extract_class_names is obsolete

hierarchical_class_names should be used instead. one test still fails.
related to #249
should fix new error in #249
Merge branch 'staging' into 249-entity_tree
rely on size-method instead of count-fields.
fast fixing the problem with explicit thing subclass sentences

its a fast fix for 249 till the tarjan algorythm is
implemented
use to_s on entity instead of explicit call.
always replace _ with whitespace for display name.
Gems updated
unset ontology_id on setting state to failed

required to pass the logic_id_check
related to #608
Revert "unset ontology_id on setting state to failed"

This reverts commit 57eba7322d74ad38e54791f9a5aea29562bf2684.
use bundle exec to start rails server
Merge pull request #743 from ontohub/fix_bundle_exec_rails_server

use bundle exec to start rails server
Merge pull request #731 from ontohub/249-entity_tree

Fixing error with explicit Thing sentences
entitry is only viewable when the classes are shown

should fix #744
Merge pull request #736 from ontohub/725-entity_display_name_issue

725 entity display name issue
Merge pull request #727 from ontohub/723-sentence_count_display_correction

rely on size-method instead of count-fields.
remove unnecessary logger portions from linkscode.
extract linktype determination into method.
add KINDS_Mapping for concrete kind checking

Also adjust order of KINDS array, since
inclusion matches would never reach 'cofree'
as 'free' would be matched first.
adjust link/mapping kind determination mechanic

use three-tries mechanic before defaulting to
'import'-kind. First we search for exact matches,
then for exact-matches which are only included
in the target string, and last for triggerword
(case-insensitive) inclusion.