Disable citations extension in writers if --citeproc is used.

Otherwise we get undesirable results, as the format's native
citation mechanism is used instead of (or in addition to) the
citeproc-generated citations. Closes #10662.

MANUAL.txt

@@ -1505,11 +1505,10 @@ header when requesting a document from a URL:
     order they appear on the command line.  For more
     information, see the section on [Citations].
 
-    Note: if your target format is `markdown`, `org`, or `typst`,
-    you will need to disable the `citations` extension (e.g., `-t
-    markdown-citations`) to see the rendered citations and
-    bibliography. Otherwise the format's own citation syntax will
-    be used.
+    Note: if this option is specified, the `citations` extension
+    will be disabled automatically in the writer, to ensure that
+    the citeproc-generated citations will be rendered instead of
+    the format's own citation syntax.
 
 `--bibliography=`*FILE*
 

src/Text/Pandoc/App/OutputSettings.hs

@@ -38,6 +38,7 @@ import System.FilePath
 import System.IO (stdout)
 import Text.Pandoc.Chunks (PathTemplate(..))
 import Text.Pandoc
+import Text.Pandoc.Filter (Filter(CiteprocFilter))
 import Text.Pandoc.App.Opt (Opt (..))
 import Text.Pandoc.App.CommandLineOptions (engines)
 import Text.Pandoc.Format (FlavoredFormat (..), applyExtensionsDiff,
@@ -121,7 +122,7 @@ optToOutputSettings scriptingEngine opts = do
                      then getAndCompile (tp <.> T.unpack format)
                      else throwError e)
 
-  (writer, writerExts, mtemplate) <-
+  (writer, writerExts', mtemplate) <-
     if "lua" `T.isSuffixOf` format
     then do
       let path = T.unpack format
@@ -150,6 +151,10 @@ optToOutputSettings scriptingEngine opts = do
         tmpl <- processCustomTemplate (compileDefaultTemplate format)
         return (w, wexts, tmpl)
 
+  -- see #10662:
+  let writerExts = if CiteprocFilter `elem` optFilters opts
+                      then disableExtension Ext_citations writerExts'
+                      else writerExts'
 
   let addSyntaxMap existingmap f = do
         res <- liftIO (parseSyntaxDefinition f)

src/Text/Pandoc/Filter.hs

@@ -41,7 +41,7 @@ import Control.Monad (foldM, when)
 data Filter = LuaFilter FilePath
             | JSONFilter FilePath
             | CiteprocFilter -- built-in citeproc
-            deriving (Show, Generic)
+            deriving (Show, Generic, Eq)
 
 instance FromJSON Filter where
  parseJSON node =

test/command/7329.md

@@ -27,7 +27,12 @@
 % pandoc -f markdown -t org -C --bibliography command/biblio.bib
 - [@item1]
 ^D
-- [cite:@item1]
+- (Doe 2005)
+
+<<refs>>
+
+<<ref-item1>>
+Doe, John. 2005. /First Book/. Cambridge: Cambridge University Press.
 ```