Imported Upstream version 1.9.1.1

1 files changed, 444 insertions, 294 deletions

diff --git a/src/pandoc.hs b/src/pandoc.hs
index 27bc2c25c..3853d360a 100644
--- a/src/pandoc.hs
+++ b/src/pandoc.hs
@@ -1,5 +1,5 @@
 {-
-Copyright (C) 2006-2011 John MacFarlane <jgm@berkeley.edu>
+Copyright (C) 2006-2012 John MacFarlane <jgm@berkeley.edu>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -18,7 +18,7 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
 {- |
    Module      : Main
-   Copyright   : Copyright (C) 2006-2011 John MacFarlane
+   Copyright   : Copyright (C) 2006-2012 John MacFarlane
    License     : GNU GPL, version 2 or above
 
    Maintainer  : John MacFarlane <jgm@berkeley@edu>
@@ -30,24 +30,26 @@ writers.
 -}
 module Main where
 import Text.Pandoc
-import Text.Pandoc.S5 (s5HeaderIncludes)
+import Text.Pandoc.PDF (tex2pdf)
+import Text.Pandoc.Readers.LaTeX (handleIncludes)
 import Text.Pandoc.Shared ( tabFilter, ObfuscationMethod (..), readDataFile,
-                            headerShift, findDataFile, normalize )
-#ifdef _HIGHLIGHTING
-import Text.Pandoc.Highlighting ( languages )
-#endif
+                            headerShift, findDataFile, normalize, err, warn )
+import Text.Pandoc.XML ( toEntities, fromEntities )
+import Text.Pandoc.SelfContained ( makeSelfContained )
+import Text.Pandoc.Highlighting ( languages, Style, tango, pygments,
+         espresso, kate, haddock, monochrome )
 import System.Environment ( getArgs, getProgName )
 import System.Exit ( exitWith, ExitCode (..) )
 import System.FilePath
 import System.Console.GetOpt
 import Data.Char ( toLower )
 import Data.List ( intercalate, isSuffixOf, isPrefixOf )
-import System.Directory ( getAppUserDataDirectory, doesFileExist )
-import System.IO ( stdout, stderr )
+import System.Directory ( getAppUserDataDirectory, doesFileExist, findExecutable )
+import System.IO ( stdout )
 import System.IO.Error ( isDoesNotExistError )
 import Control.Exception.Extensible ( throwIO )
 import qualified Text.Pandoc.UTF8 as UTF8
-import Text.CSL
+import qualified Text.CSL as CSL
 import Text.Pandoc.Biblio
 import Control.Monad (when, unless, liftM)
 import Network.HTTP (simpleHTTP, mkRequest, getResponseBody, RequestMethod(..))
@@ -55,35 +57,34 @@ import Network.URI (parseURI, isURI, URI(..))
 import qualified Data.ByteString.Lazy as B
 import Data.ByteString.Lazy.UTF8 (toString )
 import Codec.Binary.UTF8.String (decodeString, encodeString)
+import Text.CSL.Reference (Reference(..))
 
 copyrightMessage :: String
-copyrightMessage = "\nCopyright (C) 2006-2011 John MacFarlane\n" ++
+copyrightMessage = "\nCopyright (C) 2006-2012 John MacFarlane\n" ++
                     "Web:  http://johnmacfarlane.net/pandoc\n" ++
                     "This is free software; see the source for copying conditions.  There is no\n" ++
                     "warranty, not even for merchantability or fitness for a particular purpose."
 
 compileInfo :: String
 compileInfo =
-  "\nCompiled with citeproc support." ++
-#ifdef _HIGHLIGHTING
-   "\nCompiled with syntax highlighting support for:\n" ++
-       wrapWords 78 languages ++
-#endif
-   ""
+  "\nCompiled with citeproc-hs " ++ VERSION_citeproc_hs ++ ", texmath " ++
+  VERSION_texmath ++ ", highlighting-kate " ++ VERSION_highlighting_kate ++
+   ".\nSyntax highlighting is supported for the following languages:\n    " ++
+       wrapWords 4 78 languages
 
 -- | Converts a list of strings into a single string with the items printed as
 -- comma separated words in lines with a maximum line length.
-wrapWords :: Int -> [String] -> String
-wrapWords c = wrap' c c where
-              wrap' _    _         []     = ""
+wrapWords :: Int -> Int -> [String] -> String
+wrapWords indent c = wrap' (c - indent) (c - indent)
+        where wrap' _    _         []     = ""
               wrap' cols remaining (x:xs) = if remaining == cols
                                                then x ++ wrap' cols (remaining - length x) xs
                                                else if (length x + 1) > remaining
-                                                       then ",\n" ++ x ++ wrap' cols (cols - length x) xs
+                                                       then ",\n" ++ replicate indent ' ' ++ x ++ wrap' cols (cols - length x) xs
                                                        else ", "  ++ x ++ wrap' cols (remaining - (length x + 2)) xs
 
-isNonTextOutput :: String -> Bool
-isNonTextOutput = (`elem` ["odt","epub"])
+nonTextFormats :: [String]
+nonTextFormats = ["odt","docx","epub"]
 
 -- | Data structure for command line options.
 data Opt = Opt
@@ -101,15 +102,19 @@ data Opt = Opt
     , optNumberSections    :: Bool    -- ^ Number sections in LaTeX
     , optSectionDivs       :: Bool    -- ^ Put sections in div tags in HTML
     , optIncremental       :: Bool    -- ^ Use incremental lists in Slidy/S5
-    , optOffline           :: Bool    -- ^ Make slideshow accessible offline
-    , optXeTeX             :: Bool    -- ^ Format latex for xetex
+    , optSelfContained     :: Bool    -- ^ Make HTML accessible offline
     , optSmart             :: Bool    -- ^ Use smart typography
+    , optOldDashes         :: Bool    -- ^ Parse dashes like pandoc <=1.8.2.1
     , optHtml5             :: Bool    -- ^ Produce HTML5 in HTML
+    , optHighlight         :: Bool    -- ^ Highlight source code
+    , optHighlightStyle    :: Style   -- ^ Style to use for highlighted code
     , optChapters          :: Bool    -- ^ Use chapter for top-level sects
     , optHTMLMathMethod    :: HTMLMathMethod -- ^ Method to print HTML math
     , optReferenceODT      :: Maybe FilePath -- ^ Path of reference.odt
+    , optReferenceDocx     :: Maybe FilePath -- ^ Path of reference.docx
     , optEPUBStylesheet    :: Maybe String   -- ^ EPUB stylesheet
     , optEPUBMetadata      :: String  -- ^ EPUB metadata
+    , optEPUBFonts         :: [FilePath] -- ^ EPUB fonts to embed
     , optDumpArgs          :: Bool    -- ^ Output command-line arguments
     , optIgnoreArgs        :: Bool    -- ^ Ignore command-line arguments
     , optStrict            :: Bool    -- ^ Use strict markdown syntax
@@ -124,8 +129,12 @@ data Opt = Opt
     , optCiteMethod        :: CiteMethod -- ^ Method to output cites
     , optBibliography      :: [String]
     , optCslFile           :: FilePath
+    , optAbbrevsFile       :: Maybe FilePath
     , optListings          :: Bool       -- ^ Use listings package for code blocks
-    , optAscii             :: Bool       -- ^ Avoid using nonascii characters
+    , optLaTeXEngine       :: String     -- ^ Program to use for latex -> pdf
+    , optSlideLevel        :: Maybe Int  -- ^ Header level that creates slides
+    , optSetextHeaders     :: Bool       -- ^ Use atx headers for markdown level 1-2
+    , optAscii             :: Bool       -- ^ Use ascii characters only in html
     }
 
 -- | Defaults for command-line options.
@@ -145,15 +154,19 @@ defaultOpts = Opt
     , optNumberSections    = False
     , optSectionDivs       = False
     , optIncremental       = False
-    , optOffline           = False
-    , optXeTeX             = False
+    , optSelfContained     = False
     , optSmart             = False
+    , optOldDashes         = False
     , optHtml5             = False
+    , optHighlight         = True
+    , optHighlightStyle    = pygments
     , optChapters          = False
     , optHTMLMathMethod    = PlainMath
     , optReferenceODT      = Nothing
+    , optReferenceDocx     = Nothing
     , optEPUBStylesheet    = Nothing
     , optEPUBMetadata      = ""
+    , optEPUBFonts         = []
     , optDumpArgs          = False
     , optIgnoreArgs        = False
     , optStrict            = False
@@ -168,7 +181,11 @@ defaultOpts = Opt
     , optCiteMethod        = Citeproc
     , optBibliography      = []
     , optCslFile           = ""
+    , optAbbrevsFile       = Nothing
     , optListings          = False
+    , optLaTeXEngine       = "pdflatex"
+    , optSlideLevel        = Nothing
+    , optSetextHeaders     = True
     , optAscii             = False
     }
 
@@ -188,50 +205,23 @@ options =
                   "FORMAT")
                  ""
 
-    , Option "s" ["standalone"]
-                 (NoArg
-                  (\opt -> return opt { optStandalone = True }))
-                 "" -- "Include needed header and footer on output"
-
     , Option "o" ["output"]
                  (ReqArg
                   (\arg opt -> return opt { optOutputFile = arg })
                   "FILENAME")
                  "" -- "Name of output file"
 
-    , Option "p" ["preserve-tabs"]
-                 (NoArg
-                  (\opt -> return opt { optPreserveTabs = True }))
-                 "" -- "Preserve tabs instead of converting to spaces"
-
-    , Option "" ["tab-stop"]
+    , Option "" ["data-dir"]
                  (ReqArg
-                  (\arg opt ->
-                      case reads arg of
-                           [(t,"")] | t > 0 -> return opt { optTabStop = t }
-                           _          -> do
-                               UTF8.hPutStrLn stderr $
-                                   "tab-stop must be a number greater than 0"
-                               exitWith $ ExitFailure 31)
-                  "NUMBER")
-                 "" -- "Tab stop (default 4)"
+                  (\arg opt -> return opt { optDataDir = Just arg })
+                 "DIRECTORY") -- "Directory containing pandoc data files."
+                ""
 
     , Option "" ["strict"]
                  (NoArg
                   (\opt -> return opt { optStrict = True } ))
                  "" -- "Disable markdown syntax extensions"
 
-    , Option "" ["normalize"]
-                 (NoArg
-                  (\opt -> return opt { optTransforms =
-                                   normalize : optTransforms opt } ))
-                 "" -- "Normalize the Pandoc AST"
-
-    , Option "" ["reference-links"]
-                 (NoArg
-                  (\opt -> return opt { optReferenceLinks = True } ))
-                 "" -- "Use reference links in parsing HTML"
-
     , Option "R" ["parse-raw"]
                  (NoArg
                   (\opt -> return opt { optParseRaw = True }))
@@ -242,145 +232,25 @@ options =
                   (\opt -> return opt { optSmart = True }))
                  "" -- "Use smart quotes, dashes, and ellipses"
 
-    , Option "5" ["html5"]
-                 (NoArg
-                  (\opt -> return opt { optHtml5 = True }))
-                 "" -- "Produce HTML5 in HTML output"
-
-    , Option "m" ["latexmathml", "asciimathml"]
-                 (OptArg
-                  (\arg opt ->
-                      return opt { optHTMLMathMethod = LaTeXMathML arg })
-                  "URL")
-                 "" -- "Use LaTeXMathML script in html output"
-
-    , Option "" ["mathml"]
-                 (OptArg
-                  (\arg opt ->
-                      return opt { optHTMLMathMethod = MathML arg })
-                   "URL")
-                 "" -- "Use mathml for HTML math"
-
-    , Option "" ["mimetex"]
-                 (OptArg
-                  (\arg opt -> do
-                      let url' = case arg of
-                                      Just u   -> u ++ "?"
-                                      Nothing  -> "/cgi-bin/mimetex.cgi?"
-                      return opt { optHTMLMathMethod = WebTeX url' })
-                  "URL")
-                 "" -- "Use mimetex for HTML math"
-
-    , Option "" ["webtex"]
-                 (OptArg
-                  (\arg opt -> do
-                      let url' = case arg of
-                                      Just u   -> u
-                                      Nothing  -> "http://chart.apis.google.com/chart?cht=tx&chl="
-                      return opt { optHTMLMathMethod = WebTeX url' })
-                  "URL")
-                 "" -- "Use web service for HTML math"
-
-    , Option "" ["jsmath"]
-                 (OptArg
-                  (\arg opt -> return opt { optHTMLMathMethod = JsMath arg})
-                  "URL")
-                 "" -- "Use jsMath for HTML math"
-
-    , Option "" ["mathjax"]
-                 (OptArg
-                  (\arg opt -> do
-                      let url' = case arg of
-                                      Just u   -> u
-                                      Nothing  -> "https://d3eoax9i5htok0.cloudfront.net/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
-                      return opt { optHTMLMathMethod = MathJax url'})
-                  "URL")
-                 "" -- "Use MathJax for HTML math"
-
-    , Option "" ["gladtex"]
-                 (NoArg
-                  (\opt -> return opt { optHTMLMathMethod = GladTeX }))
-                 "" -- "Use gladtex for HTML math"
-
-    , Option "i" ["incremental"]
-                 (NoArg
-                  (\opt -> return opt { optIncremental = True }))
-                 "" -- "Make list items display incrementally in Slidy/S5"
-
-    , Option "" ["offline"]
-                 (NoArg
-                  (\opt -> return opt { optOffline = True,
-                                        optStandalone = True }))
-                 "" -- "Make slide shows include all the needed js and css"
-
-    , Option "" ["xetex"]
+    , Option "" ["old-dashes"]
                  (NoArg
-                  (\opt -> do
-                     UTF8.hPutStrLn stderr $ "pandoc: --xetex is deprecated. "
-                       ++ "It is no longer needed for use with XeTeX."
-                     return opt { optXeTeX = True }))
-                 "" -- "Format latex for processing by XeTeX"
-
-    , Option "" ["chapters"]
-                 (NoArg
-                  (\opt -> return opt { optChapters = True }))
-                 "" -- "Use chapter for top-level sections in LaTeX, DocBook"
-
-    , Option "N" ["number-sections"]
-                 (NoArg
-                  (\opt -> return opt { optNumberSections = True }))
-                 "" -- "Number sections in LaTeX"
-
-    , Option "" ["listings"]
-                 (NoArg
-                  (\opt -> return opt { optListings = True }))
-                 "" -- "Use listings package for LaTeX code blocks"
-
-    , Option "" ["section-divs"]
-                 (NoArg
-                  (\opt -> return opt { optSectionDivs = True }))
-                 "" -- "Put sections in div tags in HTML"
-
-    , Option "" ["no-wrap"]
-                 (NoArg
-                  (\opt -> return opt { optWrapText = False }))
-                 "" -- "Do not wrap text in output"
+                  (\opt -> return opt { optSmart = True
+                                      , optOldDashes = True }))
+                 "" -- "Use smart quotes, dashes, and ellipses"
 
-    , Option "" ["columns"]
+    , Option "" ["base-header-level"]
                  (ReqArg
                   (\arg opt ->
                       case reads arg of
-                           [(t,"")] | t > 0 -> return opt { optColumns = t }
-                           _          -> do
-                               UTF8.hPutStrLn stderr $
-                                   "columns must be a number greater than 0"
-                               exitWith $ ExitFailure 33)
-                 "NUMBER")
-                 "" -- "Length of line in characters"
-
-    , Option "" ["ascii"]
-                 (NoArg
-                  (\opt -> return opt { optAscii = True }))
-                 "" -- "Avoid using non-ascii characters in output"
-
-    , Option "" ["email-obfuscation"]
-                 (ReqArg
-                  (\arg opt -> do
-                     method <- case arg of
-                            "references" -> return ReferenceObfuscation
-                            "javascript" -> return JavascriptObfuscation
-                            "none"       -> return NoObfuscation
-                            _            -> UTF8.hPutStrLn stderr ("Error: Unknown obfuscation method: " ++ arg) >>
-                                            exitWith (ExitFailure 6)
-                     return opt { optEmailObfuscation = method })
-                  "none|javascript|references")
-                 "" -- "Method for obfuscating email in HTML"
-
-     , Option "" ["id-prefix"]
-                  (ReqArg
-                   (\arg opt -> return opt { optIdentifierPrefix = arg })
-                   "STRING")
-                  "" -- "Prefix to add to automatically generated HTML identifiers"
+                           [(t,"")] | t > 0 -> do
+                               let oldTransforms = optTransforms opt
+                               let shift = t - 1
+                               return opt{ optTransforms =
+                                           headerShift shift : oldTransforms }
+                           _          -> err 19
+                                       "base-header-level must be a number > 0")
+                  "NUMBER")
+                 "" -- "Headers base level"
 
      , Option "" ["indented-code-classes"]
                   (ReqArg
@@ -389,26 +259,31 @@ options =
                    "STRING")
                   "" -- "Classes (whitespace- or comma-separated) to use for indented code-blocks"
 
-    , Option "" ["toc", "table-of-contents"]
-                (NoArg
-                 (\opt -> return opt { optTableOfContents = True }))
-               "" -- "Include table of contents"
+    , Option "" ["normalize"]
+                 (NoArg
+                  (\opt -> return opt { optTransforms =
+                                   normalize : optTransforms opt } ))
+                 "" -- "Normalize the Pandoc AST"
 
-    , Option "" ["base-header-level"]
+    , Option "p" ["preserve-tabs"]
+                 (NoArg
+                  (\opt -> return opt { optPreserveTabs = True }))
+                 "" -- "Preserve tabs instead of converting to spaces"
+
+    , Option "" ["tab-stop"]
                  (ReqArg
                   (\arg opt ->
                       case reads arg of
-                           [(t,"")] | t > 0 -> do
-                               let oldTransforms = optTransforms opt
-                               let shift = t - 1
-                               return opt{ optTransforms =
-                                           headerShift shift : oldTransforms }
-                           _          -> do
-                               UTF8.hPutStrLn stderr $
-                                   "base-header-level must be a number > 0"
-                               exitWith $ ExitFailure 19)
+                           [(t,"")] | t > 0 -> return opt { optTabStop = t }
+                           _                -> err 31
+                                          "tab-stop must be a number greater than 0")
                   "NUMBER")
-                 "" -- "Headers base level"
+                 "" -- "Tab stop (default 4)"
+
+    , Option "s" ["standalone"]
+                 (NoArg
+                  (\opt -> return opt { optStandalone = True }))
+                 "" -- "Include needed header and footer on output"
 
     , Option "" ["template"]
                  (ReqArg
@@ -425,21 +300,62 @@ options =
                           (k,_:v) -> do
                             let newvars = optVariables opt ++ [(k,v)]
                             return opt{ optVariables = newvars }
-                          _  -> do
-                            UTF8.hPutStrLn stderr $ "Could not parse `" ++ arg ++ "' as a key/value pair (k=v or k:v)"
-                            exitWith $ ExitFailure 17)
+                          _  -> err 17 $
+                            "Could not parse `" ++ arg ++ "' as a key/value pair (k=v or k:v)")
                   "KEY:VALUE")
                  "" -- "Use custom template"
 
-    , Option "c" ["css"]
+    , Option "D" ["print-default-template"]
                  (ReqArg
-                  (\arg opt -> do
-                     -- add new link to end, so it is included in proper order
-                     let newvars = optVariables opt ++ [("css",arg)]
-                     return opt { optVariables = newvars,
-                                  optStandalone = True })
-                  "URL")
-                 "" -- "Link to CSS style sheet"
+                  (\arg _ -> do
+                     templ <- getDefaultTemplate Nothing arg
+                     case templ of
+                          Right t -> UTF8.hPutStr stdout t
+                          Left e  -> error $ show e
+                     exitWith ExitSuccess)
+                  "FORMAT")
+                 "" -- "Print default template for FORMAT"
+
+    , Option "" ["no-wrap"]
+                 (NoArg
+                  (\opt -> return opt { optWrapText = False }))
+                 "" -- "Do not wrap text in output"
+
+    , Option "" ["columns"]
+                 (ReqArg
+                  (\arg opt ->
+                      case reads arg of
+                           [(t,"")] | t > 0 -> return opt { optColumns = t }
+                           _          -> err 33 $
+                                   "columns must be a number greater than 0")
+                 "NUMBER")
+                 "" -- "Length of line in characters"
+
+    , Option "" ["toc", "table-of-contents"]
+                (NoArg
+                 (\opt -> return opt { optTableOfContents = True }))
+               "" -- "Include table of contents"
+
+    , Option "" ["no-highlight"]
+                (NoArg
+                 (\opt -> return opt { optHighlight = False }))
+                 "" -- "Don't highlight source code"
+
+    , Option "" ["highlight-style"]
+                (ReqArg
+                 (\arg opt -> do
+                   newStyle <- case map toLower arg of
+                                     "pygments"   -> return pygments
+                                     "tango"      -> return tango
+                                     "espresso"   -> return espresso
+                                     "kate"       -> return kate
+                                     "monochrome" -> return monochrome
+                                     "haddock"    -> return haddock
+                                     _            -> err 39 $
+                                         "Unknown style :" ++ arg
+                   return opt{ optHighlightStyle = newStyle })
+                 "STYLE")
+                 "" -- "Style for highlighted code"
 
     , Option "H" ["include-in-header"]
                  (ReqArg
@@ -474,6 +390,100 @@ options =
                   "FILENAME")
                  "" -- "File to include after document body"
 
+    , Option "" ["self-contained"]
+                 (NoArg
+                  (\opt -> return opt { optSelfContained = True,
+                                        optVariables = ("slidy-url","slidy") :
+                                                       optVariables opt,
+                                        optStandalone = True }))
+                 "" -- "Make slide shows include all the needed js and css"
+
+    , Option "" ["offline"]
+                 (NoArg
+                  (\opt -> do warn $ "--offline is deprecated. Use --self-contained instead."
+                              return opt { optSelfContained = True,
+                                           optStandalone = True }))
+                 "" -- "Make slide shows include all the needed js and css"
+                 -- deprecated synonym for --self-contained
+
+    , Option "5" ["html5"]
+                 (NoArg
+                  (\opt -> do
+                     warn $ "--html5 is deprecated. "
+                       ++ "Use the html5 output format instead."
+                     return opt { optHtml5 = True }))
+                 "" -- "Produce HTML5 in HTML output"
+
+    , Option "" ["ascii"]
+                 (NoArg
+                  (\opt -> return opt { optAscii = True }))
+                 ""  -- "Use ascii characters only in HTML output"
+
+    , Option "" ["reference-links"]
+                 (NoArg
+                  (\opt -> return opt { optReferenceLinks = True } ))
+                 "" -- "Use reference links in parsing HTML"
+
+    , Option "" ["atx-headers"]
+                 (NoArg
+                  (\opt -> return opt { optSetextHeaders = False } ))
+                 "" -- "Use atx-style headers for markdown"
+
+    , Option "" ["chapters"]
+                 (NoArg
+                  (\opt -> return opt { optChapters = True }))
+                 "" -- "Use chapter for top-level sections in LaTeX, DocBook"
+
+    , Option "N" ["number-sections"]
+                 (NoArg
+                  (\opt -> return opt { optNumberSections = True }))
+                 "" -- "Number sections in LaTeX"
+
+    , Option "" ["listings"]
+                 (NoArg
+                  (\opt -> return opt { optListings = True }))
+                 "" -- "Use listings package for LaTeX code blocks"
+
+    , Option "i" ["incremental"]
+                 (NoArg
+                  (\opt -> return opt { optIncremental = True }))
+                 "" -- "Make list items display incrementally in Slidy/S5"
+
+    , Option "" ["slide-level"]
+                 (ReqArg
+                  (\arg opt -> do
+                      case reads arg of
+                           [(t,"")] | t >= 1 && t <= 6 ->
+                                    return opt { optSlideLevel = Just t }
+                           _          -> err 39 $
+                                    "slide level must be a number between 1 and 6")
+                 "NUMBER")
+                 "" -- "Force header level for slides"
+
+    , Option "" ["section-divs"]
+                 (NoArg
+                  (\opt -> return opt { optSectionDivs = True }))
+                 "" -- "Put sections in div tags in HTML"
+
+    , Option "" ["email-obfuscation"]
+                 (ReqArg
+                  (\arg opt -> do
+                     method <- case arg of
+                            "references" -> return ReferenceObfuscation
+                            "javascript" -> return JavascriptObfuscation
+                            "none"       -> return NoObfuscation
+                            _            -> err 6
+                               ("Unknown obfuscation method: " ++ arg)
+                     return opt { optEmailObfuscation = method })
+                  "none|javascript|references")
+                 "" -- "Method for obfuscating email in HTML"
+
+     , Option "" ["id-prefix"]
+                  (ReqArg
+                   (\arg opt -> return opt { optIdentifierPrefix = arg })
+                   "STRING")
+                  "" -- "Prefix to add to automatically generated HTML identifiers"
+
     , Option "T" ["title-prefix"]
                  (ReqArg
                   (\arg opt -> do
@@ -483,6 +493,16 @@ options =
                   "STRING")
                  "" -- "String to prefix to HTML window title"
 
+    , Option "c" ["css"]
+                 (ReqArg
+                  (\arg opt -> do
+                     -- add new link to end, so it is included in proper order
+                     let newvars = optVariables opt ++ [("css",arg)]
+                     return opt { optVariables = newvars,
+                                  optStandalone = True })
+                  "URL")
+                 "" -- "Link to CSS style sheet"
+
     , Option "" ["reference-odt"]
                  (ReqArg
                   (\arg opt -> do
@@ -490,6 +510,13 @@ options =
                   "FILENAME")
                  "" -- "Path of custom reference.odt"
 
+    , Option "" ["reference-docx"]
+                 (ReqArg
+                  (\arg opt -> do
+                    return opt { optReferenceDocx = Just arg })
+                  "FILENAME")
+                 "" -- "Path of custom reference.docx"
+
     , Option "" ["epub-stylesheet"]
                  (ReqArg
                   (\arg opt -> do
@@ -514,16 +541,22 @@ options =
                   "FILENAME")
                  "" -- "Path of epub metadata file"
 
-    , Option "D" ["print-default-template"]
+    , Option "" ["epub-embed-font"]
                  (ReqArg
-                  (\arg _ -> do
-                     templ <- getDefaultTemplate Nothing arg
-                     case templ of
-                          Right t -> UTF8.hPutStr stdout t
-                          Left e  -> error $ show e
-                     exitWith ExitSuccess)
-                  "FORMAT")
-                 "" -- "Print default template for FORMAT"
+                  (\arg opt -> do
+                     return opt{ optEPUBFonts = arg : optEPUBFonts opt })
+                  "FILE")
+                 "" -- "Directory of fonts to embed"
+
+    , Option "" ["latex-engine"]
+                 (ReqArg
+                  (\arg opt -> do
+                     let b = takeBaseName arg
+                     if (b == "pdflatex" || b == "lualatex" || b == "xelatex")
+                        then return opt { optLaTeXEngine = arg }
+                        else err 45 "latex-engine must be pdflatex, lualatex, or xelatex.")
+                  "PROGRAM")
+                 "" -- "Name of latex program to use in generating PDF"
 
     , Option "" ["bibliography"]
                  (ReqArg
@@ -537,6 +570,12 @@ options =
                   "FILENAME")
                  ""
 
+    , Option "" ["citation-abbreviations"]
+                 (ReqArg
+                  (\arg opt -> return opt { optAbbrevsFile = Just arg })
+                  "FILENAME")
+                 ""
+
     , Option "" ["natbib"]
                  (NoArg
                   (\opt -> return opt { optCiteMethod = Natbib }))
@@ -547,11 +586,60 @@ options =
                   (\opt -> return opt { optCiteMethod = Biblatex }))
                  "" -- "Use biblatex cite commands in LaTeX output"
 
-    , Option "" ["data-dir"]
-                 (ReqArg
-                  (\arg opt -> return opt { optDataDir = Just arg })
-                 "DIRECTORY") -- "Directory containing pandoc data files."
-                ""
+    , Option "m" ["latexmathml", "asciimathml"]
+                 (OptArg
+                  (\arg opt ->
+                      return opt { optHTMLMathMethod = LaTeXMathML arg })
+                  "URL")
+                 "" -- "Use LaTeXMathML script in html output"
+
+    , Option "" ["mathml"]
+                 (OptArg
+                  (\arg opt ->
+                      return opt { optHTMLMathMethod = MathML arg })
+                   "URL")
+                 "" -- "Use mathml for HTML math"
+
+    , Option "" ["mimetex"]
+                 (OptArg
+                  (\arg opt -> do
+                      let url' = case arg of
+                                      Just u   -> u ++ "?"
+                                      Nothing  -> "/cgi-bin/mimetex.cgi?"
+                      return opt { optHTMLMathMethod = WebTeX url' })
+                  "URL")
+                 "" -- "Use mimetex for HTML math"
+
+    , Option "" ["webtex"]
+                 (OptArg
+                  (\arg opt -> do
+                      let url' = case arg of
+                                      Just u   -> u
+                                      Nothing  -> "http://chart.apis.google.com/chart?cht=tx&chl="
+                      return opt { optHTMLMathMethod = WebTeX url' })
+                  "URL")
+                 "" -- "Use web service for HTML math"
+
+    , Option "" ["jsmath"]
+                 (OptArg
+                  (\arg opt -> return opt { optHTMLMathMethod = JsMath arg})
+                  "URL")
+                 "" -- "Use jsMath for HTML math"
+
+    , Option "" ["mathjax"]
+                 (OptArg
+                  (\arg opt -> do
+                      let url' = case arg of
+                                      Just u   -> u
+                                      Nothing  -> "https://d3eoax9i5htok0.cloudfront.net/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
+                      return opt { optHTMLMathMethod = MathJax url'})
+                  "URL")
+                 "" -- "Use MathJax for HTML math"
+
+    , Option "" ["gladtex"]
+                 (NoArg
+                  (\opt -> return opt { optHTMLMathMethod = GladTeX }))
+                 "" -- "Use gladtex for HTML math"
 
     , Option "" ["dump-args"]
                  (NoArg
@@ -579,14 +667,15 @@ options =
                      UTF8.hPutStr stdout (usageMessage prg options)
                      exitWith ExitSuccess ))
                  "" -- "Show help"
+
     ]
 
 -- Returns usage message
 usageMessage :: String -> [OptDescr (Opt -> IO Opt)] -> String
 usageMessage programName = usageInfo
   (programName ++ " [OPTIONS] [FILES]" ++ "\nInput formats:  " ++
-  (intercalate ", " $ map fst readers) ++ "\nOutput formats:  " ++
-  (intercalate ", " $ map fst writers ++ ["odt","epub"]) ++ "\nOptions:")
+  (wrapWords 16 78 $ map fst readers) ++ "\nOutput formats: " ++
+  (wrapWords 16 78 $ map fst writers ++ nonTextFormats) ++ "\nOptions:")
 
 -- Determine default reader based on source file extensions
 defaultReaderName :: String -> [FilePath] -> String
@@ -637,8 +726,11 @@ defaultWriterName x =
     ".texinfo"  -> "texinfo"
     ".db"       -> "docbook"
     ".odt"      -> "odt"
+    ".docx"     -> "docx"
     ".epub"     -> "epub"
     ".org"      -> "org"
+    ".asciidoc" -> "asciidoc"
+    ".pdf"      -> "latex"
     ['.',y] | y `elem` ['1'..'9'] -> "man"
     _          -> "html"
 
@@ -654,10 +746,8 @@ main = do
                                   else getOpt Permute options rawArgs
 
   unless (null errors) $
-    do name <- getProgName
-       mapM_ (\e -> UTF8.hPutStr stderr (name ++ ": ") >> UTF8.hPutStr stderr e) errors
-       UTF8.hPutStrLn stderr $ "Try " ++ name ++ " --help for more information."
-       exitWith $ ExitFailure 2
+     err 2 $ concat $ errors ++
+        ["Try " ++ prg ++ " --help for more information."]
 
   let defaultOpts' = if compatMode
                        then defaultOpts { optReader = "markdown"
@@ -682,14 +772,19 @@ main = do
               , optNumberSections    = numberSections
               , optSectionDivs       = sectionDivs
               , optIncremental       = incremental
-              , optOffline           = offline
+              , optSelfContained     = selfContained
               , optSmart             = smart
+              , optOldDashes         = oldDashes
               , optHtml5             = html5
+              , optHighlight         = highlight
+              , optHighlightStyle    = highlightStyle
               , optChapters          = chapters
               , optHTMLMathMethod    = mathMethod
               , optReferenceODT      = referenceODT
+              , optReferenceDocx     = referenceDocx
               , optEPUBStylesheet    = epubStylesheet
               , optEPUBMetadata      = epubMetadata
+              , optEPUBFonts         = epubFonts
               , optDumpArgs          = dumpArgs
               , optIgnoreArgs        = ignoreArgs
               , optStrict            = strict
@@ -702,8 +797,12 @@ main = do
               , optDataDir           = mbDataDir
               , optBibliography      = reffiles
               , optCslFile           = cslfile
+              , optAbbrevsFile       = cslabbrevs
               , optCiteMethod        = citeMethod
               , optListings          = listings
+              , optLaTeXEngine       = latexEngine
+              , optSlideLevel        = slideLevel
+              , optSetextHeaders     = setextHeaders
               , optAscii             = ascii
              } = opts
 
@@ -726,17 +825,35 @@ main = do
                                              then "html"
                                              else "markdown"
                            in  defaultReaderName fallback sources
-                      else readerName 
+                      else readerName
 
   let writerName' = if null writerName
                       then defaultWriterName outputFile
                       else writerName
 
+  let pdfOutput = map toLower (takeExtension outputFile) == ".pdf"
+
+  when pdfOutput $ do
+    -- make sure writer is latex or beamer
+    unless (writerName' == "latex" || writerName' == "beamer" ||
+            writerName' == "latex+lhs") $
+      err 47 $ "cannot produce pdf output with " ++ writerName' ++ " writer"
+    -- check for latex program
+    mbLatex <- findExecutable latexEngine
+    case mbLatex of
+         Nothing  -> err 41 $
+           latexEngine ++ " not found. " ++
+           latexEngine ++ " is needed for pdf output."
+         Just _   -> return ()
+
   reader <- case (lookup readerName' readers) of
      Just r  -> return r
-     Nothing -> error ("Unknown reader: " ++ readerName')
+     Nothing -> err 7 ("Unknown reader: " ++ readerName')
+
+  let standalone' = standalone || writerName' `elem` nonTextFormats || pdfOutput
 
   templ <- case templatePath of
+                _ | not standalone' -> return ""
                 Nothing -> do
                            deftemp <- getDefaultTemplate datadir writerName'
                            case deftemp of
@@ -756,57 +873,57 @@ main = do
                                              (\_ -> throwIO e)
                                        else throwIO e)
 
-  let standalone' = standalone || isNonTextOutput writerName'
-
-  variables' <- case (writerName', standalone', offline) of
-                      ("s5", True, True) -> do
-                        inc <- s5HeaderIncludes datadir
-                        return $ ("s5includes", inc) : variables
-                      ("slidy", True, True) -> do
-                        slidyJs <- readDataFile datadir $
-                                      "slidy" </> "slidy.min.js"
-                        slidyCss <- readDataFile datadir $
-                                      "slidy" </> "slidy.css"
-                        return $ ("slidy-js", slidyJs) :
-                            ("slidy-css", slidyCss) : variables
-                      _ -> return variables
+  let slideVariant = case writerName' of
+                           "s5"       -> S5Slides
+                           "slidy"    -> SlidySlides
+                           "dzslides" -> DZSlides
+                           _          -> NoSlides
 
-  variables'' <- case mathMethod of
+  variables' <- case mathMethod of
                       LaTeXMathML Nothing -> do
                          s <- readDataFile datadir $ "data" </> "LaTeXMathML.js"
-                         return $ ("mathml-script", s) : variables'
+                         return $ ("mathml-script", s) : variables
                       MathML Nothing -> do
                          s <- readDataFile datadir $ "data"</>"MathMLinHTML.js"
-                         return $ ("mathml-script", s) : variables'
-                      _ -> return variables'
+                         return $ ("mathml-script", s) : variables
+                      _ -> return variables
+
+  variables'' <- case slideVariant of
+                      DZSlides  -> do
+                        dztempl <- readDataFile datadir $ "dzslides" </> "template.html"
+                        let dzcore = unlines $ dropWhile (not . isPrefixOf "<!-- {{{{ dzslides core")
+                                             $ lines dztempl
+                        return $ ("dzslides-core", dzcore) : variables'
+                      _         -> return variables'
 
-  refs <- mapM (\f -> catch (readBiblioFile f) $ \e -> do
-         UTF8.hPutStrLn stderr $ "Error reading bibliography `" ++ f ++ "'"
-         UTF8.hPutStrLn stderr $ show e
-         exitWith (ExitFailure 23)) reffiles >>= \rs -> return $ concat rs
+  -- unescape reference ids, which may contain XML entities, so
+  -- that we can do lookups with regular string equality
+  let unescapeRefId ref = ref{ refId = fromEntities (refId ref) }
+
+  refs <- mapM (\f -> catch (CSL.readBiblioFile f) $ \e ->
+             err 23 $ "Error reading bibliography `" ++ f ++ "'" ++ "\n" ++ show e)
+          reffiles >>=
+           return . map unescapeRefId . concat
 
   let sourceDir = if null sources
                      then "."
                      else takeDirectory (head sources)
 
-  let slideVariant = case writerName' of
-                           "s5"    -> S5Slides
-                           "slidy" -> SlidySlides
-                           _       -> NoSlides
-
   let startParserState =
          defaultParserState { stateParseRaw        = parseRaw,
                               stateTabStop         = tabStop,
                               stateLiterateHaskell = "+lhs" `isSuffixOf` readerName' ||
                                                      lhsExtension sources,
                               stateStandalone      = standalone',
-                              stateCitations       = map refId refs,
+                              stateCitations       = map CSL.refId refs,
                               stateSmart           = smart || writerName' `elem`
-                                                              ["latex", "context", "latex+lhs", "man"],
+                                                     ["latex", "context", "latex+lhs", "beamer"],
+                              stateOldDashes       = oldDashes,
                               stateColumns         = columns,
                               stateStrict          = strict,
                               stateIndentedCodeClasses = codeBlockClasses,
-                              stateApplyMacros     = writerName' `notElem` ["latex", "latex+lhs"] }
+                              stateApplyMacros     = writerName' `notElem`
+                                                     ["latex", "latex+lhs", "beamer"] }
 
   let writerOptions = defaultWriterOptions
                                     { writerStandalone       = standalone',
@@ -836,16 +953,20 @@ main = do
                                       writerIdentifierPrefix = idPrefix,
                                       writerSourceDirectory  = sourceDir,
                                       writerUserDataDir      = datadir,
-                                      writerHtml5            = html5 &&
-                                                               "html" `isPrefixOf` writerName',
-                                      writerChapters         = chapters, 
+                                      writerHtml5            = html5 ||
+                                           slideVariant == DZSlides,
+                                      writerChapters         = chapters,
                                       writerListings         = listings,
-                                      writerAscii            = ascii }
+                                      writerBeamer           = writerName' == "beamer",
+                                      writerSlideLevel       = slideLevel,
+                                      writerHighlight        = highlight,
+                                      writerHighlightStyle   = highlightStyle,
+                                      writerSetextHeaders    = setextHeaders
+                                      }
 
-  when (isNonTextOutput writerName' && outputFile == "-") $
-    do UTF8.hPutStrLn stderr ("Error:  Cannot write " ++ writerName ++ " output to stdout.\n" ++
-                               "Specify an output file using the -o option.")
-       exitWith $ ExitFailure 5
+  when (writerName' `elem` nonTextFormats&& outputFile == "-") $
+    err 5 $ "Cannot write " ++ writerName' ++ " output to stdout.\n" ++
+            "Specify an output file using the -o option."
 
   let readSources [] = mapM readSource ["-"]
       readSources srcs = mapM readSource srcs
@@ -859,7 +980,14 @@ main = do
 
   let convertTabs = tabFilter (if preserveTabs then 0 else tabStop)
 
-  doc <- fmap (reader startParserState . convertTabs . intercalate "\n") (readSources sources)
+  let handleIncludes' = if readerName' == "latex" || readerName' == "beamer" ||
+                           readerName' == "latex+lhs" ||
+                           readerName' == "context"
+                           then handleIncludes
+                           else return
+
+  doc <- (reader startParserState) `fmap` (readSources sources >>=
+             handleIncludes' . convertTabs . intercalate "\n")
 
   let doc0 = foldr ($) doc transforms
 
@@ -881,19 +1009,41 @@ main = do
                                             replaceDirectory
                                             (replaceExtension cslfile "csl")
                                             csldir
-                processBiblio cslfile' refs doc1
+                processBiblio cslfile' cslabbrevs refs doc1
              else return doc1
 
+  let writeBinary :: B.ByteString -> IO ()
+      writeBinary = B.writeFile (encodeString outputFile)
+
+  let writerFn :: FilePath -> String -> IO ()
+      writerFn "-" = UTF8.putStr
+      writerFn f   = UTF8.writeFile f
+
   case lookup writerName' writers of
-        Nothing | writerName' == "epub" ->
-           writeEPUB epubStylesheet writerOptions doc2
-           >>= B.writeFile (encodeString outputFile)
-        Nothing | writerName' == "odt"  ->
-           writeODT referenceODT writerOptions doc2
-           >>= B.writeFile (encodeString outputFile)
-        Just r  -> writerFn outputFile result
-            where writerFn "-" = UTF8.putStr
-                  writerFn f   = UTF8.writeFile f
-                  result       = r writerOptions doc2 ++
-                                 ['\n' | not standalone']
-        Nothing -> error $ "Unknown writer: " ++ writerName'
+        Nothing
+          | writerName' == "epub" ->
+              writeEPUB epubStylesheet epubFonts writerOptions doc2
+               >>= writeBinary
+          | writerName' == "odt"  ->
+              writeODT referenceODT writerOptions doc2 >>= writeBinary
+          | writerName' == "docx"  ->
+              writeDocx referenceDocx writerOptions doc2 >>= writeBinary
+          | otherwise -> err 9 ("Unknown writer: " ++ writerName')
+        Just _
+          | pdfOutput  -> do
+              res <- tex2pdf latexEngine $ writeLaTeX writerOptions doc2
+              case res of
+                   Right pdf -> writeBinary pdf
+                   Left err' -> err 43 $ toString err'
+        Just r
+          | htmlFormat && ascii ->
+                  writerFn outputFile =<< selfcontain (toEntities result)
+          | otherwise ->
+                  writerFn outputFile =<< selfcontain result
+          where result       = r writerOptions doc2 ++ ['\n' | not standalone']
+                htmlFormat = writerName' `elem`
+                               ["html","html+lhs","html5","html5+lhs",
+                               "s5","slidy","dzslides"]
+                selfcontain = if selfContained && htmlFormat
+                                 then makeSelfContained datadir
+                                 else return