No output written when Browserify.opts.basedir is set

When `Browserify.opts.basedir` is set, all content is written to the common file, and the outputs specified by `{ outputs: [...] }` are blank. Before I realized that it was the `Browserify.opts.basedir` setting, I found that printing out the `row` and `groups` from the `threashold` function showed some differences (which thus led me to the `basedir` setting). Below are the outputs from the `threashold` function using the homepage sample.
# `basedir` not set

```
var browserify = require("browserify");
var fs = require("fs");

var files = ["./Scripts/test/x.js", "./Scripts/test/y.js"];
var b = browserify(files);
b
.plugin(factor, {
outputs: ["wwwroot/test/x.js", "wwwroot/test/y.js"], threshold: function (row, groups) {
console.log(row);
console.log(groups);

return this._defaultThreshold(row, groups);
}
});
b
.bundle()
.pipe(fs.createWriteStream("wwwroot/common.js"));
```

*Note the `groups` array is non-empty and there are 3 files emitted

```
{ entry: true,
expose: false,
basedir: undefined,
file: './Scripts/test/y.js',
id: 2,
order: 1,
source: 'var z = require(\'./z.js\');\r\nconsole.log(z(2) + 111);',
deps: { './z.js': 4 },
index: 2,
indexDeps: { './z.js': 4 } }
[ 'C:\\path\to\\Scripts\\test\\y.js' ]

{ entry: true,
expose: false,
basedir: undefined,
file: './Scripts/test/x.js',
id: 1,
order: 0,
source: 'var z = require(\'./z.js\');\r\nvar w = require(\'./w.js\');\r\nconsole.log(z(5) * w(2));',
deps: { './z.js': 4, './w.js': 3 },
index: 1,
indexDeps: { './z.js': 4, './w.js': 3 } }
[ 'C:\\path\to\\Scripts\\test\\x.js' ]

{ id: 4,
source: 'module.exports = function (n) { return n * 111 }',
deps: {},
file: 'C:\\path\to\\Scripts\\test\\z.js',
index: 4,
indexDeps: {} }
[ 'C:\\path\to\\Scripts\\test\\y.js',
'C:\\path\to\\Scripts\\test\\x.js' ]
{ id: 3,
source: 'module.exports = function (n) { return n * 50 }',
deps: {},
file: 'C:\\path\to\\Scripts\\test\\w.js',
index: 3,
indexDeps: {} }
[ 'C:\\path\to\\Scripts\\test\\x.js' ]
```
# `basedir` set

```
var browserify = require("browserify");
var fs = require("fs");

var files = ["./test/x.js", "./test/y.js"];
var b = browserify(files, { basedir: "./Scripts" });
b
.plugin(factor, {
outputs: ["wwwroot/test/x.js", "wwwroot/test/y.js"], threshold: function (row, groups) {
console.log(row);
console.log(groups);

return this._defaultThreshold(row, groups);
}
});
b
.bundle()
.pipe(fs.createWriteStream("wwwroot/common.js"));
```

_Note the `groups` array is always empty, and only 2 files are emitted_

```
{ entry: true,
expose: false,
basedir: './Scripts',
file: './test/y.js',
id: 2,
order: 1,
source: 'var z = require(\'./z.js\');\r\nconsole.log(z(2) + 111);',
deps: { './z.js': 4 },
index: 2,
indexDeps: { './z.js': 4 } }
[]

{ entry: true,
expose: false,
basedir: './Scripts',
file: './test/x.js',
id: 1,
order: 0,
source: 'var z = require(\'./z.js\');\r\nvar w = require(\'./w.js\');\r\nconsole.log(z(5) * w(2));',
deps: { './z.js': 4, './w.js': 3 },
index: 1,
indexDeps: { './z.js': 4, './w.js': 3 } }
[]
```

Environment:
Windows 8.1 x64
Node.js v0.10.33
Browserify 8.0.2
factor-bundle 2.3.3