Fix scaffold creation via CreateAutomaticDocumentation
Do not convert .bib to xml

First off, the manual does not currently use the bibliography at all.
Secondly, GAPDoc can handle .bib files directly, there is no need to
manually convert them to XML. Just write
  <Bibliography Databases="AutoDoc.bib"/>
and it will work.
Merge branch 'simplify-bib' of https://github.com/fingolfin/AutoDoc

* 'simplify-bib' of https://github.com/fingolfin/AutoDoc:
  Do not convert .bib to xml
Remove default entities list
Added new methods with options. Not tested yet.
Merge branch 'master' of github.com:mohamed-barakat/AutoDoc

* 'master' of github.com:mohamed-barakat/AutoDoc:
  again .gitignore
Tested new commands, fixed bugs.
Added a default chapter method.

Tested.
Merge branch 'option_files'

* option_files:
  Tested new commands, fixed bugs.
  Added new methods with options. Not tested yet.
Highered Version.