Force UNIX style line endings for shell scripts.

Shell scripts must have UNIX style endings even on Windows so that when the projects is built, packaged and run on Linux they work without errors.
Fix BrooklyCatalog.createSpec, was creating the spec as if a regular app, not catalog item.

BrooklynAssemblyTemplateInstantiator.createSpec couldn't realize that the passed in plan was created from a catalog item - it was checking with the wrong id (plan name instead of catalog id). Fix the problem by passing a loader explicitly, making it the caller's responsibility to decide if it is a catalog item plan or a regular plan.
This closes #135
This closes #134