cleanup fix for Unresolved reference while instantiating Encoding

PR cebe#68

Merge pull request cebe#59 from cebe/fix-writer-yaml-empty-array

Fix writing empty array to YAML

added test case for cebe#54

it is a duplicate of cebe#57

fixes cebe#54

only allow $ref in array, a map may have a $ref property

Merge pull request cebe#41 from cebe/more-reference-issues

Fix issue with loading reference that points to a reference

Merge pull request cebe#39 from cebe/fix-resolving-references

Fix resolving recursive references

improved error messages when reading or writing files fails

Update README.md

fix PHPdoc to reflect the fact that properties are writeable now