Fix for #226,#282

For #226 The fix is to make sure relative paths are rooted:
(ScriptOptions.makeAbsolute <| project.BaseDirectory.ToString())

For #282 project reference do not return all dependencies so we have to
iterate over project type references and add them ourselves.
Removed reverse pipes, corrected project references to have the correct root path.
Merge pull request #283 from 7sharp9/master

Fix for #226,#282