[INTERNAL] mv bam_io file from extras to core
[INTERNAL] mv basic file from extras to core
[INTERNAL] mv consensus files from extras to core
[INTERNAL] mv extras/include/seqan/* from extras to core
[INTERNAL] fix apps after moving includes to core
[FIX] uninclude headers again
[INTERNAL] mv extras/tests/* to core
[INTERNAL] mv extras/demos/* to core
[INTERNAL] mv extras/apps/* to core
[INTERNAL] rm extras
[INTERNAL] rm sandbox
[INTERNAL] rm docs and docs2
[INTERNAL] rm misc/iorev*
[INTERNAL] rm misc cruft
[INTERNAL] remove lpthread from test, since it is now globally included
[INTERNAL] move ./core/* to ./ and adapt cmake
[INTERNAL] Humongous text replacing commit, removing "core" directory hierarchy.

Includes adjustments to the build and documentation system.
Merge pull request #716 from h-2/mergeCoreExtras

Removing core/extras directory layer