I've noticed that by using a 'silent' ringtone from another source (zedge) that messages do not vibrate the phone either, even if the entire phone is set to vibrate silent mode. This kind of sucks to be perfectly honest. I really wish they would change it back to two separate sources.
You can go in the individual APP settings and mute. mt yahoo email had a turn off and google has a silent option in tones.
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