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We do this with Flare but we do not use the Alias file solution described by Daniel Freedman. I'm pretty certain our solution is tailored to our product but something similar may work for you.
The UX team identifies MOOPPOPs (Moments Of Opportunity Or Pain) in the software and they add a little question mark button in the UI in these locations. Our software has Page IDs and each UI element also has a Help ID.
The writers writes the text for each popup as a separate Flare topic and publishes them normally (in a folder called PopUps).
The developer provides the writers with the page ID and UI element ID of each question mark button.
The writer uses an internal (to our company) tool to add an entry to a database table in the software which links the pop-up help topic to the question mark button for each UI element (using Page ID and Help ID). This tool also allows us to include a 'Read more' link to the pop-up which links out to a topic in the help system.
I'm happy to provide screenshots off-list if it helps.
Cheers,
Sion
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