Fix to obey --build-dir when copying files

Currently, Shifter does not obey the `--build-dir` option for any files it needs to generate with the `copy` directive. Note: In the core library, `copy` is only used in Uploader's [build.json](https://github.com/yui/yui3/blob/master/src/uploader/build.json#L6).

By not respecting `--build-dir`, everything outputs to the yui3 repo's root `/build/` directory.

For example...

    yui3/src/uploader $ shifter --build-dir ../../foo
    [... lots of Shifter output, including ...]
         shifter [info] copying from /Users/derek/src/yui/yui3/src/uploader/swf/flashuploader.swf to /Users/derek/src/yui/yui3/build/uploader/assets/flashuploader.swf

    # Now let's see what files ended up where?
    yui/yui3/src/uploader $ ls -1 ../../foo/
    uploader
    uploader-flash
    uploader-html5
    uploader-queue

    yui/yui3/src/uploader $ ls -1 ../../foo/uploader/
    assets
    uploader-coverage.js
    uploader-debug.js
    uploader-min.js
    uploader.js

    yui/yui3/src/uploader $ ls -1 ../../foo/uploader/assets/
    uploader-flash-core.css

    # Wait, where is flashuploader.swf?

    yui3/src/uploader $ ls ../../build/uploader/assets/flashuploader.swf 
    ../../build/uploader/assets/flashuploader.swf

After this update

     yui/yui3/src/ $ find ../../foo -name *.swf
     ../../foo/build/uploader/assets/flashuploader.swf


This change will also require an update to any build.json files that utilize `copy` so the 2nd path will be relative to the output directory.  See https://github.com/derek/yui3/commit/9eec5ed579ba014fd4650a6889c8b92faf71c71b