Closure compiler: variable define is undeclared - google-closure-compiler

Question

I'm trying to write a Coldfusion script that compresses JavaScript files using a recent version of Google's closure compiler.
This program ends with two errors:
JSC_UNDEFINED_VARIABLE. variable module is undeclared at jquery-3.1.1.js line 9767 : 12
JSC_UNDEFINED_VARIABLE. variable define is undeclared at jquery-3.1.1.js line 9784 : 13
I wonder what's the magic. module and define are common JS variables; I trust Closure knows them. What setting am I missing? Is there an extern missing? Do I have to set a certain CompilerOption?
<cfset options = createObject( "java", "com.google.javascript.jscomp.CompilerOptions" ).init()>
<cfset cl = createObject( "java", "com.google.javascript.jscomp.CompilationLevel" )>
<cfset wl = createObject( "java", "com.google.javascript.jscomp.WarningLevel" )>
<cfset cl.SIMPLE_OPTIMIZATIONS.setOptionsForCompilationLevel(options)>
<cfset cl.SIMPLE_OPTIMIZATIONS.setDebugOptionsForCompilationLevel(options)>
<cfset lm = createobject( "java", "com.google.javascript.jscomp.CompilerOptions$LanguageMode" )>
<cfset options.setEnvironment(options.Environment.BROWSER)>
<cfset schar = createobject( "java", "java.nio.charset.StandardCharsets")>
<cfset options.setOutputCharset( schar.UTF_8 )>
<cfset wl.VERBOSE.setOptionsForWarningLevel(options)>
<cfset comp = createObject( "java", "com.google.javascript.jscomp.Compiler" ).init()>
<cfset clr = createObject( "java", "com.google.javascript.jscomp.CommandLineRunner" )>
<cfset sourceFile = createObject( "java", "com.google.javascript.jscomp.SourceFile" )>
<cfset arrInputs = createObject( "java", "java.util.ArrayList" ).init()>
<cfset arrExterns = createObject( "java", "java.util.ArrayList" ).init()>
<cfset arrInputs.add(
sourceFile.fromCode(
javaCast( "string", "jquery-3.1.1.js" ),
javaCast( "string", fileRead( expandPath( "../advanced/js/jquery-3.1.1.js" ), "utf-8" ) )
)
)>
<cfset arrExterns.addAll( clr.getBuiltinExterns(options.Environment) )>
<cfset result = comp.compile( arrExterns, arrInputs , options )>
<cfoutput>
|#result.success#|
<cfloop from="1" to="#arrayLen( result.errors )#" index="i">
err: #result.errors[i]#<br>
</cfloop>
</cfoutput>

Answer 1

module and define are common JS variables
module is typically an indicator of the CommonJS module system. define is used by the AMD module system. Neither are default JS variables or known to browsers.
jQuery is using a Universal Module Definition pattern to export the jQuery object either as a module (CommonJS or AMD as appropriate), or if none are found, as a global variable. Closure-compiler can recognize this pattern and remove the module specific parts when the --process_common_js_modules flag is specified.