Ok i'm going to answer my own question.
First of all thank Michael Dibbets and wtjones for your answers.
--disable-web-security and --allow-file-access-from-files
did not work.
I did not go for native plugins and for extending chrome from its source as it seems to take time.
The solution:
I used chromedriver with selenium java to automate chrome.
and with the help of Slanec's Answer to this question i was able select the file pragmatically.
Here's the java code:
System.setProperty("webdriver.chrome.driver", "C:/.../chromedriver.exe");
WebDriver driver = new ChromeDriver();
driver.get("URL_OF_THE_PAGE");
WebElement link = driver.findElement(By.linkText("TEXT_IN_THE_LINK"));
link.click();
WebElement choose_file_input = driver.findElement(By.className("CLASS_OF_THE_INPUT"));
choose_file_input.sendKeys("PATH_TO_FILE");
Thanks!
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