content)
-    with open(svg, 'w') as fp:
-        fp.write(content)
+        # Post-process generated SVG to remove title elements which most browsers
+        # render as redundant (and annoying) tooltips.
+        with open(svg, 'r') as fp:
+            content = fp.read()
+        content = re.sub('<title>.*</title>', '', content)
+        content = re.sub('xlink:title="[^"]*"', '', content)
+        with open(svg, 'w') as fp:
+            fp.write(content)
 
-    # Post-process generated overview-summary.html files    
-    top = join(args.base, 'all', 'overview-summary.html')
-    for root, _, files in os.walk(args.base):
-        for f in files:
-            if f == 'overview-summary.html':
-                path = join(root, f)
-                topLink = ''
-                if top != path:
-                    link = os.path.relpath(join(args.base, 'all', 'index.html'), dirname(path))
-                    topLink = '<p><a href="' + link + '", target="_top">[return to the overall Graal documentation]</a></p>'
-                _fix_overview_summary(path, topLink)
-    
-    print 'Created website - root is ' + join(unified, 'index.html')
-    
+        # Post-process generated overview-summary.html files
+        top = join(tmpbase, 'all', 'overview-summary.html')
+        for root, _, files in os.walk(tmpbase):
+            for f in files:
+                if f == 'overview-summary.html':
+                    path = join(root, f)
+                    topLink = ''
+                    if top != path:
+                        link = os.path.relpath(join(tmpbase, 'all', 'index.html'), dirname(path))
+                        topLink = '<p><a href="' + link + '", target="_top"><b>[return to the overall Graal documentation]</b></a></p>'
+                    _fix_overview_summary(path, topLink)
+
+
+        if exists(args.base):
+            shutil.rmtree(args.base)
+        shutil.move(tmpbase, args.base)
+
+        print 'Created website - root is ' + join(args.base, 'all', 'index.html')
+
+    finally:
+        if exists(tmpbase):
+            shutil.rmtree(tmpbase)
+
 def mx_init():
     _vmbuild = 'product'
     commands = {
@@ -1177,7 +1164,7 @@
         'vmg': [vmg, '[-options] class [args...]'],
         'vmfg': [vmfg, '[-options] class [args...]']
     }
-    
+
     mx.add_argument('--jacoco', help='instruments com.oracle.* classes using JaCoCo', default='off', choices=['off', 'on', 'append'])
 
     if (_vmSourcesAvailable):
@@ -1186,12 +1173,12 @@
         mx.add_argument('--debug', action='store_const', dest='vmbuild', const='debug', help='select the debug build of the VM')
         mx.add_argument('--fastdebug', action='store_const', dest='vmbuild', const='fastdebug', help='select the fast debug build of the VM')
         mx.add_argument('--ecl', action='store_true', dest='make_eclipse_launch', help='create launch configuration for running VM execution(s) in Eclipse')
-        
+
         commands.update({
             'export': [export, '[-options] [zipfile]'],
             'build': [build, '[-options] [product|debug|fastdebug]...']
         })
-    
+
     mx.commands.update(commands)
 
 def mx_post_parse_cmd_line(opts):
@@ -1202,7 +1189,7 @@
     major = int(parts[1])
     if not major >= 7:
         mx.abort('Requires Java version 1.7 or greater, got version ' + version)
-    
+
     if (_vmSourcesAvailable):
         if hasattr(opts, 'vm') and opts.vm is not None:
             global _vm