What is Selenium Automation-Atoms

I noticed selenium-atoms project in selenium repository. According to the wiki this project exposes some common APIs similar to selenium language implementations like click, type and findElement. I don't see anything related to this project being used by selenium-ide.

Initially my understanding was, the language implementation sends calls to the driver (for example, chromedriver.exe) where it sends another call to specific browser in a language only that browser understands.

(Java Language implementation) ------ json wire protocol -----> (chromedriver.exe) ------> (chrome.exe)

Is this how web drivers actually executing actions on browser? If so,

1. How is it being injected to the web page?
2. How sendKeys on to a <input type="file"> is handled (since JavaScript cannot possibly access files in the user's file system) or alert.accept() where in JavaScript's thread is blocked?

If not, how is this being used?