diff --git a/jsdoc.js b/jsdoc.js
index b1f27885..6312f1c9 100644
--- a/jsdoc.js
+++ b/jsdoc.js
@@ -61,6 +61,13 @@ require('lib/jsdoc/util/global').env = {
     */
     opts: {},
 
+    /**
+     * The source files that JSDoc will parse.
+     * @type Array
+     * @memberof env
+     */
+    sourceFiles: [],
+    
     /**
      * The JSDoc version number and revision date.
      * 
@@ -220,7 +227,8 @@ function main() {
     if (env.conf.source && env.opts._.length > 0) { // are there any files to scan and parse?
         filter = new jsdoc.src.filter.Filter(env.conf.source);
 
-        sourceFiles = app.jsdoc.scanner.scan(env.opts._, (env.opts.recurse? 10 : undefined), filter);
+        env.sourceFiles = sourceFiles = app.jsdoc.scanner.scan(env.opts._,
+            (env.opts.recurse? 10 : undefined), filter);
 
         jsdoc.src.handlers.attachTo(app.jsdoc.parser);
 
diff --git a/lib/jsdoc/path.js b/lib/jsdoc/path.js
index 4ddb031d..ea405e8c 100644
--- a/lib/jsdoc/path.js
+++ b/lib/jsdoc/path.js
@@ -51,7 +51,10 @@ function prefixReducer(previousPath, current) {
  * @return {string} The common prefix, or an empty string if there is no common prefix.
  */
 exports.commonPrefix = function(paths) {
-    var common = paths.reduce(prefixReducer, undefined);
+    var common;
+
+    paths = paths || [];
+    common = paths.reduce(prefixReducer, undefined) || [];
 
     // if there's anything left (other than a placeholder for a leading slash), add a placeholder
     // for a trailing slash
diff --git a/lib/jsdoc/tag/dictionary/definitions.js b/lib/jsdoc/tag/dictionary/definitions.js
index cb96cbf7..b37e0753 100644
--- a/lib/jsdoc/tag/dictionary/definitions.js
+++ b/lib/jsdoc/tag/dictionary/definitions.js
@@ -7,7 +7,19 @@
     @license Apache License 2.0 - See file 'LICENSE.md' in this project.
  */
 
-var path = require('path');
+var path = require('jsdoc/path');
+
+function filepathMinusPrefix(filepath) {
+    var sourceFiles = env.sourceFiles || [];
+    var commonPrefix = path.commonPrefix( sourceFiles.concat(env.opts._ || []) );
+    var result = (filepath + '/').replace(commonPrefix, '');
+
+    if (result.length > 0 && result[result.length - 1] !== '/') {
+        result += '/';
+    }
+
+    return result;
+}
 
 /** @private */
 function setDocletKindToTitle(doclet, tag) {
@@ -34,12 +46,11 @@ function setDocletDescriptionToValue(doclet, tag) {
 }
 
 function setNameToFile(doclet, tag) {
-    var name = '';
+    var name;
+
     if (doclet.meta.filename) {
-        // TODO: find the shortest path shared by all input files, and remove that from
-        // doclet.meta.path
-        name += path.basename(doclet.meta.path) + '/';
-        doclet.addTag( 'name', name + doclet.meta.filename );
+        name = filepathMinusPrefix(doclet.meta.path) + doclet.meta.filename;
+        doclet.addTag('name', name);
     }
 }
 
@@ -64,17 +75,13 @@ function applyNamespace(docletOrNs, tag) {
 }
 
 function setDocletNameToFilename(doclet, tag) {
-    // TODO: find the shortest path shared by all input files, and remove that from doclet.meta.path
-    var name = doclet.meta.path ? path.basename(doclet.meta.path) + '/' : '';
-    name += doclet.meta.filename;
-    name = name.replace(/\.js$/i, '');
-    
-    for (var i = 0, len = env.opts._.length; i < len; i++) {
-        if (name.indexOf(env.opts._[i]) === 0) {
-            name = name.replace(env.opts._[0], '');
-            break;
-        }
+    var name = '';
+
+    if (doclet.meta.path) {
+        name = filepathMinusPrefix(doclet.meta.path);
     }
+    name += doclet.meta.filename.replace(/\.js$/i, '');
+
     doclet.name = name;
 }
 
diff --git a/lib/jsdoc/util/templateHelper.js b/lib/jsdoc/util/templateHelper.js
index c85a5665..c14f33cb 100644
--- a/lib/jsdoc/util/templateHelper.js
+++ b/lib/jsdoc/util/templateHelper.js
@@ -52,6 +52,8 @@ function makeFilenameUnique(filename, str) {
 }
 
 function cleanseFilename(str) {
+    str = str || '';
+
     // allow for namespace prefix
     return str.replace(/^(event|module|external|package):/, '$1-')
         // use - instead of ~ to denote 'inner'
@@ -702,28 +704,46 @@ function getFilename(longname) {
 
 /** Turn a doclet into a URL. */
 exports.createLink = function(doclet) {
+    var filename;
+    var fragment;
+    var match;
+    var fakeContainer;
+
     var url = '';
     var longname = doclet.longname;
-    var filename;
-
-    var fakeContainerMatch = /(\S+):/.exec(longname);
     
+    // handle doclets in which doclet.longname implies that the doclet gets its own HTML file, but
+    // doclet.kind says otherwise. this happens due to mistagged JSDoc (for example, a module that
+    // somehow has doclet.kind set to `member`).
+    // TODO: generate a warning (ideally during parsing!)
+    if (containers.indexOf(doclet.kind) === -1) {
+        match = /(\S+):/.exec(longname);
+        if (match && containers.indexOf(match[1]) !== -1) {
+            fakeContainer = match[1];
+        }
+    }
+
     // the doclet gets its own HTML file
     if ( containers.indexOf(doclet.kind) !== -1 || isModuleFunction(doclet) ) {
-        url = getFilename(longname);
+        filename = getFilename(longname);
     }
-    // the doclet's longname suggests that it should get its own HTML file, but doclet.kind says
-    // otherwise. this happens due to mistagged JSDoc (for example, a module that somehow has
-    // doclet.kind set to `member`). use the container's filename plus a fragment.
-    else if ( containers.indexOf(doclet.kind) === -1 && fakeContainerMatch &&
-        containers.indexOf(fakeContainerMatch[1]) !== -1 ) {
-        url = getFilename(longname) + '#' + doclet.name;
+    // mistagged version of a doclet that gets its own HTML file
+    else if ( containers.indexOf(doclet.kind) === -1 && fakeContainer ) {
+        filename = getFilename(doclet.memberof || longname);
+        if (doclet.name === doclet.longname) {
+            fragment = '';
+        }
+        else {
+            fragment = doclet.name || '';
+        }
     }
     // the doclet is within another HTML file
     else {
         filename = getFilename(doclet.memberof || exports.globalName);
-        url = filename + '#' + getNamespace(doclet.kind) + doclet.name;
+        fragment = getNamespace(doclet.kind) + (doclet.name || '');
     }
+
+    url = fragment ? (filename + '#' + fragment) : filename;
     
     return url;
 };
diff --git a/test/specs/documentation/modules.js b/test/specs/documentation/modules.js
index 52481150..2c025d29 100644
--- a/test/specs/documentation/modules.js
+++ b/test/specs/documentation/modules.js
@@ -1,14 +1,20 @@
-/*global beforeEach: true, describe: true, env: true, expect: true, it: true */
+/*global afterEach: true, beforeEach: true, describe: true, env: true, expect: true, it: true */
 describe("module names", function() {
-    var parser = require('jsdoc/src/parser'),
-        srcParser = null, doclets;
+    var parser = require('jsdoc/src/parser');
+    var srcParser = null;
+    var doclets;
+    var sourcePaths = env.opts._.slice(0);
 
     beforeEach(function() {
-        env.opts._ = [__dirname + '/test/fixtures/modules/'];
+        env.opts._ = [__dirname + '/test/fixtures/modules/data/'];
         srcParser = new parser.Parser();
         require('jsdoc/src/handlers').attachTo(srcParser);
     });
 
+    afterEach(function() {
+        env.opts._ = sourcePaths;
+    });
+
     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');
         expect(doclets.length).toBeGreaterThan(1);
diff --git a/test/specs/jsdoc/util/templateHelper.js b/test/specs/jsdoc/util/templateHelper.js
index 3ae04851..c3266177 100644
--- a/test/specs/jsdoc/util/templateHelper.js
+++ b/test/specs/jsdoc/util/templateHelper.js
@@ -1379,20 +1379,53 @@ describe("jsdoc/util/templateHelper", function() {
         it('should create a url for a doclet with the wrong kind (caused by incorrect JSDoc tags', function() {
             var moduleDoclet = {
                 kind: 'module',
-                longname: 'module:bar',
-                name: 'module:bar'
+                longname: 'module:baz',
+                name: 'module:baz'
             };
             var badDoclet = {
                 kind: 'member',
-                longname: 'module:bar',
-                name: 'module:bar'
+                longname: 'module:baz',
+                name: 'module:baz'
             };
 
             var moduleDocletUrl = helper.createLink(moduleDoclet);
             var badDocletUrl = helper.createLink(badDoclet);
 
-            expect(moduleDocletUrl).toBe('module-bar.html');
-            expect(badDocletUrl).toBe('module-bar.html#module:bar');
+            expect(moduleDocletUrl).toBe('module-baz.html');
+            expect(badDocletUrl).toBe('module-baz.html');
+        });
+
+        it('should create a url for a function that is a member of a doclet with the wrong kind', function() {
+            var badModuleDoclet = {
+                kind: 'member',
+                longname: 'module:qux',
+                name: 'module:qux'
+            };
+            var memberDoclet = {
+                kind: 'function',
+                name: 'frozzle',
+                memberof: 'module:qux',
+                scope: 'instance',
+                longname: 'module:qux#frozzle'
+            };
+
+            var badModuleDocletUrl = helper.createLink(badModuleDoclet);
+            var memberDocletUrl = helper.createLink(memberDoclet);
+
+            expect(badModuleDocletUrl).toBe('module-qux.html');
+            expect(memberDocletUrl).toBe('module-qux.html#frozzle');
+        });
+
+        it('should create a url for an empty package definition', function() {
+            var packageDoclet = {
+                kind: 'package',
+                name: undefined,
+                longname: 'package:undefined'
+            };
+
+            var packageDocletUrl = helper.createLink(packageDoclet);
+
+            expect(packageDocletUrl).toBe('global.html');
         });
     });
 
diff --git a/test/specs/tags/overviewtag.js b/test/specs/tags/overviewtag.js
index 6087be5b..f78761fc 100644
--- a/test/specs/tags/overviewtag.js
+++ b/test/specs/tags/overviewtag.js
@@ -1,18 +1,28 @@
-/*global describe: true, env: true, expect: true, it: true */
+/*global beforeEach: true, afterEach: true, describe: true, env: true, expect: true, it: true */
 
 describe("@overview tag", function() {
-    var parser = require('jsdoc/src/parser'),
-        srcParser = new parser.Parser(),
-        doclets;
+    var parser = require('jsdoc/src/parser');
+    var srcParser = null;
+    var doclets;
+    var sourcePaths = env.opts._.slice(0);
 
-    require('jsdoc/src/handlers').attachTo(srcParser);
-    doclets = srcParser.parse(__dirname + '/test/fixtures/file.js');
+    beforeEach(function() {
+        env.opts._ = [__dirname + '/test/fixtures/'];
+        srcParser = new parser.Parser();
+        require('jsdoc/src/handlers').attachTo(srcParser);
+    });
+
+    afterEach(function() {
+        env.opts._ = sourcePaths;
+    });
 
     it('When a file overview tag appears in a doclet, the name of the doclet should contain the path to the file.', function() {
+        doclets = srcParser.parse(__dirname + '/test/fixtures/file.js');
         expect(doclets[0].name).toMatch(/^(fixtures[\/\\]file\.js)$/);
     });
 
     it("The name and longname should be equal", function() {
+        doclets = srcParser.parse(__dirname + '/test/fixtures/file.js');
         expect(doclets[0].name).toBe(doclets[0].longname);
     });
 });