Github user mattf-horton commented on the issue:

    https://github.com/apache/metron/pull/656
  
    Hi @nickwallen , regarding problems with links:  Item 5 in the header 
comments for site-book/bin/fix-md-dialect.py says:
    ```
    5. Relative links need to be re-written.  ... 
    as best we can we will re-write named anchors referring to tags 
autogenerated from headers.            
    The problem with generated tags is that Github-MD forces header text to 
lower-case, and                
    replaces blank spaces with hyphens, while doxia-markdown leaves case 
unchanged, and replaces           
    blanks with underscores.  Fortunately we seem to have a culture of using 
link references that          
    are typographically the same as the header text, so we have some basis for 
fixing most links.
    ```
    You've done several links to doc headers (which have autogenerated anchor 
tags) that _don't_ use the header text as the link reference text.  That means 
the tool is unable to re-synthesize the link tags, which will therefore be 
wrong.
    
    To fix this, replace things that look like:
    ```
    Build the Metron RPMs by [following these 
instructions](../../metron-deployment#rpm).
    ```
    with something like this:
    ```
    Build the Metron RPMs by following these instructions: 
[RPM](../../metron-deployment#rpm).
    ```
    This will cause the link in Doxia to be correctly re-written as 
`../../metron-deployment#RPM`
    
    If this seems stilted you could go back and retitle the section you're 
pointing at to be something like `Building RPMs`, then the above reference 
becomes:
    ```
    Create the Metron RPMs by following these instructions: [Building 
RPMs](../../metron-deployment#building-rpms)
    or
    Create the Metron RPMs by following the instructions for [Building 
RPMs](../../metron-deployment#building-rpms)
    ```
    which will also be correctly fixed-up by the re-write script.


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