diff --git a/jsdoc.js b/jsdoc.js
index 6e13842e..54ee1ccf 100644
--- a/jsdoc.js
+++ b/jsdoc.js
@@ -8,33 +8,6 @@
 
 //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
 
-/** The absolute path to the base directory of the jsdoc application.
-    @type string
-    @global
- */
-__dirname = '.',
-args = Array.prototype.slice.call(arguments, 0);
-
-// rhino has no native way to get the base dirname of the currently running script
-// so this information must be manually passed in from the command line
-for (var i = 0; i < args.length; i++) {
-    if ( /^--dirname(?:=(.+?)(\/|\/\.)?)?$/i.test(args[i]) ) {
-        if (RegExp.$1) {
-            __dirname = RegExp.$1; // last wins
-            args.splice(i--, 1); // remove --dirname opt from arguments
-        }
-        else {
-            __dirname = args[i + 1];
-            args.splice(i--, 2);
-        }
-    }
-}
-
-load(__dirname + '/lib/rhino-shim.js');
-
-//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
-
-
 /** Data representing the environment in which this app is running.
     @namespace
 */
@@ -49,8 +22,7 @@ env = {
         The command line arguments passed into jsdoc.
         @type Array
     */
-    args: Array.prototype.slice.call(args, 0),
-
+    args: [],
 
     /**
         The parsed JSON data from the configuration file.
@@ -58,6 +30,12 @@ env = {
     */
     conf: {},
 
+    /** 
+        The absolute path to the base directory of the jsdoc application.
+        @type string
+    */
+    dirname: '.',
+
     /**
         The command line arguments, parsed into a key/value hash.
         @type Object
@@ -66,6 +44,29 @@ env = {
     opts: {}
 };
 
+args = Array.prototype.slice.call(arguments, 0);
+
+// rhino has no native way to get the base dirname of the currently running script
+// so this information must be manually passed in from the command line
+for (var i = 0; i < args.length; i++) {
+    if ( /^--dirname(?:=(.+?)(\/|\/\.)?)?$/i.test(args[i]) ) {
+        if (RegExp.$1) {
+            env.dirname = RegExp.$1; // last wins
+            args.splice(i--, 1); // remove --dirname opt from arguments
+        }
+        else {
+            env.dirname = args[i + 1];
+            args.splice(i--, 2);
+        }
+    }
+}
+
+env.args = args;
+
+load(env.dirname + '/lib/rhino-shim.js');
+
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
+
 
 /** @global
     @param {string} filepath The path to the script file to include (read and execute).
@@ -76,7 +77,7 @@ function include(filepath) {
         load(filepath);
     }
     catch (e) {
-        console.log('Cannot include "' + __dirname + '/' + filepath + '": '+e);
+        console.log('Cannot include "' + env.dirname + '/' + filepath + '": '+e);
     }
 }
 include.resolve = function(filepath) {
@@ -84,7 +85,7 @@ include.resolve = function(filepath) {
         return filepath;
     }
     
-    return __dirname + '/' + filepath;
+    return env.dirname + '/' + filepath;
 }
 
 
@@ -188,13 +189,13 @@ function main() {
     env.opts = jsdoc.opts.parser.parse(env.args);
 
     try {
-        env.conf = new Config( fs.readFileSync( env.opts.configure || __dirname + '/conf.json' ) ).get();
+        env.conf = new Config( fs.readFileSync( env.opts.configure || env.dirname + '/conf.json' ) ).get();
     }
     catch (e) {
         try {
             //Try to copy over the example conf
-            var example = fs.readFileSync(__dirname + '/conf.json.EXAMPLE', 'utf8');
-            fs.writeFileSync(__dirname + '/conf.json', example, 'utf8');
+            var example = fs.readFileSync(env.dirname + '/conf.json.EXAMPLE', 'utf8');
+            fs.writeFileSync(env.dirname + '/conf.json', example, 'utf8');
             env.conf = JSON.parse(example);
         }
         catch(e) {
diff --git a/lib/rhino-shim.js b/lib/rhino-shim.js
index 08cdda85..19f68398 100644
--- a/lib/rhino-shim.js
+++ b/lib/rhino-shim.js
@@ -31,5 +31,5 @@ process = {
         n = n || 0;
         java.lang.System.exit(n);
     },
-    argv: [__dirname + '/jsdoc.js'].concat(Array.prototype.slice.call(arguments, 0))
+    argv: [env.dirname + '/jsdoc.js'].concat(Array.prototype.slice.call(arguments, 0))
 };
diff --git a/plugins/test/specs/railsTemplate.js b/plugins/test/specs/railsTemplate.js
index 7541f95b..00a649fc 100644
--- a/plugins/test/specs/railsTemplate.js
+++ b/plugins/test/specs/railsTemplate.js
@@ -8,7 +8,7 @@ describe("railsTemplate plugin", function() {
 
     it("should remove <% %> rails template tags from the source of *.erb files", function() {
         var path = require("path"),
-            docSet = parser.parse([path.join(__dirname, "plugins/test/fixtures/railsTemplate.js.erb")]);
+            docSet = parser.parse([path.join(env.dirname, "plugins/test/fixtures/railsTemplate.js.erb")]);
 
         expect(docSet[2].description).toEqual("Remove rails tags from the source input (e.g. )");
     });
diff --git a/rhino_modules/jsdoc/opts/parser.js b/rhino_modules/jsdoc/opts/parser.js
index 96128f47..03839914 100644
--- a/rhino_modules/jsdoc/opts/parser.js
+++ b/rhino_modules/jsdoc/opts/parser.js
@@ -17,7 +17,7 @@ var argParser = new common.args.ArgParser(),
 	};
 
 argParser.addOption('t', 'template',    true,  'The name of the template to use. Default: the "default" template');
-argParser.addOption('c', 'configure',   true,  'The path to the configuration file. Default: jsdoc __dirname + /conf.json');
+argParser.addOption('c', 'configure',   true,  'The path to the configuration file. Default: jsdoc env.dirname + /conf.json');
 argParser.addOption('e', 'encoding',    true,  'Assume this encoding when reading all source files. Default: utf-8');
 argParser.addOption('T', 'test',        false, 'Run all tests and quit.');
 argParser.addOption('d', 'destination', true,  'The path to the output folder. Use "console" to dump data to the console. Default: console');
diff --git a/templates/default/publish.js b/templates/default/publish.js
index 8a96d7ff..85f554d4 100644
--- a/templates/default/publish.js
+++ b/templates/default/publish.js
@@ -16,7 +16,7 @@
         var defaultTemplatePath = 'templates/default';
         var templatePath = (opts.template) ? opts.template : defaultTemplate;
         var out = '',
-            view = new template.Template(__dirname + '/' + templatePath + '/tmpl');
+            view = new template.Template(env.dirname + '/' + templatePath + '/tmpl');
         
         // set up templating
         view.layout = 'layout.tmpl';
@@ -177,7 +177,7 @@
         fs.mkPath(outdir);
 
         // copy static files to outdir
-        var fromDir = __dirname + '/' + templatePath + '/static',
+        var fromDir = env.dirname + '/' + templatePath + '/static',
             staticFiles = fs.ls(fromDir, 3);
             
         staticFiles.forEach(function(fileName) {
diff --git a/test/fixtures/typekind.js b/test/fixtures/typekind.js
index 687eb7d7..aacfcc70 100644
--- a/test/fixtures/typekind.js
+++ b/test/fixtures/typekind.js
@@ -8,7 +8,7 @@ module.exports = require('connect').createServer(
   Connect.favicon(),
   Connect.cache(),
   Connect.gzip(),
-  require('wheat')(__dirname)
+  require('wheat')(env.dirname)
 );
 
 /**
diff --git a/test/jasmine-jsdoc.js b/test/jasmine-jsdoc.js
index eac659c9..e2c20299 100644
--- a/test/jasmine-jsdoc.js
+++ b/test/jasmine-jsdoc.js
@@ -15,7 +15,7 @@ jasmine.loadHelpersInFolder = function(folder, matcher) {
     helpers = helperCollection.getSpecs();
     for ( var i = 0, len = helpers.length; i < len; ++i) {
         var file = helpers[i].path();
-        var helper = require(file.replace(/\\/g, '/').replace(new RegExp('^' + __dirname + '/'), "").replace(/\.*$/, ""));
+        var helper = require(file.replace(/\\/g, '/').replace(new RegExp('^' + env.dirname + '/'), "").replace(/\.*$/, ""));
 
         for (var key in helper) {
             this[key] = helper[key];
@@ -79,7 +79,7 @@ jasmine.executeSpecsInFolder = function(folder, done, verbose, matcher) {
     var specsList = specs.getSpecs();
     for ( var i = 0, len = specsList.length; i < len; ++i) {
         var filename = specsList[i];
-        require(filename.path().replace(/\\/g, '/').replace(new RegExp('^' + __dirname + '/'), "").replace(/\.\w+$/, ""));
+        require(filename.path().replace(/\\/g, '/').replace(new RegExp('^' + env.dirname + '/'), "").replace(/\.\w+$/, ""));
     }
 
     //Run Jasmine
diff --git a/test/spec-collection.js b/test/spec-collection.js
index 1093c1a9..146d9833 100644
--- a/test/spec-collection.js
+++ b/test/spec-collection.js
@@ -33,7 +33,7 @@ exports.load = function(loadpath, matcher, clear) {
     }
     var wannaBeSpecs = wrench.readdirSyncRecursive(loadpath);
     for (var i = 0; i < wannaBeSpecs.length; i++) {
-        var file = path.join(__dirname, loadpath, wannaBeSpecs[i]);
+        var file = path.join(env.dirname, loadpath, wannaBeSpecs[i]);
         try {
             if (fs.statSync(file).isFile()) {
                 if (!/.*node_modules.*/.test(file) && matcher.test(path.filename(file))) {
diff --git a/test/specs/documentation/modules.js b/test/specs/documentation/modules.js
index e682c757..c3b7debd 100644
--- a/test/specs/documentation/modules.js
+++ b/test/specs/documentation/modules.js
@@ -3,19 +3,19 @@ describe("module names", function() {
         srcParser = null, doclets;
 
     beforeEach(function() {
-        env.opts._ = [__dirname + '/test/fixtures/modules/'];
+        env.opts._ = [env.dirname + '/test/fixtures/modules/'];
         srcParser = new parser.Parser();
         require('jsdoc/src/handlers').attachTo(srcParser);
     });
 
     it("should create a name from the file path when no documented module name exists", function() {
-        doclets = srcParser.parse(__dirname + '/test/fixtures/modules/data/mod-1.js');
+        doclets = srcParser.parse(env.dirname + '/test/fixtures/modules/data/mod-1.js');
         expect(doclets.length).toBeGreaterThan(1);
         expect(doclets[0].longname).toEqual('module:data/mod-1');
     });
 
     it("should use the documented module name if available", function() {
-        doclets = srcParser.parse(__dirname + '/test/fixtures/modules/data/mod-2.js');
+        doclets = srcParser.parse(env.dirname + '/test/fixtures/modules/data/mod-2.js');
         expect(doclets.length).toBeGreaterThan(1);
         expect(doclets[0].longname).toEqual('module:my/module/name');
     });
diff --git a/test/specs/helpers.js b/test/specs/helpers.js
index 88d39db4..91af9678 100644
--- a/test/specs/helpers.js
+++ b/test/specs/helpers.js
@@ -1,7 +1,7 @@
 var hasOwnProperty = Object.prototype.hasOwnProperty;
 
 exports.getDocSetFromFile = function(filename, parser) {
-    var sourceCode = readFile(__dirname + '/' + filename),
+    var sourceCode = readFile(env.dirname + '/' + filename),
         testParser = parser || new (require('jsdoc/src/parser')).Parser(),
         doclets;
 
diff --git a/test/specs/jsdoc/functions/include.js b/test/specs/jsdoc/functions/include.js
index dbfa1694..29d07a6e 100644
--- a/test/specs/jsdoc/functions/include.js
+++ b/test/specs/jsdoc/functions/include.js
@@ -15,8 +15,8 @@ describe("include", function() {
         expect( include.resolve('/a/b/c.js') ).toEqual('/a/b/c.js');
     });
     
-    it("should resolve relative filepaths relative to the __dirname", function() {
-        expect( include.resolve('a/b/c') ).toEqual(__dirname+'/'+'a/b/c');
+    it("should resolve relative filepaths relative to the env.dirname", function() {
+        expect( include.resolve('a/b/c') ).toEqual(env.dirname+'/'+'a/b/c');
     });
     
 });
\ No newline at end of file
diff --git a/test/specs/jsdoc/src/parser.js b/test/specs/jsdoc/src/parser.js
index 113c96d7..2162583e 100644
--- a/test/specs/jsdoc/src/parser.js
+++ b/test/specs/jsdoc/src/parser.js
@@ -43,7 +43,7 @@ describe("jsdoc/src/parser", function() {
             it("should be able to parse its own source file", function() {
                 var fs = require("fs"),
                     path = require("path"),
-                    parserSrc = "javascript:" + fs.readFileSync( path.join(__dirname,
+                    parserSrc = "javascript:" + fs.readFileSync( path.join(env.dirname,
                         "rhino_modules", "jsdoc", "src", "parser.js") ),
                     parse = function() {
                         parser.parse(parserSrc);
diff --git a/test/specs/jsdoc/src/scanner.js b/test/specs/jsdoc/src/scanner.js
index e9f127e7..206d286e 100644
--- a/test/specs/jsdoc/src/scanner.js
+++ b/test/specs/jsdoc/src/scanner.js
@@ -4,10 +4,10 @@ describe("jsdoc/src/scanner", function() {
             includePattern: new RegExp(".+\\.js(doc)?$"),
             excludePattern: new RegExp("(^|\\/)_")
         }),
-        sourceFiles = scanner.scan([__dirname+'/test/fixtures/src/'], 3, filter);
+        sourceFiles = scanner.scan([env.dirname+'/test/fixtures/src/'], 3, filter);
 
     sourceFiles = sourceFiles.map(function($) {
-        return $.replace(__dirname, '');
+        return $.replace(env.dirname, '');
     });
 
     it("should return the correct source files", function() {
diff --git a/test/specs/jshint/jshint-clean.js b/test/specs/jshint/jshint-clean.js
index fa1b7461..436aaab3 100644
--- a/test/specs/jshint/jshint-clean.js
+++ b/test/specs/jshint/jshint-clean.js
@@ -2,7 +2,7 @@
 var fs = require("fs"),
     path = require("path");
 
-var config = JSON.parse( fs.readFileSync( path.join(__dirname, ".jshintrc"), "utf-8" ) );
+var config = JSON.parse( fs.readFileSync( path.join(env.dirname, ".jshintrc"), "utf-8" ) );
 
 function jsHintCheck(filename, source, conf) {
     var JSHINT = require("jshint/jshint").JSHINT;
@@ -46,7 +46,7 @@ describe("jshint-clean", function() {
         };
         filter = new (require('jsdoc/src/filter').Filter)(source);
 
-        files = app.jsdoc.scanner.scan([__dirname], 10, filter);
+        files = app.jsdoc.scanner.scan([env.dirname], 10, filter);
 
         check = function() {
             jsHintCheck(files[i]);
diff --git a/test/specs/tags/overviewtag.js b/test/specs/tags/overviewtag.js
index 21a688f3..5104fbf4 100644
--- a/test/specs/tags/overviewtag.js
+++ b/test/specs/tags/overviewtag.js
@@ -4,7 +4,7 @@ describe("@overview tag", function() {
         doclets;
 
     require('jsdoc/src/handlers').attachTo(srcParser);
-    doclets = srcParser.parse(__dirname + '/test/fixtures/file.js');
+    doclets = srcParser.parse(env.dirname + '/test/fixtures/file.js');
 
     it('When a file overview tag appears in a doclet, the name of the doclet should start with file: and should end with the path to the file.', function() {
         expect(doclets[0].name).toMatch(/^.*([\/\\]fixtures[\/\\]file\.js)$/);