Fixed handling of links

This PR fixes two issues with the handling of links:

* `CodexRepositoryGit` was passing in full filesystem paths to the `MarkdownHelper`.
* `MarkdownHelper`'s path matching regexp was too greedy, and it misses multiple links on a single line.

You can see both problems in action on niceframework.com. This fix seems to take care of all linking issues, and should be considered for 1.1.1.