[FIX,INTERNAL] Fixing dox system when using <code>.

The internal representation of @code was as a <code> node.  This is now done
as <dox:code> which allows to distinguish both without @htmlonly.
[DOC] First full version of language_entities.dox

Providing each part of language_entities.dox with some documentation.
We might need to extend this, but for now it should be OK.
Merge pull request #14 from holtgrewe/feature/language_entities_doc

Fixing language_entities.dox
[FIX] Gustaf: paired-end input and vcf out
Merge branch 'pr/16' into develop

# By Kathrin Trappe
# Via Kathrin Trappe
* pr/16:
  [FIX] Gustaf: paired-end input and vcf out
Merge pull request #16 from ktrappe/hotfix/gustaf_input

[FIX] Gustaf: paired-end input and vcf out
[FEATURE] Build System: added SEQAN_DATE and SEQAN_REVISION from git or svn
[FIX] Search/Join: fixed date and revision
[FIX] Build System: removed duplicated git_wc_info macro
[FEATURE] Build System: added macro seqan_get_repository_info()

Conflicts:
	util/cmake/FindSeqAn.cmake
Merge branch 'hotfix/date_revision' into develop

* hotfix/date_revision:
  [FEATURE] Build System: added macro seqan_get_repository_info()
  [FIX] Build System: removed duplicated git_wc_info macro
  [FIX] Search/Join: fixed date and revision
  [FEATURE] Build System: added SEQAN_DATE and SEQAN_REVISION from git or svn

Conflicts:
	util/cmake/FindSeqAn.cmake