Your problem surfaces here: https://github.com/jekyll/jekyll/blob/master/lib/jekyll/cleaner.rb#L56. Cleaner messages Document#destination before Document#read is done, resulting in Document#permalink returning nil which leads to converters.first.output_ext being messaged with document.extname instead of File.extname with document.permalink in Renderer#output_ext which leads to Document@output_ext being cached with ".html"

To add, the Document is actually being read and is fully populated. Document@output_ext just ended up being cached early leading to this order problem. Your source works, it's higher up the chain an order problem surfaces a bug.

Cleaner messages Document#destination before Document#read is done, resulting in Document#permalink returning nil which leads to converters.first.output_ext being messaged with document.extname instead of File.extname with document.permalink in Renderer#output_ext which leads to Document@output_ext being cached with ".html"

I think you're right, but I'm not sure why quite yet.

Consider Site#process:

    def process
      reset
      read
      generate
      render
      cleanup
      write
      print_stats
    end

cleanup is called after read, and read has to complete before cleanup can be called. cleanup calls Cleaner#cleanup! which calls Cleaner#obsolete_files which calls Cleaner#new_dirs which calls Cleaner#new_files, which calls, for each site document, Document#destination. So I'm not really sure what's up. Especially because the failing tests use Site#process...

Only test failures are the ones currently on master:

Failure:
TestKramdown#test_: kramdown when a custom highlighter is chosen should support legacy enable_coderay... for now.  [/home/travis/build/jekyll/jekyll/test/test_kramdown.rb:93]
Minitest::Assertion: Failed refutation, no message given
Failure:
TestKramdown#test_: kramdown when a custom highlighter is chosen should use the chosen highlighter if it's available.  [/home/travis/build/jekyll/jekyll/test/test_kramdown.rb:73]
Minitest::Assertion: Failed refutation, no message given

@jekyllbot: merge +bug