Is it possible to write Markdown links in a way that satisfies both Github and Doxygen?

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My project's current directory structure is <ProjectRooot>/wiki, and there are three Markdown files within the wiki directory.

One of them links to the other two, and I have tried two ways of writing the links.

First Way

[Kernel API & Core Negotiation Protocol](wiki/KernelAPI.md)
[Priorities & Starvation](wiki/Priorities.md)

Second Way

[Kernel API & Core Negotiation Protocol](KernelAPI.md)
[Priorities & Starvation](Priorities.md)

Under the first way, the links work correctly in the generated Doxygen and are broken when accessed on github.com. Under the second way, the links work correctly on github.com, but Doxygen does not even try to link at all.

Is there a way to write the links that will satisfy both?

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Is there a way to write the links that will satisfy both?

No, but you could:

smudge
(image from "Customizing Git - Git Attributes", from "Pro Git book")