Added first version of refactor.
Updated release notes.
Updated files for html documentation.
Changed code from class to module.

This is for #43.
The change was done as there are only static method.
Made update optionally recursive

For #43.
Changed package ordering and avoided to add files such as Resources

For #43
Added constants to package.order
Merge branch 'master' into issue43_refactor
Merge branch 'master' into issue43_refactor
Merge branch 'master' into issue43_refactor
Removed unused import
Changed name to a hidden file name
Corrected bug that caused reference results not to be added to copiedFiles.txt
Revised file to make copy entries as a relative path
Merge pull request #45 from lbl-srg/issue43_refactor

Issue43 refactor