Use doPublish instead of publish('Stage', 'Live')

From what I understand, doPublish does the same thing as publish, but it has the onBeforePublish and onAfterPublish hooks
Merge pull request #1 from dnadesign/apply_extensions_via_config_yml

Apply extensions via config yml instead of static context
Avoid direct querying where possible, replace with calls to Versioned::get_by_stage()
Replace calls to htmlspecialchars() with Convert::raw2xml()
No need for an empty _config.php file
Merge pull request #2 from dnadesign/avoid_direct_querying_where_possible

Avoid direct querying where possible
Merge pull request #3 from dnadesign/remove_empty_config_file

No need for an empty _config.php file
Merge pull request #4 from dnadesign/use_convert_class_instead_of_htmlspecialchars

Replace calls to htmlspecialchars() with Convert::raw2xml()
Merge pull request #5 from Leapfrognz/patch-1

Use doPublish instead of publish('Stage', 'Live')
added hook
Fallback to standard publish for objects without a doPublish
Merge pull request #16 from dnadesign/master

Misc fixes.