Discourse has fine-grained quoting rules and capabilities, but if you read and reply primarily by email, you will lose much of the nuance. The Web interface is the truth.
A few notes:
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Clicking the gray Reply button under a specific post replies to that post and links the two. Clicking the blue button at the bottom of the entire topic replies generally, such that there is no linking.
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Selecting a small amount of text in a message and clicking the Quote button (or pressing q) creates a reply that is linked.
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When there is a link based on a simple reply, the person making the original message is linked in the upper right corner. If you click their name, you jump to the original message.
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When there is a link based on a quoted reply, there is a two-part control that looks like a down-pointing caret and an up-pointing arrow in the right corner.
- Click the down-point caret to see more context for the quoted text.
- Click the up-pointing arrow to move up to the original message.



