[DOC,FEATURE,FIX,INTERNAL] Improvements and fixes to the dox build system.

git-svn-id: http://svn.seqan.de/seqan/trunk@14403 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Fixing problems in dox documentation all over the library.

git-svn-id: http://svn.seqan.de/seqan/trunk@14404 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] Disabling pair_align for being built for workflow plugin.

git-svn-id: http://svn.seqan.de/seqan/trunk@14405 e6417c60-b987-48fd-844e-b20f0fcc1017