Markdown->Latex and Inline Links referencing included subdirectory files

[Mike Crowe <drmikecrowe-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>]

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Hey folks,

So, I'm building a PDF from bunch of markdown files.  Starting at the top 
file, I build a list of all the files references in a link, such as [Some 
Topic](file1.md), [Another Topic](file2.md).  My list would then contain:

README.md
file1.md
file2.md

etc.

However, I have subdirectories of markdown files, so my list of files is 
more like:

README.md
file1.md
file2.md
topic1/file3.md
topic1/file4.md
topic2/file5.md
topic2/file6.md

To build the PDF, I'm essentially calling pandoc as follows:

pandoc --template templates/mytemplate.latex --listings --file-scope 
--self-contained \
        -f gfm \
        -s $(cat files.lis) \
        -o $OUTPUT.pdf

Overall, this is working great for all the markdown files in the root 
directory (so file1.md, file2.md).  However, all the markdown files in a 
subdirectory (such as topic1/file3) show up as a link in the PDF, rather 
than an inline link, and try to open up topic1/file3.md rather than jump to 
the anchor.

As an aside, it *appears* that pandoc is creating the anchor for 
topic1/file3.md as file3, though I'd prefer it were topic1file3.






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