I am only first year degree student. I am only capable to object oriented programming and not learning data structure yet. 
Data structure? What data structure?

I don't even use Unity3D and GameMaker, at worst, not even cannot to make my own maps and conditioning Lua for Warcraft 3. (I will learn from my friend after this)
This is bad. :/
When I try move through the your Danmagine V1.2 files via Notepad, I cannot tell how the library linked up to another file so it is my negligence I am afraid. 
.dll libraries are sort of back-end, and are likely to be not of your any interest, at least because you won't get any useful information.
.lua files, on the other end, contain higher level code. It is splitted in several "packages", each of which describe its own level of objects:
- Engine contain implementations of basic entities, such as Class (an entity which implements some principles of OOP), Actor (game entity, anything that exists in game world), SpriteComponent (an attachable component which shown Actor on screen), UserInputHandler (part of gameplay object dealing with all user input, including keyboard events) and others.
- DammakuGame contains code which describes common rules of danmaku. It introduces Player (actor representing protagonist and controlled by actual player), Bullet (danmaku bullet), Enemy and others.
- Game contains resources, specific to one particular shmup. Currently it contains just simple dueld between a generic player and flying TV box.
All this data is placed in "Content" folder, every package has its own folder.
Client application runs some predefined scripts, in this order:
- some nearly internal code,
- Engine.Main,
- DammakuGame.Main,
- Game.Players.0.Main (currently does nothing),
- Game.MainStage.
All scripts are loaded from .pkg files found in Output directory, which also contai executables themselves. Those packages are built by "Packer.exe", with their structure determined by .tpkg files. E. g. DammakuGame's structure is described in Content\DammakuGame\Index.pkg, which lists all first-level items along with two sub-packages. You may wath "PackGame.bat" to see how the program is called.
If you want to change game's content files, you must not forget to rebuild changed package, since the application doesn't directly use files from "Content" folder, instead, it uses .pkg files lying in the sam folder with binaries.
Since there is too many question to ask when I need to compare of other doujin game to this engine and how to make exactly one doujin game, I need to catch a breath there and try algorithm my intention to make one.
...As I said, my program is not a good choice for beginners.
two stages... conversation... conversation box... character sprite animation...
Oh, wait, wait, not that fast, I need to implement those things first: probably nobody except for me will write appropriate files, among those who can, and it takes time.