adding final docs and creating nav

Docs-Home.md

@@ -0,0 +1,20 @@
+---
+layout: default
+title: User Documentation
+
+---
+
+<div class="doclist">
+    {% assign navigation_pages = site.html_pages | sort: 'navigation_weight' %}
+    {% for p in navigation_pages %}
+      {% if p.navigation_weight %}
+       
+        <h3>
+          <a href="{{ p.url }}" {% if p.url == page.url %}class="active"{% endif %}>
+            {{ p.title }}
+          </a>
+          </h3>
+        
+      {% endif %}
+    {% endfor %}
+</div>

Ingestible-Package-Guide.md

@@ -0,0 +1,206 @@
+---
+layout: default
+title: Ingestible Package Guide
+navigation_weight: 0
+
+---
+
+# Introduction
+
+This guide will walk you through creating, ingesting, and publishing an article package in Ambra.
+For instructions for setting up the Ambra stack, please see the Quickstart-Guide.
+
+# Table of Contents:
+
+1. The JATS standard
+1. The article package
+    1. manifest.xml
+    1. manuscript.xml
+        1. eISSN
+        1. JATS deviations
+    1. printable
+    1. graphics
+        1. required sizes
+1. Ingesting an article into Rhino
+    1. Creating a Content Repo bucket
+    1. Uploading the article
+    1. Adding an article revision
+1. Viewing the article
+
+# The JATS standard
+
+JATS is a standardized markup for journal articles. When ingesting your article into Ambra, you will have to provide an XML version of your manuscript that complies with JATS.
+
+Rhino supports JATS `1.1d2` and `1.1d3`.
+
+The JATS standard will tell you which tags to use for an abstract, author list, references, etc. Find the standard [here](https://jats.nlm.nih.gov/index.html).
+
+You can find example articles for the 1.1d3 version of JATS [here](https://jats.nlm.nih.gov/publishing/tag-library/1.1d3/chapter/samples.html).
+
+# The Article Package
+
+The article package is a zip file that contains all of the article content within a single directory. There are a few required files, which are detailed below.
+
+## manifest.xml
+
+The manifest is an XML file that tells Rhino what is in the article package. It must be named `manifest.xml`.
+
+All files present in the article package zip *must* be represented in the manifest XML, and the names must match.
+
+Verify the layout of your `manifest.xml` with a DTD. It is kept in Rhino, at `/src/main/resources/manifest.dtd`. The DTD also contains a PLOS-specific manifest example.
+
+It is optional to include `manifest.dtd` in your article package. If you choose include it, it must be mentioned in the `ancillary` section of `manifest.xml`.
+
+### Manifest XML Example
+
+```xml
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE manifest SYSTEM "manifest.dtd">
+<manifest>
+  <articleBundle>
+    <article uri="info:doi/my-article-id">
+      <representation entry="my-article-id_xml" key="my-article-id_xml" mimetype="application/xml" type="manuscript"/>
+      <representation entry="my-article-id_pdf" key="my-article-id_pdf" mimetype="application/pdf" type="printable"/>
+    </article>
+    <object type="figure" uri="info:doi/my-article-id_g001">
+      <representation entry="my-article-id_g001.tif" key="my-article-id_g001.tif" mimetype="image/tiff" type="original"/>
+      <representation entry="my-article-id_g001_medium.png" key="my-article-id_g001_medium.png" mimetype="image/png" type="medium"/>
+      <representation entry="my-article-id_g001_large.png" key="my-article-id_g001_large.png" mimetype="image/png" type="large"/>
+      <representation entry="my-article-id_g001_inline.png" key="my-article-id_g001_inline.png" mimetype="image/png" type="inline"/>
+      <representation entry="my-article-id_g001_small.png" key="my-article-id_g001_small.png" mimetype="image/png" type="small"/>
+    </object>
+    <object type="graphic" uri="info:doi/my-article-id_e001">
+      <representation entry="my-article-id_e001.tif" key="my-article-id_e001.tif" mimetype="image/tiff" type="original"/>
+      <representation entry="my-article-id_e001_inline.png" key="my-article-id_e001_inline.png" mimetype="image/png" type="inline"/>
+    </object>
+    <object type="supplementaryMaterial" uri="info:doi/my-article-id_s001">
+      <representation entry="my-article-id_s001.docx" key="my-article-id_s001.docx" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" type="supplementary"/>
+    </object>
+    <object type="table" uri="info:doi/my-article-id_t001">
+      <representation entry="my-article-id_t001.tif" key="my-article-id_t001.tif" mimetype="image/tiff" type="original"/>
+      <representation entry="my-article-id_t001_medium.png" key="my-article-id_t001_medium.png" mimetype="image/png" type="medium"/>
+      <representation entry="my-article-id_t001_large.png" key="my-article-id_t001_large.png" mimetype="image/png" type="large"/>
+      <representation entry="my-article-id_t001_inline.png" key="my-article-id_t001_inline.png" mimetype="image/png" type="inline"/>
+      <representation entry="my-article-id_t001_small.png" key="my-article-id_t001_small.png" mimetype="image/png" type="small"/>
+    </object>
+  </articleBundle>
+  <ancillary>
+    <file entry="manifest.xml" key="my-article-id_manifest.xml" mimetype="application/xml"/>
+    <file entry="my-article-id_xml.orig" key="my-article-id_manifest.xml.orig" mimetype="application/xml"/>
+  </ancillary>
+</manifest>
+```
+
+### Required tags
+
+The example above, as well as the manifest DTD, define all required tags.
+
+1. The `xml` and `DOCTYPE` tags are required and can be copied verbatim from the example.
+1. `manifest` must be used as the top-level container tag.
+1. `articleBundle` contains everything used to display the article.
+1. `article` defines the article uri (DOI).
+    1. must contain a `representation` tag for the XML and printable versions of your article.
+1. `object` is a general container tag for graphics and supplementary material. It also requires `representation` tags, but the requirements differ based on object type. Graphics will be covered in more detail later in the guide.
+1. `representation` requirements:
+    1. `entry` - value is identical to the filename
+    1. `key` - unique identifier for the asset
+    1. `mimetype` - MIME type of the asset
+    1. `type` - varies based on object type, covered in "Graphics" below.
+1. `ancillary` contains any extra files, represented in `file` nodes. Both `manifest.xml` and `manifest.dtd` are required.
+    1. `file` nodes require `entry`, `key`, and `mimetype` attributes.
+
+## Manuscript.xml
+
+The manuscript XML contains the text for your article, including references to images. 
+
+There are standard tags to use for the abstract, author list, citations, etc. Please consult the [JATS standard](https://jats.nlm.nih.gov/index.html) or refer to the example article package [here](TODO).
+
+### eISSN
+
+The eISSN defined in your manuscript XML *must match* a journal eISSN defined in your Ambra database.
+
+Example:
+ ```xml
+ <issn pub-type="epub">1932-6203</issn> 
+ ```
+
+### JATS deviations
+
+There are two known issues when rendering a JATS article in Wombat:
+
+1. The `<!DOCTYPE` tag should not be included. 
+    * If included, the article will not render, and Wombat will throw a DTD-not-found exception.
+1. The `<copyright-statement>` tag is not rendered. Use the `<license-p>` tag instead.
+
+PLOS is actively working to resolve these issues.
+
+## Printable
+
+The `Printable` is a print-ready version of your article, generally a PDF.
+
+## Article Assets (figures, tables, an supplementary material) 
+
+An article can have any number of article assets included, as long as they are defined in the manuscript AND the manifest.
+
+Each included article asset requires at least one resized copy. The copy, or copies, will be one of the following types:
+
+### Article Asset Types
+
+1. figure - A standard image that will fit most use cases. Requires *original*, *large*, *medium*, *small*, and *inline* representations.
+1. graphic - used for inline images. Requires *original* and *inline* representations.
+1. table - used for tabular data. Requires *original*, *large*, *medium*, *small*, and *inline* representations.
+1. supplementaryMaterial - used for supplementary material such as videos or other media. Requires *only* the supplementary type.
+
+#### Figure and Table Size Types
+
+1. original - the original image with original dimensions. 
+1. large - used in the stand-alone image view and the image viewer. Should be able to fit on a standard computer screen.
+1. medium - used on the homepage. Should be less than half the size of the large version.
+1. small - used in issues and the current issue on the homepage. Should be less than half the size of the medium version.
+1. inline - used for inline equations. Should be able to fit close to a line in the text.
+
+The sizes for these images are not strict and tweaking may be necessary.
+
+These requirements are also defined in the example XML above.
+
+# Ingesting an article into Rhino
+
+Ingesting an article into Rhino takes three steps.
+
+1. A bucket must exist in Content Repo with the same name defined in `rhino.yaml`.
+1. Upload the article to Rhino
+1. Create a revision in Rhino
+
+## Creating a Content Repo bucket
+
+1. Visit the Content Repo root page where you'll see a swagger interface.
+1. Click on `Create a bucket` within the `buckets` section.
+1. You'll see a bucket creation form. Enter `corpus` as the name.
+1. Click the `Try it out!` button.
+
+## Uploading an article
+
+1. Visit the Rhino root page where you'll see a swagger interface.
+1. Click on `ingestible-zip-controller`.
+1. Click on `zipUpload` or anywhere on the green bar.
+1. Click the `Browse...` button and upload your article package zipfile.
+1. Click the `Try it out!` button.
+
+This will ingest the article into Rhino and save the data to the database and content repo. 
+
+Ambra is designed versioning in mind. This means when you ingest an article, we save the data to the `ArticleIngestion` table. In order to actually view an article you will need to add a new revision.  
+
+## Adding an article revision
+
+1. Visit the Rhino root page where you'll see a swagger interface.
+1. Click on `article-crud-controller`.
+1. Click on `writeRevision`.
+1. Enter the doi. Because of a quirk in the DOI standard, if your doi includes a slash `/` it must be replaced with `++`.
+1. Enter the ingestion number.
+1. Click the `Try it out!` button.
+
+# Viewing the article
+
+Navigate to the article in Wombat: http://localhost:<$WOMBAT_PORT>/wombat/<$SITE_NAME>/article?id=<$DOI>
+
+For example: http://localhost:8123/wombat/Desktop/article?id=my-article-id 

quickstart.md → Quickstart-Guide.md

@@ -1,7 +1,9 @@
 ---
 layout: default
-title: Hank Quinlan, Horrible Cop
+title: Quickstart Guide
+
 ---
+
 ✮ = missing info
 
 # Introduction
@@ -11,7 +13,7 @@ Welcome to the Ambra Quickstart guide, brought to you by PLoS
 
 # Table of Contents:
 
-1. Walkthrough of the Ambra core components
+1. [Walkthrough of the Ambra core components](#walkthrough-of-the-ambra-core-components)
     1. Wombat
     1. Rhino
     1. Content Repo
@@ -76,7 +78,8 @@ Add a journal to the database. For example:
 
 ```sql
 INSERT INTO journal (`journalKey`, `title`) VALUES ("PLOS", "PLOSWorld");
-```
+
+
 
 Note that `journalKey` *must* be identical to the key configured in `journal.yaml` (see below)     
 
@@ -148,6 +151,16 @@ For example to override `email.yaml`:
     1. In Wombat this file is located at `src/main/webapp/WEB-INF/themes/root/config/email.yaml`
     1. In your theme, this file should be located at `$YOUR_THEME_PATH/config/email.yaml`
 
+#### Homepage
+
+You can get started by setting your homepage content with a theme override. The homepage body is defined by the theme file `$YOUR_THEME_PATH/ftl/home/body.ftl`. Create a file at this path in your theme and fill it with the HTML or FreeMarker code for your homepage content.
+
+To define new resources to use in your homepage, such as images or CSS files, place the files at the `$YOUR_THEME_PATH/resource` theme path. Any files placed here can be linked at the `resource/` path, relative to your homepage URL. For example, you could place an image named `banner.jpg` in the `resource` path and then link to it from your homepage with
+
+```html
+<img src="resource/banner.jpg" />
+```
+
 ## Compiling Content Repo (crepo)
 
 1. Clone the [crepo github project](https://github.com/PLOS/content-repo.git) into your projects folder. This will be your crepo working directory.
@@ -193,4 +206,4 @@ Go to `http://localhost:<PORT>` to view the root page for each application
 
 PLoS provides some sample article package zip files for ingestion, located [here](✮).
 
-You can ingest and publish an article package using the Rhino Swagger interface. For complete instructions, see "Ingesting the article into Rhino" in the Ingestible-Package-Guide. 
+You can ingest and publish an article package using the Rhino Swagger interface. For complete instructions, see "Ingesting the article into Rhino" in the Ingestible-Package-Guide. 

Releases.md

@@ -0,0 +1,5 @@
+---
+layout: default
+title: Releases
+
+---

_layouts/default.html

@@ -11,10 +11,13 @@
   <body>
     <section class="page-header">
       <h1 class="project-name"><a href="{{ 'index.html' | relative_url }}">{{ site.title | default: site.github.repository_name }}</a></h1>
+
       <h2 class="project-tagline">{{ site.description | default: site.github.project_tagline }}</h2>
-        <a href="{{ 'quickstart.html' | relative_url }}" class="btn">Quickstart</a>
-        <a href="{{ 'docs_home.md' | relative_url }}" class="btn">User Documentation</a>
-         <a href="{{ 'releases.md' | relative_url }}" class="btn">releases</a>
+      <nav>
+        <a href="{{ 'Quickstart-Guide.html' | relative_url }}" class="btn">Quickstart</a>
+        <a href="{{ 'Docs-Home.html' | relative_url }}" class="btn">User Documentation</a>
+         <a href="{{ 'releases.html' | relative_url }}" class="btn">Releases</a>
+         </nav>
     </section>
 
     <section class="main-content">