v1.4.0
If installed from Package Manager, previous version would not open files (default settings and help file) from menu, it was due to path naming, since now it uses Transparency directory instead of SublimeTextTrans.
Git cloning was not affected.
It was also used sublime_api on ST3 to apply opacity settings, more faster than finding out all Windows applications whose windows belong to ST3 in order to apply transparency levels.
However, ST2 still uses the old approach, since it doesn't have sublime_api.
Issue #3 was also fixed.
Calling external executable was also limited to only call it if ST's window is not capable to adjust opacity levels. It means, it might only be called once each restart of Sublime Text.