Fix parsing of footnotes in --metadata-file.

Closes #7813.

pandoc.cabal

@@ -246,6 +246,7 @@ extra-source-files:
                  test/command/bar.tex
                  test/command/bar-endinput.tex
                  test/command/yaml-metadata.yaml
+                 test/command/7813-meta.yaml
                  test/command/3510-subdoc.org
                  test/command/3510-export.latex
                  test/command/3510-src.hs

src/Text/Pandoc/Readers/Markdown.hs

@@ -81,8 +81,12 @@ yamlToMeta opts mbfp bstr = do
         oldPos <- getPosition
         setPosition $ initialPos (fromMaybe "" mbfp)
         meta <- yamlBsToMeta (fmap B.toMetaValue <$> parseBlocks) bstr
+        checkNotes
         setPosition oldPos
-        return $ runF meta defaultParserState
+        st <- getState
+        let result = runF meta st
+        reportLogMessages
+        return result
   parsed <- readWithM parser def{ stateOptions = opts } ("" :: Text)
   case parsed of
     Right result -> return result
@@ -103,7 +107,11 @@ yamlToRefs idpred opts mbfp bstr = do
           Nothing -> return ()
           Just fp -> setPosition $ initialPos fp
         refs <- yamlBsToRefs (fmap B.toMetaValue <$> parseBlocks) idpred bstr
-        return $ runF refs defaultParserState
+        checkNotes
+        st <- getState
+        let result = runF refs st
+        reportLogMessages
+        return result
   parsed <- readWithM parser def{ stateOptions = opts } ("" :: Text)
   case parsed of
     Right result -> return result
@@ -308,7 +316,17 @@ parseMarkdown = do
   optional titleBlock
   blocks <- parseBlocks
   st <- getState
-  -- check for notes with no corresponding note references
+  checkNotes
+  let doc = runF (do Pandoc _ bs <- B.doc <$> blocks
+                     meta <- stateMeta' st
+                     return $ Pandoc meta bs) st
+  reportLogMessages
+  return doc
+
+-- check for notes with no corresponding note references
+checkNotes :: PandocMonad m => MarkdownParser m ()
+checkNotes = do
+  st <- getState
   let notesUsed = stateNoteRefs st
   let notesDefined = M.keys (stateNotes' st)
   mapM_ (\n -> unless (n `Set.member` notesUsed) $
@@ -317,11 +335,7 @@ parseMarkdown = do
                    Nothing -> throwError $
                      PandocShouldNeverHappenError "note not found")
          notesDefined
-  let doc = runF (do Pandoc _ bs <- B.doc <$> blocks
-                     meta <- stateMeta' st
-                     return $ Pandoc meta bs) st
-  reportLogMessages
-  return doc
+
 
 referenceKey :: PandocMonad m => MarkdownParser m (F Blocks)
 referenceKey = try $ do

test/command/7813-meta.yaml

@@ -0,0 +1,6 @@
+---
+abstract: |
+    a footnote[^1] in abstract.
+
+    [^1]: content
+...

test/command/7813.md

@@ -0,0 +1,26 @@
+```
+% pandoc --metadata-file command/7813-meta.yaml -t native -s
+Hi
+^D
+Pandoc
+  Meta
+    { unMeta =
+        fromList
+          [ ( "abstract"
+            , MetaBlocks
+                [ Para
+                    [ Str "a"
+                    , Space
+                    , Str "footnote"
+                    , Note [ Para [ Str "content" ] ]
+                    , Space
+                    , Str "in"
+                    , Space
+                    , Str "abstract."
+                    ]
+                ]
+            )
+          ]
+    }
+  [ Para [ Str "Hi" ] ]
+```