A first pass at documenting build plugins

Documentation for the CompileStep is only in the source right now
Allow CompileStep#addAsset to accept Strings for content
Fix bug where backcompat for registerBuildPlugin didn't work
Document packageName
Document Buffer or String argument in addAsset
Add newlines between CompileStep methods
Consistently name path variables
Fix link
Add fullInputPath to public API
Document arch

Fix documentation typo
Rename appendDocument to addHtml
Rename back pathForSourceMap
Fix a big typo
Fix incorrect packageName docs
Pass through 'bare' option to compiled js source files
Add link to Wiki, add warning that comments aren't used
Fix typo
Deprecate amplify,backbone,bootstrap,d3

packages/deprecated/README:

```
These packages are no longer actively maintained by MDG.  Seek
community alternatives instead.

Note that these packages still exist in atmosphere, and you can still
build a package that depends on one of them by specifying an explicit
package version.
```

Nothing technically prevents us from publishing further versions of these packages (like the ones in packages/non-core).
Fix small documentation issues
Re-run doc script to pick up doc changes