I see that this was fixed in commit https://github.com/jgm/pandoc/commit/37e68a818bd0adafa4b90048eab0efc94a4980c4 but it I noticed today that it's back.

pandoc version:
pandoc 2.14.0.1
Compiled with pandoc-types 1.22, texmath 0.12.3, skylighting 0.10.5.1,
citeproc 0.4.0.1, ipynb 0.1.0.1

OS Version: 
Mac OS X, Version 10.15.7, Build 19H1030

To reproduce, run 
pandoc -r rst -w native -o simple.native simple.rst

give the following two files (delimited by lines with equals signs)
===== simple.rst ===========================================
.. include:: three.txt
   :code:
============================================================
===== three.txt ============================================
1st line.
2nd line.
3rd line.
============================================================

That produces:
===== simple.native ========================================
[CodeBlock ("",[""],[("code","")]) "1st line.\n2nd line.\n3rd line.\n\n"]
============================================================

Notice the two newlines at the end.

On Sunday, July 12, 2020 at 4:48:44 PM UTC-4 John MacFarlane wrote:

Okay, I see how to fix this and will push a fix soon.

John MacFarlane <j...@berkeley.edu> writes:

> I see why this is happening. In the RST reader, at line 487, we
> have
>
> let contents' = T.unlines contentLines'' <> "\n"
>
> which will produce \n\n. I have no idea why the "\n" was added
> originally.
>
> This was added in 8fcf66453cc4f9d1cf9413aa466477e56290d733
>
>
> "T. Kurt Bond" <tkur...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
>
>> Note
>>
>> *The ``text/plain`` alternative may look … odd.*
>>
>> I'm trying to make this readable both as text/html e-mail and text/plain but
>> have little control over how the text/plain alternative comes out. I've
>> added extra horizontal rules before the included files to make the file
>> contents stand out more, even though the text/html alternative doesn't need
>> it. Unfortunately, the automatic process that converts the text/html
>> alternative
>> into the text/plan alternative leaves blank lines before and after the file
>> contents, which is distressing since the bug I'm talking about is about an
>> extra blank line. Gmail, sometimes I hate you.
>>
>> It turns out that the -w native output of an RST input file with an
>> include directive
>> with the :code: option shows that there is an extra blank line at the end
>> of the CodeBlock in the AST. This causes the generated output for HTML, ms,
>> LaTeX, and ConTeXt to have extra blank lines at the ends of those code
>> blocks.
>>
>> My Pandoc version is:
>>
>> pandoc 2.9.2.1
>> Compiled with pandoc-types 1.20, texmath 0.12.0.1, skylighting 0.8.3.2
>>
>> My OS information is:
>>
>> Mac OS X, Version 10.15.4, Build 19E287
>>
>> I generated the output to check with the following commands:
>>
>> pandoc -r rst -w native --output=elii-rst.native elii.rst
>> pandoc -r rst -w html --output=elii-rst.html elii.rst
>> pandoc -r rst -w ms --output=elii-rst.ms elii.rst
>> pandoc -r rst -w latex --pdf-engine=xelatex --output=elii-rst.ltx elii.rst
>> pandoc -r rst -w context --output=elii-rst.ctx elii.rst
>>
>> (I'm only going to include the native and HTML output in this message, but
>> I did check the other output formats.)
>>
>> So, for the ReStructuredText input (file elii.rst):
>> ------------------------------
>>
>> Extra Line in Include Directive Output for HTML, ms, LaTeX, and ConTeXt Output
>> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
>>
>> Here's a ``include`` directive **without** a ``:code:`` option:
>>
>> .. include:: three.txt
>>
>> Did it have an extra line at the end? **No**, in HTML, ms, LaTeX,
>> and ConTeXt output. Note that this will not show up when the HTML is
>> rendered as a web page, just in the HTML source itself.
>>
>> Here's a ``include`` directive with a ``:code:`` option:
>>
>> .. include:: three.txt
>> :code:
>>
>> Did it have an extra line at the end? **Yes**, in HTML, ms, LaTeX,
>> and ConTeXt output.
>>
>> ------------------------------
>>
>> which includes a text file (three.txt) using the include directive with a
>> :code: option:
>> ------------------------------
>>
>> 1st line.
>> 2nd line.
>> 3rd line.
>>
>> ------------------------------
>>
>> the resulting native output (elii-rst.native) is generated:
>> ------------------------------
>>
>> [Header 1 ("extra-line-in-include-directive-output-for-html-ms-latex-and-context-output",[],[])
>> [Str "Extra",Space,Str "Line",Space,Str "in",Space,Str
>> "Include",Space,Str "Directive",Space,Str "Output",Space,Str
>> "for",Space,Str "HTML,",Space,Str "ms,",Space,Str "LaTeX,",Space,Str
>> "and",Space,Str "ConTeXt",Space,Str "Output"]
>> ,Para [Str "Here's",Space,Str "a",Space,Code ("",[],[])
>> "include",Space,Str "directive",Space,Strong [Str "without"],Space,Str
>> "a",Space,Code ("",[],[]) ":code:",Space,Str "option:"]
>> ,Para [Str "1st",Space,Str "line.",SoftBreak,Str "2nd",Space,Str
>> "line.",SoftBreak,Str "3rd",Space,Str "line."]
>> ,Para [Str "Did",Space,Str "it",Space,Str "have",Space,Str
>> "an",Space,Str "extra",Space,Str "line",Space,Str "at",Space,Str
>> "the",Space,Str "end?",Space,Strong [Str "No"],Str ",",Space,Str
>> "in",Space,Str "HTML,",Space,Str "ms,",Space,Str
>> "LaTeX,",SoftBreak,Str "and",Space,Str "ConTeXt",Space,Str
>> "output.",Space,Str "Note",Space,Str "that",Space,Str "this",Space,Str
>> "will",Space,Str "not",Space,Str "show",Space,Str "up",Space,Str
>> "when",Space,Str "the",Space,Str "HTML",Space,Str "is",SoftBreak,Str
>> "rendered",Space,Str "as",Space,Str "a",Space,Str "web",Space,Str
>> "page,",Space,Str "just",Space,Str "in",Space,Str "the",Space,Str
>> "HTML",Space,Str "source",Space,Str "itself."]
>> ,Para [Str "Here's",Space,Str "a",Space,Code ("",[],[])
>> "include",Space,Str "directive",Space,Str "with",Space,Str
>> "a",Space,Code ("",[],[]) ":code:",Space,Str "option:"]
>> ,CodeBlock ("",[""],[]) "1st line.\n2nd line.\n3rd line.\n\n"
>> ,Para [Str "Did",Space,Str "it",Space,Str "have",Space,Str
>> "an",Space,Str "extra",Space,Str "line",Space,Str "at",Space,Str
>> "the",Space,Str "end?",Space,Strong [Str "Yes"],Str ",",Space,Str
>> "in",Space,Str "HTML,",Space,Str "ms,",Space,Str
>> "LaTeX,",SoftBreak,Str "and",Space,Str "ConTeXt",Space,Str "output."]]
>>
>> ------------------------------
>>
>> If you look at the CodeBlock element you can see it ends with \n\n. The
>> original included text file ends with just one \n.
>>
>> The HTML output (elii-rst.html) is:
>> ------------------------------
>>
>> <h1 id="extra-line-in-include-directive-output-for-html-ms-latex-and-context-output">Extra
>> Line in Include Directive Output for HTML, ms, LaTeX, and ConTeXt
>> Output</h1>
>> <p>Here's a <code>include</code> directive <strong>without</strong> a
>> <code>:code:</code> option:</p>
>> <p>1st line. 2nd line. 3rd line.</p>
>> <p>Did it have an extra line at the end? <strong>No</strong>, in HTML,
>> ms, LaTeX, and ConTeXt output. Note that this will not show up when
>> the HTML is rendered as a web page, just in the HTML source
>> itself.</p>
>> <p>Here's a <code>include</code> directive with a <code>:code:</code>
>> option:</p>
>> <pre class=""><code>1st line.
>> 2nd line.
>> 3rd line.
>>
>> </code></pre>
>> <p>Did it have an extra line at the end? <strong>Yes</strong>, in
>> HTML, ms, LaTeX, and ConTeXt output.</p>
>>
>> ------------------------------
>>
>> I've checked and HTML, ms, LaTeX, and ConTeXt output all have these blank
>> lines at the end of generated text for those code blocks.
>> ------------------------------
>>
>> *Note:* This message was written as RST input with include directives with
>> the :code: option but does not have the extra blank lines at the ends of
>> the included code (at least in the text/html alternative, see the note
>> about the text/plain alternative at the beginning of this message) because
>> I preprocessed it with
>>
>> pandoc -s -r rst -w rst -o elii-email.rst elii-email-in.rst
>>
>> which converted the include directives with the :code: option to
>> inline code directives,
>> which don't the extra lines at the end. Very useful workaround. I use *GNU
>> Make* to build all the various generated files.
>>
>> --
>> T. Kurt Bond, tkur...@gmail.com, https://tkurtbond.github.io
>>
>> --
>> You received this message because you are subscribed to the Google Groups "pandoc-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
>> To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/CAN1EhV_L54%3DmKnSxiNwKNoKZ2CXNe7pVXM8ZtBe_D%2BkAZ_KURg%40mail.gmail.com.

--
You received this message because you are subscribed to the Google Groups "pandoc-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/74b0adbe-6552-4553-98c4-f31e3afcdc31n%40googlegroups.com.