How do we know? Hillary's plan was, as it appeared on the surface, to send unsecured emails to soldiers and operatives in the field with what appeared to be low-level / relatively harmless information (of course nothing at this level of government is "harmless"--but that's a different story). However, encoded into her emails were the signals to warn the parties she KNEW would be intercepting them about what could happen.
It is starting to appear that Hillary's server was not, as we'd been led to believe, a way to circumvent government rules--but rather an intentionally insecure environment to facilitate illegal communication with various parties. It's like this: let the Russians or ISIS know you have an unsecured open-server and then you can leave messages for them all you want with plenty of deniability.
Any message you send can have additional "piggy-back" information--and as everyone is watching, you can easily get the word out. In this case, she was letting them know the "heat level" (likelihood of the strike going through) and specific targets.
How Did She Do It?
The technical answer is "Stegonographic Equidistant Letter Sequences"--but it is more commonly referred to as "the Bible Code." It's essentially a way to write a fairly normal seeming sentence that, if chopped up the right way, and every Xth letter taken, provides a hidden message. Hillary's emails, run through statistical sieves to look for these anomalies find messages that are almost 1-in-a-billion chances of happening accidentally.