From b8d17f7ae8ed37784adcfaa4f89d0d28f52fffff Mon Sep 17 00:00:00 2001
From: John MacFarlane <jgm@berkeley.edu>
Date: Sat, 14 Nov 2020 15:00:17 -0800
Subject: Markdown reader: don't increment stateNoteNumber for example refs.

Background:  syntactically, references to example list items
can't be distinguished from citations; we only know which they
are after we've parsed the whole document (and this is resolved
in the `runF` stage).

This means that pandoc's calculation of `citationNoteNum`
can sometimes be wrong when there are example list references.

This commit partially addresses #6836, but only for the case
where the example list references refer to list items defined
previously in the document.
---
 src/Text/Pandoc/Readers/Markdown.hs | 12 ++++++++++++
 test/command/6836.md                | 17 +++++++++++++++++
 test/markdown-reader-more.native    |  2 +-
 3 files changed, 30 insertions(+), 1 deletion(-)
 create mode 100644 test/command/6836.md

diff --git a/src/Text/Pandoc/Readers/Markdown.hs b/src/Text/Pandoc/Readers/Markdown.hs
index 64a2db288..e62a8a978 100644
--- a/src/Text/Pandoc/Readers/Markdown.hs
+++ b/src/Text/Pandoc/Readers/Markdown.hs
@@ -1535,6 +1535,11 @@ ltSign = do
   char '<'
   return $ return $ B.str "<"
 
+-- Note that if the citations extension is enabled, example refs will be
+-- parsed as citations, and handled by a clause in the parser for citations,
+-- since we won't know whether we have an example ref until the
+-- whole document has been parsed.  But we need this parser
+-- here in case citations is disabled.
 exampleRef :: PandocMonad m => MarkdownParser m (F Inlines)
 exampleRef = try $ do
   guardEnabled Ext_example_lists
@@ -2066,6 +2071,13 @@ cite = do
 textualCite :: PandocMonad m => MarkdownParser m (F Inlines)
 textualCite = try $ do
   (suppressAuthor, key) <- citeKey
+  -- If this is a reference to an earlier example list item,
+  -- then don't parse it as a citation.  If the example list
+  -- item comes later, we'll parse it here and figure out in
+  -- the runF stage if it's a citation.  But it helps with
+  -- issue #6836 to filter out known example list references
+  -- at this stage, so we don't increment stateNoteNumber.
+  getState >>= guard . isNothing . M.lookup key . stateExamples
   noteNum <- stateNoteNumber <$> getState
   let first = Citation{ citationId      = key
                       , citationPrefix  = []
diff --git a/test/command/6836.md b/test/command/6836.md
new file mode 100644
index 000000000..c35048045
--- /dev/null
+++ b/test/command/6836.md
@@ -0,0 +1,17 @@
+```
+pandoc -t native
+[@buchanan]
+
+(@foo)
+
+See @foo.
+
+[@buchanan]
+^D
+[Para [Cite [Citation {citationId = "buchanan", citationPrefix = [], citationSuffix = [], citationMode = NormalCitation, citationNoteNum = 1, citationHash = 0}] [Str "[@buchanan]"]]
+,OrderedList (1,Example,TwoParens)
+ [[]]
+,Para [Str "See",Space,Str "1."]
+,Para [Cite [Citation {citationId = "buchanan", citationPrefix = [], citationSuffix = [], citationMode = NormalCitation, citationNoteNum = 2, citationHash = 0}] [Str "[@buchanan]"]]]
+```
+
diff --git a/test/markdown-reader-more.native b/test/markdown-reader-more.native
index 2f643cab0..5ac4facb8 100644
--- a/test/markdown-reader-more.native
+++ b/test/markdown-reader-more.native
@@ -328,7 +328,7 @@ Pandoc (Meta {unMeta = fromList [("author",MetaList [MetaInlines [Str "Author",S
 ,Header 2 ("reference-link-fallbacks",[],[]) [Str "Reference",Space,Str "link",Space,Str "fallbacks"]
 ,Para [Str "[",Emph [Str "not",Space,Str "a",Space,Str "link"],Str "]",Space,Str "[",Emph [Str "nope"],Str "]\8230"]
 ,Header 2 ("reference-link-followed-by-a-citation",[],[]) [Str "Reference",Space,Str "link",Space,Str "followed",Space,Str "by",Space,Str "a",Space,Str "citation"]
-,Para [Str "MapReduce",Space,Str "is",Space,Str "a",Space,Str "paradigm",Space,Str "popularized",Space,Str "by",Space,Link ("",[],[]) [Str "Google"] ("http://google.com",""),Space,Cite [Citation {citationId = "mapreduce", citationPrefix = [], citationSuffix = [], citationMode = NormalCitation, citationNoteNum = 3, citationHash = 0}] [Str "[@mapreduce]"],Space,Str "as",Space,Str "its",SoftBreak,Str "most",Space,Str "vocal",Space,Str "proponent."]
+,Para [Str "MapReduce",Space,Str "is",Space,Str "a",Space,Str "paradigm",Space,Str "popularized",Space,Str "by",Space,Link ("",[],[]) [Str "Google"] ("http://google.com",""),Space,Cite [Citation {citationId = "mapreduce", citationPrefix = [], citationSuffix = [], citationMode = NormalCitation, citationNoteNum = 2, citationHash = 0}] [Str "[@mapreduce]"],Space,Str "as",Space,Str "its",SoftBreak,Str "most",Space,Str "vocal",Space,Str "proponent."]
 ,Header 2 ("empty-reference-links",[],[]) [Str "Empty",Space,Str "reference",Space,Str "links"]
 ,Para [Str "bar"]
 ,Para [Link ("",[],[]) [Str "foo2"] ("","")]
-- 
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