Remove static classes #206; Reactivate PHPCPD and PHPMD

As #206, three static classes, i.e. Footnotes, Endnotes, and TOC, are replaced by non-static version. I'll continue the refactoring to Media, Settings, and Style, but I won't refactor static clasess in Shared folder.

We've also passed PHPCPD and PHPMD, so I reactivate those tests in Travis.