You need to create manual Markdown links to each page.
[[documentation]] and [[Help|get help]] style links are wikilinks and generally only used in wikis. They are not part of the standard Markdown syntax and not supported by Jekyll (which GitHub Pages uses under the hood). Note that GitHub Wiki supports both styles, so you could edit your links before importing if you like.
Either any, you need to edit your links to manually point to the appropriate pages:
Read the [documentation](path/to/documentation/) or [Help](path/to/get_help.html]
Of course, you will need to adjust the above paths to point at the correct location. As an alternative you may be able to use Jekyll permalinks, which could provide a shortcut for you to identify specific pages without specifying a full path.