You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@joshua.apache.org by mj...@apache.org on 2016/04/09 05:10:52 UTC

[43/44] incubator-joshua-site git commit: First attempt

First attempt


Project: http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/commit/53cc3005
Tree: http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/tree/53cc3005
Diff: http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/diff/53cc3005

Branch: refs/heads/asf-site
Commit: 53cc30052ec9bdbb0582347967d84b8cf00eb7ee
Parents: 6e1230a
Author: Matt Post <po...@cs.jhu.edu>
Authored: Fri Apr 8 23:09:25 2016 -0400
Committer: Matt Post <po...@cs.jhu.edu>
Committed: Fri Apr 8 23:09:25 2016 -0400

----------------------------------------------------------------------
 4.0/decoder.html                                | 1240 ++++
 4.0/decoder.md                                  |  910 ---
 4.0/faq.html                                    |  257 +
 4.0/faq.md                                      |    7 -
 4.0/features.html                               |  257 +
 4.0/features.md                                 |    7 -
 4.0/file-formats.html                           |  341 +
 4.0/file-formats.md                             |   78 -
 4.0/index.html                                  |  309 +
 4.0/index.md                                    |   48 -
 4.0/large-lms.html                              |  455 ++
 4.0/large-lms.md                                |  192 -
 4.0/lattice.html                                |  267 +
 4.0/lattice.md                                  |   17 -
 4.0/packing.html                                |  357 +
 4.0/packing.md                                  |   76 -
 4.0/pipeline.html                               |  929 +++
 4.0/pipeline.md                                 |  576 --
 4.0/step-by-step-instructions.html              |  177 +-
 4.0/thrax.html                                  |  264 +
 4.0/thrax.md                                    |   14 -
 4.0/tms.html                                    |  377 ++
 4.0/tms.md                                      |  106 -
 4.0/zmert.html                                  |  339 +
 4.0/zmert.md                                    |   83 -
 5.0/advanced.html                               |  170 +
 5.0/advanced.md                                 |    7 -
 5.0/bundle.html                                 |  189 +
 5.0/bundle.md                                   |   24 -
 5.0/decoder.html                                |  637 ++
 5.0/decoder.md                                  |  374 --
 5.0/faq.html                                    |  170 +
 5.0/faq.md                                      |    7 -
 5.0/features.html                               |  170 +
 5.0/features.md                                 |    6 -
 5.0/file-formats.html                           |  248 +
 5.0/file-formats.md                             |   72 -
 5.0/index.html                                  |  255 +
 5.0/index.md                                    |   77 -
 5.0/jacana.html                                 |  309 +
 5.0/jacana.md                                   |  139 -
 5.0/large-lms.html                              |  368 +
 5.0/large-lms.md                                |  192 -
 5.0/packing.html                                |  270 +
 5.0/packing.md                                  |   76 -
 5.0/pipeline.html                               |  919 +++
 5.0/pipeline.md                                 |  640 --
 5.0/server.html                                 |  196 +
 5.0/server.md                                   |   30 -
 5.0/thrax.html                                  |  177 +
 5.0/thrax.md                                    |   14 -
 5.0/tms.html                                    |  290 +
 5.0/tms.md                                      |  106 -
 5.0/tutorial.html                               |  368 +
 5.0/tutorial.md                                 |  174 -
 5.0/zmert.html                                  |  252 +
 5.0/zmert.md                                    |   83 -
 6                                               |    1 -
 6.0/advanced.html                               |  192 +
 6.0/advanced.md                                 |    7 -
 6.0/bundle.html                                 |  297 +
 6.0/bundle.md                                   |  100 -
 6.0/decoder.html                                |  671 ++
 6.0/decoder.md                                  |  385 --
 6.0/faq.html                                    |  376 ++
 6.0/faq.md                                      |  161 -
 6.0/features.html                               |  192 +
 6.0/features.md                                 |    6 -
 6.0/file-formats.html                           |  270 +
 6.0/file-formats.md                             |   72 -
 6.0/index.html                                  |  210 +
 6.0/index.md                                    |   24 -
 6.0/install.html                                |  301 +
 6.0/install.md                                  |   88 -
 6.0/jacana.html                                 |  331 +
 6.0/jacana.md                                   |  139 -
 6.0/large-lms.html                              |  390 ++
 6.0/large-lms.md                                |  192 -
 6.0/packing.html                                |  277 +
 6.0/packing.md                                  |   74 -
 6.0/pipeline.html                               |  966 +++
 6.0/pipeline.md                                 |  666 --
 6.0/quick-start.html                            |  251 +
 6.0/quick-start.md                              |   59 -
 6.0/server.html                                 |  218 +
 6.0/server.md                                   |   30 -
 6.0/thrax.html                                  |  199 +
 6.0/thrax.md                                    |   14 -
 6.0/tms.html                                    |  312 +
 6.0/tms.md                                      |  106 -
 6.0/tutorial.html                               |  407 ++
 6.0/tutorial.md                                 |  187 -
 6.0/whats-new.html                              |  200 +
 6.0/whats-new.md                                |   12 -
 6.0/zmert.html                                  |  274 +
 6.0/zmert.md                                    |   83 -
 6/advanced.html                                 |  192 +
 6/bundle.html                                   |  297 +
 6/decoder.html                                  |  671 ++
 6/faq.html                                      |  376 ++
 6/features.html                                 |  192 +
 6/file-formats.html                             |  270 +
 6/index.html                                    |  210 +
 6/install.html                                  |  301 +
 6/jacana.html                                   |  331 +
 6/large-lms.html                                |  390 ++
 6/packing.html                                  |  277 +
 6/pipeline.html                                 |  966 +++
 6/quick-start.html                              |  251 +
 6/server.html                                   |  218 +
 6/thrax.html                                    |  199 +
 6/tms.html                                      |  312 +
 6/tutorial.html                                 |  407 ++
 6/whats-new.html                                |  200 +
 6/zmert.html                                    |  274 +
 _config.yml                                     |    5 -
 _data/joshua.yaml                               |    2 -
 _layouts/default.html                           |  169 -
 _layouts/default4.html                          |   94 -
 _layouts/default6.html                          |  200 -
 _layouts/documentation.html                     |   60 -
 bootstrap/css/bootstrap-responsive.css          | 1109 +++
 bootstrap/css/bootstrap-responsive.min.css      |    9 +
 bootstrap/css/bootstrap.css                     | 6167 +++++++++++++++++
 bootstrap/css/bootstrap.min.css                 |    9 +
 bootstrap/img/glyphicons-halflings-white.png    |  Bin 0 -> 8777 bytes
 bootstrap/img/glyphicons-halflings.png          |  Bin 0 -> 12799 bytes
 bootstrap/js/bootstrap.js                       | 2280 +++++++
 bootstrap/js/bootstrap.min.js                   |    6 +
 contributors.html                               |  232 +
 data/fisher-callhome-corpus/images/lattice.png  |  Bin 0 -> 22684 bytes
 data/fisher-callhome-corpus/index.html          |  149 +
 data/index.html                                 |    7 +
 data/indian-parallel-corpora/images/map1.png    |  Bin 0 -> 59635 bytes
 data/indian-parallel-corpora/images/map2.png    |  Bin 0 -> 51311 bytes
 data/indian-parallel-corpora/index.html         |  166 +
 devel/index.html                                |   16 +
 dist/css/bootstrap-theme.css                    |  470 ++
 dist/css/bootstrap-theme.css.map                |    1 +
 dist/css/bootstrap-theme.min.css                |    5 +
 dist/css/bootstrap.css                          | 6332 ++++++++++++++++++
 dist/css/bootstrap.css.map                      |    1 +
 dist/css/bootstrap.min.css                      |    5 +
 dist/fonts/glyphicons-halflings-regular.eot     |  Bin 0 -> 20335 bytes
 dist/fonts/glyphicons-halflings-regular.svg     |  229 +
 dist/fonts/glyphicons-halflings-regular.ttf     |  Bin 0 -> 41280 bytes
 dist/fonts/glyphicons-halflings-regular.woff    |  Bin 0 -> 23320 bytes
 dist/js/bootstrap.js                            | 2320 +++++++
 dist/js/bootstrap.min.js                        |    7 +
 dist/js/npm.js                                  |   13 +
 fisher-callhome-corpus/index.html               |    1 +
 images/desert.jpg                               |  Bin 0 -> 121958 bytes
 images/joshua-logo-small.png                    |  Bin 0 -> 29235 bytes
 images/joshua-logo.jpg                          |  Bin 0 -> 236977 bytes
 images/joshua-logo.pdf                          |  Bin 0 -> 1465851 bytes
 images/joshua-logo.png                          |  Bin 0 -> 858713 bytes
 images/logo-credits.txt                         |    1 +
 images/sponsors/NSF-logo.jpg                    |  Bin 0 -> 38008 bytes
 images/sponsors/darpa-logo.jpg                  |  Bin 0 -> 11552 bytes
 images/sponsors/euromatrix.png                  |  Bin 0 -> 59093 bytes
 images/sponsors/hltcoe-logo1.jpg                |  Bin 0 -> 8278 bytes
 images/sponsors/hltcoe-logo1.png                |  Bin 0 -> 22031 bytes
 images/sponsors/hltcoe-logo2.jpg                |  Bin 0 -> 8803 bytes
 images/sponsors/hltcoe-logo2.png                |  Bin 0 -> 9767 bytes
 images/sponsors/hltcoe-logo3.png                |  Bin 0 -> 34899 bytes
 index.html                                      |  237 +
 index5.html                                     |  237 +
 indian-parallel-corpora/index.html              |    1 +
 joshua.bib                                      |   12 +
 joshua.css                                      |   44 +
 joshua4.css                                     |  184 +
 joshua6.css                                     |  220 +
 language-packs.csv                              |    2 +
 language-packs/ar-en-phrase/index.html          |   16 +
 language-packs/es-en-phrase/index.html          |   16 +
 language-packs/index.html                       |  261 +
 language-packs/paraphrase/index.html            |  194 +
 language-packs/zh-en-hiero/index.html           |   16 +
 publications/joshua-2.0.pdf                     |  Bin 0 -> 95757 bytes
 publications/joshua-3.0.pdf                     |  Bin 0 -> 198854 bytes
 ...lkit-for-statistical-machine-translation.pdf |  Bin 0 -> 105762 bytes
 releases.html                                   |  235 +
 releases/5.0/index.html                         |   16 +
 releases/6.0/index.0                            |    8 +
 releases/6.0/index.html                         |    0
 releases/current/index                          |    8 +
 releases/current/index.html                     |    0
 releases/index.html                             |  199 +
 releases/runtime/index                          |    8 +
 releases/runtime/index.html                     |    0
 style.css                                       |  237 +
 support/index.html                              |  207 +
 192 files changed, 45111 insertions(+), 7078 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/blob/53cc3005/4.0/decoder.html
----------------------------------------------------------------------
diff --git a/4.0/decoder.html b/4.0/decoder.html
new file mode 100644
index 0000000..b63855c
--- /dev/null
+++ b/4.0/decoder.html
@@ -0,0 +1,1240 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <link rel="stylesheet" type="text/css" media="screen,print" href="../joshua4.css" />
+    <title>Joshua | Decoder configuration parameters</title>
+  </head>
+
+  <body>
+
+    <div id="navbar">
+      <a href="http://joshua-decoder.org/">
+        <img src="../images/joshua-logo-small.png" width="130px" 
+             alt="Joshua logo (picture of a Joshua tree)" />
+      </a>
+
+      <p class="infobox">
+        <b>Stable version</b><br />
+        4.1<br/><br/>
+        <b>Release date</b><br />
+        2013 January
+      </p>
+
+<!--       <div class="infobox"> -->
+<!--         <b>AUTO LINKS</b><br/> -->
+<!--         <ul> -->
+<!--            -->
+<!--           <li> Advanced features</li> -->
+<!--            -->
+<!--           <li> Advanced features</li> -->
+<!--            -->
+<!--           <li> Advanced features</li> -->
+<!--            -->
+<!--           <li> Building a language pack</li> -->
+<!--            -->
+<!--           <li> Building a language pack</li> -->
+<!--            -->
+<!--           <li> Bundling a configuration</li> -->
+<!--            -->
+<!--           <li> Contributors</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Frequently Asked Questions</li> -->
+<!--            -->
+<!--           <li> Common problems</li> -->
+<!--            -->
+<!--           <li> Frequently Asked Questions</li> -->
+<!--            -->
+<!--           <li> Common problems</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> Fisher and CALLHOME Spanish English Speech Translation Corpus</li> -->
+<!--            -->
+<!--           <li> Indian Languages Parallel Corpora</li> -->
+<!--            -->
+<!--           <li> Joshua 4.0 User Documentation</li> -->
+<!--            -->
+<!--           <li> Language packs</li> -->
+<!--            -->
+<!--           <li> Paraphrase Packs</li> -->
+<!--            -->
+<!--           <li> Joshua releases</li> -->
+<!--            -->
+<!--           <li> Support</li> -->
+<!--            -->
+<!--           <li> Getting Started</li> -->
+<!--            -->
+<!--           <li> Welcome to Joshua</li> -->
+<!--            -->
+<!--           <li> Joshua documentation</li> -->
+<!--            -->
+<!--           <li> Joshua documentation</li> -->
+<!--            -->
+<!--           <li> Installation</li> -->
+<!--            -->
+<!--           <li> Installation</li> -->
+<!--            -->
+<!--           <li> Alignment with Jacana</li> -->
+<!--            -->
+<!--           <li> Alignment with Jacana</li> -->
+<!--            -->
+<!--           <li> Alignment with Jacana</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Lattice decoding</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> Quick Start</li> -->
+<!--            -->
+<!--           <li> Quick Start</li> -->
+<!--            -->
+<!--           <li> Releases</li> -->
+<!--            -->
+<!--           <li> Server mode</li> -->
+<!--            -->
+<!--           <li> Server mode</li> -->
+<!--            -->
+<!--           <li> Server mode</li> -->
+<!--            -->
+<!--           <li> Installing and running the Joshua Decoder</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Pipeline tutorial</li> -->
+<!--            -->
+<!--           <li> Pipeline tutorial</li> -->
+<!--            -->
+<!--           <li> Pipeline tutorial</li> -->
+<!--            -->
+<!--           <li> What's New</li> -->
+<!--            -->
+<!--           <li> What's New</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--         </ul> -->
+<!--       </div>   -->
+
+      <div class="infobox">
+
+        <b>Links</b><br />
+        <ul>
+          <li> <a href="../index.html">Main</a> </li>
+          <li> <a href="pipeline.html">Pipeline</a> </li>
+          <li> <a href="step-by-step-instructions.html">Manual walkthrough</a> </li>
+          <li> <a href="decoder.html">Decoder</a> </li>
+          <li> <a href="server.html">Decoder Server</a> </li>
+          <li> <a href="file-formats.html">File formats</a> </li>
+          <li> <a href="thrax.html">Grammar Extraction</a> </li>
+          <li> <a href="../releases.html">Releases</a> </li>
+        </ul>
+      </div>
+
+      <div class="infobox">
+        <b>Advanced</b><br />
+        <ul>
+<!--          <li> <a href="packing.html">Grammar packing</a> </li> -->
+          <li> <a href="large-lms.html">Building large LMs</a> </li>
+          <li> <a href="zmert.html">Running Z-MERT</a> </li>
+          <li> <a href="lattice.html">Lattices</a> </li>
+          <li> <a href="server.html">TCP/IP server</a> </li>
+          <li> <a href="bundle.html">Bundled configuration</a> </li>
+        </ul>
+      </div>
+
+      <div class="infobox">
+        <b>Help</b><br />
+        <ul>
+          <li> <a href="faq.html">Answers</a> </li>
+          <li> <a href="https://groups.google.com/d/forum/joshua_support">Archive</a> </li>
+        </ul>
+      </div>
+
+      <div class="footer">
+        Last updated on April 08, 2016
+      </div>
+
+    </div>
+
+    <div id="main">
+      <div id="title">
+        <h1>Decoder configuration parameters</h1>
+      </div>
+
+      <div id="content">
+        
+        <p>Joshua configuration parameters affect the runtime behavior of the decoder itself.  This page
+describes the complete list of these parameters and describes how to invoke the decoder manually.</p>
+
+<p>To run the decoder, a convenience script is provided that loads the necessary Java libraries.
+Assuming you have set the environment variable <code class="highlighter-rouge">$JOSHUA</code> to point to the root of your installation,
+its syntax is:</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code>$JOSHUA/joshua-decoder [-m memory-amount] [-c config-file other-joshua-options ...]
+</code></pre>
+</div>
+
+<p>The <code class="highlighter-rouge">-m</code> argument, if present, must come first, and the memory specification is in Java format
+(e.g., 400m, 4g, 50g).  Most notably, the suffixes “m” and “g” are used for “megabytes” and
+“gigabytes”, and there cannot be a space between the number and the unit.  The value of this
+argument is passed to Java itself in the invocation of the decoder, and the remaining options are
+passed to Joshua.  The <code class="highlighter-rouge">-c</code> parameter has special import because it specifies the location of the
+configuration file.</p>
+
+<p>The Joshua decoder works by reading from STDIN and printing translations to STDOUT as they are
+received, according to a number of <a href="#output">output options</a>.  If no run-time parameters are
+specified (e.g., no translation model), sentences are simply pushed through untranslated.  Blank
+lines are similarly pushed through as blank lines, so as to maintain parallelism with the input.</p>
+
+<p>Parameters can be provided to Joshua via a configuration file and from the command
+line.  Command-line arguments override values found in the configuration file.  The format for
+configuration file parameters is</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code>parameter = value
+</code></pre>
+</div>
+
+<p>Command-line options are specified in the following format</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code>-parameter value
+</code></pre>
+</div>
+
+<p>Values are one of four types (which we list here mostly to call attention to the boolean format):</p>
+
+<ul>
+  <li>STRING, an arbitrary string (no spaces)</li>
+  <li>FLOAT, a floating-point value</li>
+  <li>INT, an integer</li>
+  <li>
+    <p>BOOLEAN, a boolean value.  For booleans, <code class="highlighter-rouge">true</code> evaluates to true, and all other values evaluate
+to false.  For command-line options, the value may be omitted, in which case it evaluates to
+true.  For example, the following are equivalent:</p>
+
+    <div class="highlighter-rouge"><pre class="highlight"><code>$JOSHUA/joshua-decoder -show-align-index true
+$JOSHUA/joshua-decoder -show-align-index
+</code></pre>
+    </div>
+  </li>
+</ul>
+
+<h2 id="joshua-configuration-file">Joshua configuration file</h2>
+
+<p>Before describing the list of Joshua parameters, we present a note about the configuration file.
+In addition to the decoder parameters described below, the configuration file contains the feature
+weight values for the model.  The weight values are distinguished from runtime parameters in two
+ways: (1) they cannot be overridden on the command line, and (2) they do not have an equals sign
+(=).  Parameters are described in further detail in the <a href="features.html">feature file</a>.  They take
+the following format, and by convention are placed at the end of the configuration file:</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code>lm 0 4.23
+phrasement pt 0 -0.2
+oovpenalty -100
+</code></pre>
+</div>
+
+<h2 id="joshua-decoder-parameters">Joshua decoder parameters</h2>
+
+<p>This section contains a list of the Joshua run-time parameters.  An important note about the
+parameters is that they are collapsed to canonical form, in which dashes (-) and underscores (-) are
+removed and case is converted to lowercase.  For example, the following parameter forms are
+equivalent (either in the configuration file or from the command line):</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code><span class="p">{</span><span class="err">top-n,</span><span class="w"> </span><span class="err">topN,</span><span class="w"> </span><span class="err">top_n,</span><span class="w"> </span><span class="err">TOP_N,</span><span class="w"> </span><span class="err">t-o-p-N</span><span class="p">}</span><span class="w">
+</span><span class="p">{</span><span class="err">poplimit,</span><span class="w"> </span><span class="err">pop-limit,</span><span class="w"> </span><span class="err">pop-limit,</span><span class="w"> </span><span class="err">popLimit</span><span class="p">}</span><span class="w">
+</span></code></pre>
+</div>
+
+<p>This basically defines equivalence classes of parameters, and relieves you of the task of having to
+remember the exact format of each parameter.</p>
+
+<p>In what follows, we group the configuration parameters in the following groups:</p>
+
+<ul>
+  <li><a href="#modes">Alternate modes of operation</a></li>
+  <li><a href="#general">General options</a></li>
+  <li><a href="#pruning">Pruning</a></li>
+  <li><a href="#tm">Translation model options</a></li>
+  <li><a href="#lm">Language model options</a></li>
+  <li><a href="#output">Output options</a></li>
+</ul>
+
+<p><a name="modes"></a></p>
+
+<h3 id="alternate-modes-of-operation">Alternate modes of operation</h3>
+
+<p>In addition to decoding (which is the default mode), Joshua can also produce synchronous parses of a
+(source,target) pair of sentences.  This mode disables the language model (since no generation is
+required) but still requires a translation model.  To enable it, you must do two things:</p>
+
+<ol>
+  <li>Set the configuration parameters <code class="highlighter-rouge">parse = true</code>.</li>
+  <li>
+    <p>Provide input in the following format:</p>
+
+    <div class="highlighter-rouge"><pre class="highlight"><code>source sentence ||| target sentence
+</code></pre>
+    </div>
+  </li>
+</ol>
+
+<p>You may also wish to display the synchronouse parse tree (<code class="highlighter-rouge">-use-tree-nbest</code>) and the alignment
+(<code class="highlighter-rouge">-show-align-index</code>).</p>
+
+<p>The synchronous parsing implementation is that of Dyer (2010)
+<a href="http://www.aclweb.org/anthology/N/N10/N10-1033">PDF</a>.</p>
+
+<p>If parsing is enabled, the following features become relevant.  If you would like more information
+about how to use these features, please ask <a href="http://cs.jhu.edu/~jonny/">Jonny Weese</a> to document
+them. </p>
+
+<ul>
+  <li>
+    <p><code class="highlighter-rouge">forest-pruning</code> — <em>false</em></p>
+
+    <p>If true, the synchronous forest will be pruned.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">forest-pruning-threshold</code> — <em>10</em></p>
+
+    <p>The threshold used for pruning.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">use-kbest-hg</code> — <em>false</em></p>
+
+    <p>The k-best hypergraph to use.</p>
+  </li>
+</ul>
+
+<p><a name="general"></a></p>
+
+<h3 id="general-decoder-options">General decoder options</h3>
+
+<ul>
+  <li>
+    <p><code class="highlighter-rouge">c</code>, <code class="highlighter-rouge">config</code> — <em>NULL</em></p>
+
+    <p>Specifies the configuration file from which Joshua options are loaded.  This feature is unique in
+ that it must be specified from the command line.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">oracle-file</code> — <em>NULL</em></p>
+
+    <p>The location of a set of oracle reference translations, parallel to the input.  When present,
+after producing the hypergraph by decoding the input sentence, the oracle is used to rescore the
+translation forest with a BLEU approximation in order to extract the oracle-translation from the
+forest.  This is useful for obtaining an (approximation to an) upper bound on your translation
+model under particular search settings.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">default-nonterminal</code> — <em>“X”</em></p>
+
+    <p>This is the nonterminal symbol assigned to out-of-vocabulary (OOV) items.  </p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">goal-symbol</code> — <em>“GOAL”</em></p>
+
+    <p>This is the symbol whose presence in the chart over the whole input span denotes a successful
+ parse (translation).  It should match the LHS nonterminal in your glue grammar.  Internally,
+ Joshua represents nonterminals enclosed in square brackets (e.g., “[GOAL]”), which you can
+ optionally supply in the configuration file.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">true-oovs-only</code> — <em>false</em></p>
+
+    <p>By default, Joshua creates an OOV entry for every word in the source sentence, regardless of
+whether it is found in the grammar.  This allows every word to be pushed through untranslated
+(although potentially incurring a high cost based on the <code class="highlighter-rouge">oovPenalty</code> feature).  If this option is
+set, then only true OOVs are entered into the chart as OOVs.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">use-sent-specific-tm</code> — <em>false</em></p>
+
+    <p>If set to true, Joshua will look for sentence-specific filtered grammars.  The location is
+determined by taking the supplied translation model (<code class="highlighter-rouge">tm-file</code>) and looking for a <code class="highlighter-rouge">filtered/</code>
+subdirectory for a file with the same name but with the (0-indexed) sentence number appended to
+it.  For example, if </p>
+
+    <div class="highlighter-rouge"><pre class="highlight"><code>tm-file = /path/to/grammar.gz
+</code></pre>
+    </div>
+
+    <p>then the sentence-filtered grammars should be found at</p>
+
+    <div class="highlighter-rouge"><pre class="highlight"><code>/path/to/filtered/grammar.0.gz
+/path/to/filtered/grammar.1.gz
+/path/to/filtered/grammar.2.gz      
+...
+</code></pre>
+    </div>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">threads</code>, <code class="highlighter-rouge">num-parallel-decoders</code> — <em>1</em></p>
+
+    <p>This determines how many simultaneous decoding threads to launch.  </p>
+
+    <p>Outputs are assembled in order and Joshua has to hold on to the complete target hypergraph until
+it is ready to be processed for output, so too many simultaneous threads could result in lots of
+memory usage if a long sentence results in many sentences being queued up.  We have run Joshua
+with as many as 48 threads without any problems of this kind, but it’s useful to keep in the back
+of your mind.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">oov-feature-cost</code> — <em>100</em></p>
+
+    <p>Each OOV word incurs this cost, which is multiplied against the <code class="highlighter-rouge">oovPenalty</code> feature (which is
+tuned but can be held fixed).</p>
+  </li>
+  <li><code class="highlighter-rouge">use-google-linear-corpus-gain</code></li>
+  <li><code class="highlighter-rouge">google-bleu-weights</code></li>
+</ul>
+
+<p><a name="pruning"></a></p>
+
+<h3 id="pruning-options">Pruning options</h3>
+
+<p>There are three different approaches to pruning in Joshua.</p>
+
+<ol>
+  <li>
+    <p>No pruning.  Exhaustive decoding is triggered by setting <code class="highlighter-rouge">pop-limit = 0</code> and
+<code class="highlighter-rouge">use-beam-and-threshold-prune = false</code>.</p>
+  </li>
+  <li>
+    <p>The old approach.  This approach uses a handful of pruning parameters whose specific roles are
+hard to understand and whose interaction is even more difficult to quantify.  It is triggered by
+setting <code class="highlighter-rouge">pop-limit = 0</code> and <code class="highlighter-rouge">use-beam-and-threshold-prune = true</code>.</p>
+  </li>
+  <li>
+    <p>Pop-limit pruning (the new approach).  The pop limit determines the number of hypotheses that are
+  popped from the candidates list for each of the O(n^2) spans of the input.  A nice feature of this
+  approach is that it provides a single value to control the size of the search space that is
+  explored (and therefore runtime).</p>
+  </li>
+</ol>
+
+<p>Selecting among these pruning methods could be made easier via a single parameter with enumerated
+values, but currently, we are stuck with this slightly more cumbersome way.  The defaults ensure
+that you don’t have to worry about them too much.  Pop-limit pruning is enabled by default, and it
+is the recommended approach; if you want to control the speed / accuracy tradeoff, you should change
+the pop limit.</p>
+
+<ul>
+  <li>
+    <p><code class="highlighter-rouge">pop-limit</code> — <em>100</em></p>
+
+    <p>The number of hypotheses to examine for each span of the input.  Higher values result in a larger
+portion of the search space being explored at the cost of an increased search time.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">use-beam-and-threshold-pruning</code> — <em>false</em></p>
+
+    <p>Enables the use of beam-and-threshold pruning, and makes the following five features relevant.</p>
+
+    <ul>
+      <li><code class="highlighter-rouge">fuzz1</code> — <em>0.1</em></li>
+      <li><code class="highlighter-rouge">fuzz2</code> — <em>0.2</em></li>
+      <li><code class="highlighter-rouge">max-n-items</code> — <em>30</em></li>
+      <li><code class="highlighter-rouge">relative-threshold</code> — <em>10.0</em></li>
+      <li><code class="highlighter-rouge">max-n-rules</code> — <em>50</em></li>
+    </ul>
+  </li>
+  <li><code class="highlighter-rouge">constrain-parse</code> — <em>false</em></li>
+  <li><code class="highlighter-rouge">use_pos_labels</code> — <em>false</em></li>
+</ul>
+
+<p><a name="tm"></a></p>
+
+<h3 id="translation-model-options">Translation model options</h3>
+
+<p>At the moment, Joshua supports only two translation models, which are designated as the (main)
+translation model and the glue grammar.  Internally, these grammars are distinguished only in that
+the <code class="highlighter-rouge">span-limit</code> parameter applies only to the glue grammar.  In the near future we plan to
+generalize the grammar specification to permit an unlimited number of translation models.</p>
+
+<p>The main translation grammar is specified with the following set of parameters:</p>
+
+<ul>
+  <li>
+    <p><code class="highlighter-rouge">tm_file STRING</code> — <em>NULL</em>, <code class="highlighter-rouge">glue_file STRING</code> — <em>NULL</em></p>
+
+    <p>This points to the file location of the translation grammar for text-based formats or to the
+directory for the <a href="packing.html">packed representation</a>.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">tm_format STRING</code> — <em>thrax</em>, <code class="highlighter-rouge">glue_format STRING</code> — <em>thrax</em></p>
+
+    <p>The format the file is in.  The permissible formats are <code class="highlighter-rouge">hiero</code> or <code class="highlighter-rouge">thrax</code> (which are equivalent),
+<code class="highlighter-rouge">packed</code> (for <a href="packing.html">packed grammars</a>), or <code class="highlighter-rouge">samt</code> (for grammars encoded in the format
+defined by <a href="http://www.cs.cmu.edu/~zollmann/samt/">Zollmann &amp; Venugopal</a>.  This parameter will be
+done away with in the near future since it is easily inferrable.  See
+<a href="file-formats.html">the formats page</a> for more information about file formats.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">phrase_owner STRING</code> — <em>pt</em>, <code class="highlighter-rouge">glue-owner STRING</code> — <em>pt</em></p>
+
+    <p>The ownership concept is used to distinguish the set of feature weights that apply to each
+grammar.  See the <a href="features.html">page on features</a> for more information.  By default, these
+parameters have the same value, meaning the grammars share a set of features.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">span-limit</code> — <em>10</em></p>
+
+    <p>This controls the maximum span of the input that grammar rules loaded from <code class="highlighter-rouge">tm-file</code> are allowed
+to apply.  The span limit is ignored for glue grammars.</p>
+  </li>
+</ul>
+
+<p><a name="lm"></a></p>
+
+<h3 id="language-model-options">Language model options</h3>
+
+<p>Joshua supports the incorporation of an arbitrary number of language models.  To add a language
+model, add a line of the following format to the configuration file:</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code>lm = lm-type order 0 0 lm-ceiling-cost lm-file
+</code></pre>
+</div>
+
+<p>where the six fields correspond to the following values:</p>
+
+<ul>
+  <li><em>lm-type</em>: one of “kenlm”, “berkeleylm”, “javalm” (not recommended), or “none”</li>
+  <li><em>order</em>: the N of the N-gram language model</li>
+  <li><em>0</em>: whether to use left equivalent state (currently not supported)</li>
+  <li><em>0</em>: whether to use right equivalent state (currently not supported)</li>
+  <li><em>lm-ceiling-cost</em>: the LM-specific ceiling cost of any n-gram (currently ignored;
+ <code class="highlighter-rouge">lm-ceiling-cost</code> applies to all language models)</li>
+  <li><em>lm-file</em>: the path to the language model file.  All types support the standard ARPA format.
+ Additionally, if the LM type is “kenlm”, this file can be compiled into KenLM’s compiled format
+ (using the program at <code class="highlighter-rouge">$JOSHUA/src/joshua/decoder/ff/lm/kenlm/build_binary</code>), and if the LM type
+ is “berkeleylm”, it can be compiled by following the directions in
+ <code class="highlighter-rouge">$JOSHUA/src/joshua/decoder/ff/lm/berkeley_lm/README</code>.</li>
+</ul>
+
+<p>For each language model, you need to specify a feature weight in the following format:</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code>lm 0 WEIGHT
+lm 1 WEIGHT
+...
+</code></pre>
+</div>
+
+<p>where the indices correspond to the language model declaration lines in order.</p>
+
+<p>For backwards compatibility, Joshua also supports a separate means of specifying the language model,
+by separately specifying each of <code class="highlighter-rouge">lm-file</code> (NULL), <code class="highlighter-rouge">lm-type</code> (kenlm), <code class="highlighter-rouge">order</code> (5), and
+<code class="highlighter-rouge">lm-ceiling-cost</code> (100).</p>
+
+<p><a name="output"></a></p>
+
+<h3 id="output-options">Output options</h3>
+
+<p>The output for a given input is a set of one or more lines with the following scheme:</p>
+
+<div class="highlighter-rouge"><pre class="highlight"><code>input ID ||| translation ||| model scores ||| score
+</code></pre>
+</div>
+
+<p>These parameters largely determine what is output by Joshua.</p>
+
+<ul>
+  <li>
+    <p><code class="highlighter-rouge">top-n</code> — <em>300</em></p>
+
+    <p>The number of translation hypotheses to output, sorted in non-increasing order of model score (i.e.,
+highest first).</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">use-unique-nbest</code> — <em>true</em></p>
+
+    <p>When constructing the n-best list for a sentence, skip hypotheses whose string has already been
+output.  This increases the amount of diversity in the n-best list by removing spurious ambiguity
+in the derivation structures.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">add-combined-cost</code> — <em>true</em></p>
+
+    <p>In addition to outputting the hypothesis number, the translation, and the individual feature
+weights, output the combined model cost.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">use-tree-nbest</code> — <em>false</em> </p>
+
+    <p>Output the synchronous derivation tree in addition to the output string, for each candidate in the
+n-best list.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">escape-trees</code> — <em>false</em></p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">include-align-index</code> — <em>false</em></p>
+
+    <p>Output the source words indices that each target word aligns to.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">mark-oovs</code> — <em>false</em></p>
+
+    <p>if <code class="highlighter-rouge">true</code>, this causes the text “_OOV” to be appended to each OOV in the output.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">visualize-hypergraph</code> — <em>false</em></p>
+
+    <p>If set to true, a visualization of the hypergraph will be displayed, though you will have to
+explicitly include the relevant jar files.  See the example usage in
+<code class="highlighter-rouge">$JOSHUA/examples/tree_visualizer/</code>, which contains a demonstration of a source sentence,
+translation, and synchronous derivation.</p>
+  </li>
+  <li>
+    <p><code class="highlighter-rouge">save-disk-hg</code> — <em>false</em> [DISABLED]</p>
+
+    <p>This feature directs that the hypergraph should be written to disk.  The code is in</p>
+
+    <div class="highlighter-rouge"><pre class="highlight"><code>$JOSHUA/src/joshua/src/DecoderThread.java
+</code></pre>
+    </div>
+
+    <p>but the feature has not been tested in some time, and is thus disabled.  It probably wouldn’t take
+much work to fix it!  If you do, you might find the
+<a href="http://aclweb.org/aclwiki/index.php?title=Hypergraph_Format">discussion on a common hypergraph format</a>
+on the ACL Wiki to be useful.</p>
+  </li>
+</ul>
+
+<!--
+
+## Full list of command-line options and arguments
+
+<table border="0">
+  <tr>
+    <th>
+      option
+    </th>
+    <th>
+      value
+    </th>
+    <th>
+      description
+    </th>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-lm</code>
+    </td>
+    <td>
+      String, e.g. <n /> <code>TYPE 5 false false 100 FILE</code>
+    </td>
+    <td markdown="1">
+      Use once for each of one or language models.
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-lm_file</code>
+    </td>
+    <td>
+      String: path the the language model file
+    </td>
+    <td>
+      ???
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-parse</code>
+    </td>
+    <td>
+      None
+    </td>
+    <td>
+      whether to parse (if not then decode)
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-tm_file</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+       path to the the translation model
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-glue_file</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      ???
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-tm_format</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-glue_format</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>-lm_type</code>
+    </td>
+    <td>
+      value
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+  <tr>
+    <td>
+      <code>lm_ceiling_cost</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>use_left_equivalent_state</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>use_right_equivalent_state</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>order</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>use_sent_specific_lm</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>span_limit</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>phrase_owner</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>glue_owner</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>default_non_terminal</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>goalSymbol</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>constrain_parse</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>oov_feature_index</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>true_oovs_only</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>use_pos_labels</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>fuzz1</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>fuzz2</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>max_n_items</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>relative_threshold</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>max_n_rules</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>use_unique_nbest</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>add_combined_cost</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>use_tree_nbest</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>escape_trees</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>include_align_index</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>top_n</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>parallel_files_prefix</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>num_parallel_decoders</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>threads</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>save_disk_hg</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>use_kbest_hg</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>forest_pruning</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>forest_pruning_threshold</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>visualize_hypergraph</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>mark_oovs</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>pop-limit</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+
+  <tr>
+    <td>
+      <code>useCubePrune</code>
+    </td>
+    <td>
+      String
+    </td>
+    <td>
+      description
+    </td>
+  </tr>
+</table>
+-->
+
+
+
+      </div>
+    </div>
+
+  </body>
+</html>
+
+
+
+
+

http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/blob/53cc3005/4.0/decoder.md
----------------------------------------------------------------------
diff --git a/4.0/decoder.md b/4.0/decoder.md
deleted file mode 100644
index e3839bf..0000000
--- a/4.0/decoder.md
+++ /dev/null
@@ -1,910 +0,0 @@
----
-layout: default4
-category: links
-title: Decoder configuration parameters
----
-
-Joshua configuration parameters affect the runtime behavior of the decoder itself.  This page
-describes the complete list of these parameters and describes how to invoke the decoder manually.
-
-To run the decoder, a convenience script is provided that loads the necessary Java libraries.
-Assuming you have set the environment variable `$JOSHUA` to point to the root of your installation,
-its syntax is:
-
-    $JOSHUA/joshua-decoder [-m memory-amount] [-c config-file other-joshua-options ...]
-    
-The `-m` argument, if present, must come first, and the memory specification is in Java format
-(e.g., 400m, 4g, 50g).  Most notably, the suffixes "m" and "g" are used for "megabytes" and
-"gigabytes", and there cannot be a space between the number and the unit.  The value of this
-argument is passed to Java itself in the invocation of the decoder, and the remaining options are
-passed to Joshua.  The `-c` parameter has special import because it specifies the location of the
-configuration file.
-
-The Joshua decoder works by reading from STDIN and printing translations to STDOUT as they are
-received, according to a number of [output options](#output).  If no run-time parameters are
-specified (e.g., no translation model), sentences are simply pushed through untranslated.  Blank
-lines are similarly pushed through as blank lines, so as to maintain parallelism with the input.
-
-Parameters can be provided to Joshua via a configuration file and from the command
-line.  Command-line arguments override values found in the configuration file.  The format for
-configuration file parameters is
-
-    parameter = value
-
-Command-line options are specified in the following format
-
-    -parameter value
-
-Values are one of four types (which we list here mostly to call attention to the boolean format):
-
-- STRING, an arbitrary string (no spaces)
-- FLOAT, a floating-point value
-- INT, an integer
-- BOOLEAN, a boolean value.  For booleans, `true` evaluates to true, and all other values evaluate
-  to false.  For command-line options, the value may be omitted, in which case it evaluates to
-  true.  For example, the following are equivalent:
-
-      $JOSHUA/joshua-decoder -show-align-index true
-      $JOSHUA/joshua-decoder -show-align-index
-
-## Joshua configuration file
-
-Before describing the list of Joshua parameters, we present a note about the configuration file.
-In addition to the decoder parameters described below, the configuration file contains the feature
-weight values for the model.  The weight values are distinguished from runtime parameters in two
-ways: (1) they cannot be overridden on the command line, and (2) they do not have an equals sign
-(=).  Parameters are described in further detail in the [feature file](features.html).  They take
-the following format, and by convention are placed at the end of the configuration file:
-
-    lm 0 4.23
-    phrasement pt 0 -0.2
-    oovpenalty -100
-
-## Joshua decoder parameters
-
-This section contains a list of the Joshua run-time parameters.  An important note about the
-parameters is that they are collapsed to canonical form, in which dashes (-) and underscores (-) are
-removed and case is converted to lowercase.  For example, the following parameter forms are
-equivalent (either in the configuration file or from the command line):
-
-    {top-n, topN, top_n, TOP_N, t-o-p-N}
-    {poplimit, pop-limit, pop-limit, popLimit}
-
-This basically defines equivalence classes of parameters, and relieves you of the task of having to
-remember the exact format of each parameter.
-
-In what follows, we group the configuration parameters in the following groups:
-
-- [Alternate modes of operation](#modes)
-- [General options](#general)
-- [Pruning](#pruning)
-- [Translation model options](#tm)
-- [Language model options](#lm)
-- [Output options](#output)
-
-<a name="modes" />
-
-### Alternate modes of operation
-
-In addition to decoding (which is the default mode), Joshua can also produce synchronous parses of a
-(source,target) pair of sentences.  This mode disables the language model (since no generation is
-required) but still requires a translation model.  To enable it, you must do two things:
-
-1. Set the configuration parameters `parse = true`.
-2. Provide input in the following format:
-   
-       source sentence ||| target sentence
-       
-You may also wish to display the synchronouse parse tree (`-use-tree-nbest`) and the alignment
-(`-show-align-index`).
-
-The synchronous parsing implementation is that of Dyer (2010)
-[PDF](http://www.aclweb.org/anthology/N/N10/N10-1033).
-
-If parsing is enabled, the following features become relevant.  If you would like more information
-about how to use these features, please ask [Jonny Weese](http://cs.jhu.edu/~jonny/) to document
-them. 
-
-- `forest-pruning` --- *false*
-
-  If true, the synchronous forest will be pruned.
-
-- `forest-pruning-threshold` --- *10*
-
-  The threshold used for pruning.
-  
-- `use-kbest-hg` --- *false*
-
-  The k-best hypergraph to use.
-
-
-<a name="general" />
-
-### General decoder options
-
-- `c`, `config` --- *NULL*
-
-   Specifies the configuration file from which Joshua options are loaded.  This feature is unique in
-   that it must be specified from the command line.
-
-- `oracle-file` --- *NULL*
-
-  The location of a set of oracle reference translations, parallel to the input.  When present,
-  after producing the hypergraph by decoding the input sentence, the oracle is used to rescore the
-  translation forest with a BLEU approximation in order to extract the oracle-translation from the
-  forest.  This is useful for obtaining an (approximation to an) upper bound on your translation
-  model under particular search settings.
-
-- `default-nonterminal` --- *"X"*
-
-   This is the nonterminal symbol assigned to out-of-vocabulary (OOV) items.  
-
-- `goal-symbol` --- *"GOAL"*
-
-   This is the symbol whose presence in the chart over the whole input span denotes a successful
-   parse (translation).  It should match the LHS nonterminal in your glue grammar.  Internally,
-   Joshua represents nonterminals enclosed in square brackets (e.g., "[GOAL]"), which you can
-   optionally supply in the configuration file.
-
-- `true-oovs-only` --- *false*
-
-  By default, Joshua creates an OOV entry for every word in the source sentence, regardless of
-  whether it is found in the grammar.  This allows every word to be pushed through untranslated
-  (although potentially incurring a high cost based on the `oovPenalty` feature).  If this option is
-  set, then only true OOVs are entered into the chart as OOVs.
-
-- `use-sent-specific-tm` --- *false*
-
-  If set to true, Joshua will look for sentence-specific filtered grammars.  The location is
-  determined by taking the supplied translation model (`tm-file`) and looking for a `filtered/`
-  subdirectory for a file with the same name but with the (0-indexed) sentence number appended to
-  it.  For example, if 
-  
-      tm-file = /path/to/grammar.gz
-  
-  then the sentence-filtered grammars should be found at
-  
-      /path/to/filtered/grammar.0.gz
-      /path/to/filtered/grammar.1.gz
-      /path/to/filtered/grammar.2.gz      
-      ...
-      
-- `threads`, `num-parallel-decoders` --- *1*
-
-  This determines how many simultaneous decoding threads to launch.  
-  
-  Outputs are assembled in order and Joshua has to hold on to the complete target hypergraph until
-  it is ready to be processed for output, so too many simultaneous threads could result in lots of
-  memory usage if a long sentence results in many sentences being queued up.  We have run Joshua
-  with as many as 48 threads without any problems of this kind, but it's useful to keep in the back
-  of your mind.
-
-- `oov-feature-cost` --- *100*
-
-  Each OOV word incurs this cost, which is multiplied against the `oovPenalty` feature (which is
-  tuned but can be held fixed).
-
-- `use-google-linear-corpus-gain`
-- `google-bleu-weights`
-
-
-<a name="pruning" />
-
-### Pruning options
-  
-There are three different approaches to pruning in Joshua.
-
-1. No pruning.  Exhaustive decoding is triggered by setting `pop-limit = 0` and
-`use-beam-and-threshold-prune = false`.
-
-1. The old approach.  This approach uses a handful of pruning parameters whose specific roles are
-hard to understand and whose interaction is even more difficult to quantify.  It is triggered by
-setting `pop-limit = 0` and `use-beam-and-threshold-prune = true`.
-
-1. Pop-limit pruning (the new approach).  The pop limit determines the number of hypotheses that are
-  popped from the candidates list for each of the O(n^2) spans of the input.  A nice feature of this
-  approach is that it provides a single value to control the size of the search space that is
-  explored (and therefore runtime).
-
-Selecting among these pruning methods could be made easier via a single parameter with enumerated
-values, but currently, we are stuck with this slightly more cumbersome way.  The defaults ensure
-that you don't have to worry about them too much.  Pop-limit pruning is enabled by default, and it
-is the recommended approach; if you want to control the speed / accuracy tradeoff, you should change
-the pop limit.
-
-- `pop-limit` --- *100*
-
-  The number of hypotheses to examine for each span of the input.  Higher values result in a larger
-  portion of the search space being explored at the cost of an increased search time.
-
-- `use-beam-and-threshold-pruning` --- *false*
-
-  Enables the use of beam-and-threshold pruning, and makes the following five features relevant.
-  
-  - `fuzz1` --- *0.1*
-  - `fuzz2` --- *0.2*
-  - `max-n-items` --- *30*
-  - `relative-threshold` --- *10.0*
-  - `max-n-rules` --- *50*
-
-- `constrain-parse` --- *false*
-- `use_pos_labels` --- *false*
-
-
-<a name="tm" />
-
-### Translation model options
-
-At the moment, Joshua supports only two translation models, which are designated as the (main)
-translation model and the glue grammar.  Internally, these grammars are distinguished only in that
-the `span-limit` parameter applies only to the glue grammar.  In the near future we plan to
-generalize the grammar specification to permit an unlimited number of translation models.
-
-The main translation grammar is specified with the following set of parameters:
-
-- `tm_file STRING` --- *NULL*, `glue_file STRING` --- *NULL*
-
-  This points to the file location of the translation grammar for text-based formats or to the
-  directory for the [packed representation](packing.html).
-  
-- `tm_format STRING` --- *thrax*, `glue_format STRING` --- *thrax*
-
-  The format the file is in.  The permissible formats are `hiero` or `thrax` (which are equivalent),
-  `packed` (for [packed grammars](packing.html)), or `samt` (for grammars encoded in the format
-  defined by [Zollmann & Venugopal](http://www.cs.cmu.edu/~zollmann/samt/).  This parameter will be
-  done away with in the near future since it is easily inferrable.  See
-  [the formats page](file-formats.html) for more information about file formats.
-
-- `phrase_owner STRING` --- *pt*, `glue-owner STRING` --- *pt*
-
-  The ownership concept is used to distinguish the set of feature weights that apply to each
-  grammar.  See the [page on features](features.html) for more information.  By default, these
-  parameters have the same value, meaning the grammars share a set of features.
-
-- `span-limit` --- *10*
-
-  This controls the maximum span of the input that grammar rules loaded from `tm-file` are allowed
-  to apply.  The span limit is ignored for glue grammars.
-
-<a name="lm" />
-
-### Language model options
-
-Joshua supports the incorporation of an arbitrary number of language models.  To add a language
-model, add a line of the following format to the configuration file:
-
-    lm = lm-type order 0 0 lm-ceiling-cost lm-file
-
-where the six fields correspond to the following values:
-
-* *lm-type*: one of "kenlm", "berkeleylm", "javalm" (not recommended), or "none"
-* *order*: the N of the N-gram language model
-* *0*: whether to use left equivalent state (currently not supported)
-* *0*: whether to use right equivalent state (currently not supported)
-* *lm-ceiling-cost*: the LM-specific ceiling cost of any n-gram (currently ignored;
-   `lm-ceiling-cost` applies to all language models)
-* *lm-file*: the path to the language model file.  All types support the standard ARPA format.
-   Additionally, if the LM type is "kenlm", this file can be compiled into KenLM's compiled format
-   (using the program at `$JOSHUA/src/joshua/decoder/ff/lm/kenlm/build_binary`), and if the LM type
-   is "berkeleylm", it can be compiled by following the directions in
-   `$JOSHUA/src/joshua/decoder/ff/lm/berkeley_lm/README`.
-
-For each language model, you need to specify a feature weight in the following format:
-
-    lm 0 WEIGHT
-    lm 1 WEIGHT
-    ...
-    
-where the indices correspond to the language model declaration lines in order.
-
-For backwards compatibility, Joshua also supports a separate means of specifying the language model,
-by separately specifying each of `lm-file` (NULL), `lm-type` (kenlm), `order` (5), and
-`lm-ceiling-cost` (100).
-
-
-<a name="output" />
-
-### Output options
-
-The output for a given input is a set of one or more lines with the following scheme:
-
-    input ID ||| translation ||| model scores ||| score
-
-These parameters largely determine what is output by Joshua.
-
-- `top-n` --- *300*
-
-  The number of translation hypotheses to output, sorted in non-increasing order of model score (i.e.,
-  highest first).
-
-- `use-unique-nbest` --- *true*
-
-  When constructing the n-best list for a sentence, skip hypotheses whose string has already been
-  output.  This increases the amount of diversity in the n-best list by removing spurious ambiguity
-  in the derivation structures.
-
-- `add-combined-cost` --- *true*
-
-  In addition to outputting the hypothesis number, the translation, and the individual feature
-  weights, output the combined model cost.
-
-- `use-tree-nbest` --- *false* 
-
-  Output the synchronous derivation tree in addition to the output string, for each candidate in the
-  n-best list.
-
-- `escape-trees` --- *false*
-
-
-- `include-align-index` --- *false*
-
-  Output the source words indices that each target word aligns to.
-
-- `mark-oovs` --- *false*
-
-  if `true`, this causes the text "_OOV" to be appended to each OOV in the output.
-
-- `visualize-hypergraph` --- *false*
-
-  If set to true, a visualization of the hypergraph will be displayed, though you will have to
-  explicitly include the relevant jar files.  See the example usage in
-  `$JOSHUA/examples/tree_visualizer/`, which contains a demonstration of a source sentence,
-  translation, and synchronous derivation.
-
-- `save-disk-hg` --- *false* [DISABLED]
-
-  This feature directs that the hypergraph should be written to disk.  The code is in
-  
-      $JOSHUA/src/joshua/src/DecoderThread.java
-      
-  but the feature has not been tested in some time, and is thus disabled.  It probably wouldn't take
-  much work to fix it!  If you do, you might find the
-  [discussion on a common hypergraph format](http://aclweb.org/aclwiki/index.php?title=Hypergraph_Format)
-  on the ACL Wiki to be useful.
-
-<!--
-
-## Full list of command-line options and arguments
-
-<table border="0">
-  <tr>
-    <th>
-      option
-    </th>
-    <th>
-      value
-    </th>
-    <th>
-      description
-    </th>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-lm</code>
-    </td>
-    <td>
-      String, e.g. <n /> <code>TYPE 5 false false 100 FILE</code>
-    </td>
-    <td markdown="1">
-      Use once for each of one or language models.
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-lm_file</code>
-    </td>
-    <td>
-      String: path the the language model file
-    </td>
-    <td>
-      ???
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-parse</code>
-    </td>
-    <td>
-      None
-    </td>
-    <td>
-      whether to parse (if not then decode)
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-tm_file</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-       path to the the translation model
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-glue_file</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      ???
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-tm_format</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-glue_format</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>-lm_type</code>
-    </td>
-    <td>
-      value
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-  <tr>
-    <td>
-      <code>lm_ceiling_cost</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>use_left_equivalent_state</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>use_right_equivalent_state</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>order</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>use_sent_specific_lm</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>span_limit</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>phrase_owner</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>glue_owner</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>default_non_terminal</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>goalSymbol</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>constrain_parse</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>oov_feature_index</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>true_oovs_only</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>use_pos_labels</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>fuzz1</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>fuzz2</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>max_n_items</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>relative_threshold</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>max_n_rules</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>use_unique_nbest</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>add_combined_cost</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>use_tree_nbest</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>escape_trees</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>include_align_index</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>top_n</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>parallel_files_prefix</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>num_parallel_decoders</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>threads</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>save_disk_hg</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>use_kbest_hg</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>forest_pruning</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>forest_pruning_threshold</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>visualize_hypergraph</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>mark_oovs</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>pop-limit</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-
-  <tr>
-    <td>
-      <code>useCubePrune</code>
-    </td>
-    <td>
-      String
-    </td>
-    <td>
-      description
-    </td>
-  </tr>
-</table>
--->
-

http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/blob/53cc3005/4.0/faq.html
----------------------------------------------------------------------
diff --git a/4.0/faq.html b/4.0/faq.html
new file mode 100644
index 0000000..d71da16
--- /dev/null
+++ b/4.0/faq.html
@@ -0,0 +1,257 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <link rel="stylesheet" type="text/css" media="screen,print" href="../joshua4.css" />
+    <title>Joshua | Common problems</title>
+  </head>
+
+  <body>
+
+    <div id="navbar">
+      <a href="http://joshua-decoder.org/">
+        <img src="../images/joshua-logo-small.png" width="130px" 
+             alt="Joshua logo (picture of a Joshua tree)" />
+      </a>
+
+      <p class="infobox">
+        <b>Stable version</b><br />
+        4.1<br/><br/>
+        <b>Release date</b><br />
+        2013 January
+      </p>
+
+<!--       <div class="infobox"> -->
+<!--         <b>AUTO LINKS</b><br/> -->
+<!--         <ul> -->
+<!--            -->
+<!--           <li> Advanced features</li> -->
+<!--            -->
+<!--           <li> Advanced features</li> -->
+<!--            -->
+<!--           <li> Advanced features</li> -->
+<!--            -->
+<!--           <li> Building a language pack</li> -->
+<!--            -->
+<!--           <li> Building a language pack</li> -->
+<!--            -->
+<!--           <li> Bundling a configuration</li> -->
+<!--            -->
+<!--           <li> Contributors</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Decoder configuration parameters</li> -->
+<!--            -->
+<!--           <li> Frequently Asked Questions</li> -->
+<!--            -->
+<!--           <li> Common problems</li> -->
+<!--            -->
+<!--           <li> Frequently Asked Questions</li> -->
+<!--            -->
+<!--           <li> Common problems</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Features</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> Joshua file formats</li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> Fisher and CALLHOME Spanish English Speech Translation Corpus</li> -->
+<!--            -->
+<!--           <li> Indian Languages Parallel Corpora</li> -->
+<!--            -->
+<!--           <li> Joshua 4.0 User Documentation</li> -->
+<!--            -->
+<!--           <li> Language packs</li> -->
+<!--            -->
+<!--           <li> Paraphrase Packs</li> -->
+<!--            -->
+<!--           <li> Joshua releases</li> -->
+<!--            -->
+<!--           <li> Support</li> -->
+<!--            -->
+<!--           <li> Getting Started</li> -->
+<!--            -->
+<!--           <li> Welcome to Joshua</li> -->
+<!--            -->
+<!--           <li> Joshua documentation</li> -->
+<!--            -->
+<!--           <li> Joshua documentation</li> -->
+<!--            -->
+<!--           <li> Installation</li> -->
+<!--            -->
+<!--           <li> Installation</li> -->
+<!--            -->
+<!--           <li> Alignment with Jacana</li> -->
+<!--            -->
+<!--           <li> Alignment with Jacana</li> -->
+<!--            -->
+<!--           <li> Alignment with Jacana</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Building large LMs with SRILM</li> -->
+<!--            -->
+<!--           <li> Lattice decoding</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> Grammar Packing</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> The Joshua Pipeline</li> -->
+<!--            -->
+<!--           <li> Quick Start</li> -->
+<!--            -->
+<!--           <li> Quick Start</li> -->
+<!--            -->
+<!--           <li> Releases</li> -->
+<!--            -->
+<!--           <li> Server mode</li> -->
+<!--            -->
+<!--           <li> Server mode</li> -->
+<!--            -->
+<!--           <li> Server mode</li> -->
+<!--            -->
+<!--           <li> Installing and running the Joshua Decoder</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Grammar extraction with Thrax</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Building Translation Models</li> -->
+<!--            -->
+<!--           <li> Pipeline tutorial</li> -->
+<!--            -->
+<!--           <li> Pipeline tutorial</li> -->
+<!--            -->
+<!--           <li> Pipeline tutorial</li> -->
+<!--            -->
+<!--           <li> What's New</li> -->
+<!--            -->
+<!--           <li> What's New</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> Z-MERT</li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--           <li> </li> -->
+<!--            -->
+<!--         </ul> -->
+<!--       </div>   -->
+
+      <div class="infobox">
+
+        <b>Links</b><br />
+        <ul>
+          <li> <a href="../index.html">Main</a> </li>
+          <li> <a href="pipeline.html">Pipeline</a> </li>
+          <li> <a href="step-by-step-instructions.html">Manual walkthrough</a> </li>
+          <li> <a href="decoder.html">Decoder</a> </li>
+          <li> <a href="server.html">Decoder Server</a> </li>
+          <li> <a href="file-formats.html">File formats</a> </li>
+          <li> <a href="thrax.html">Grammar Extraction</a> </li>
+          <li> <a href="../releases.html">Releases</a> </li>
+        </ul>
+      </div>
+
+      <div class="infobox">
+        <b>Advanced</b><br />
+        <ul>
+<!--          <li> <a href="packing.html">Grammar packing</a> </li> -->
+          <li> <a href="large-lms.html">Building large LMs</a> </li>
+          <li> <a href="zmert.html">Running Z-MERT</a> </li>
+          <li> <a href="lattice.html">Lattices</a> </li>
+          <li> <a href="server.html">TCP/IP server</a> </li>
+          <li> <a href="bundle.html">Bundled configuration</a> </li>
+        </ul>
+      </div>
+
+      <div class="infobox">
+        <b>Help</b><br />
+        <ul>
+          <li> <a href="faq.html">Answers</a> </li>
+          <li> <a href="https://groups.google.com/d/forum/joshua_support">Archive</a> </li>
+        </ul>
+      </div>
+
+      <div class="footer">
+        Last updated on April 08, 2016
+      </div>
+
+    </div>
+
+    <div id="main">
+      <div id="title">
+        <h1>Common problems</h1>
+      </div>
+
+      <div id="content">
+        
+        <p>Solutions to common problems will be posted here as we become aware of them.</p>
+
+
+      </div>
+    </div>
+
+  </body>
+</html>
+
+
+
+
+

http://git-wip-us.apache.org/repos/asf/incubator-joshua-site/blob/53cc3005/4.0/faq.md
----------------------------------------------------------------------
diff --git a/4.0/faq.md b/4.0/faq.md
deleted file mode 100644
index f0a4151..0000000
--- a/4.0/faq.md
+++ /dev/null
@@ -1,7 +0,0 @@
----
-layout: default4
-category: help
-title: Common problems
----
-
-Solutions to common problems will be posted here as we become aware of them.