Document-sharing with edits being tracked is the big one, though (like the article raised).
Also, Signal being tied to a phone number is a nightmare.
I disagree. Sitting on a phone and sweet-talking sources isn't high-tech, and neither is bundling up five tweets to make a clickbait.
But as soon as you're talking about doing public records research, tracking the activities and ownership of a multi-national company, working in a team with people from 30 countries on a single story, try to manage your confidential evidence across five years, it becomes quite technical.
Calendaring system: Google Calendar, iCal
Contacts databases: GMail Contacts, Apple Contacts
Location coordination tools: Google Latitude, Find My Friends.
Some of those programs don't exist, as far as I'm aware. A Wiki/Etherpad/Word style change tracking mashup, and Map-based storytelling and analysis systems are two that I'd like to see implemented.