Merge branch 'master' into 1786-replace-jekyll-with-zenweb

diff --combined doc/admin/cheat_sheet.textile
index 32015f2ccade4c98ea1d24d51b64a6203d1b0820,78841f434914a8212b0dcfcef5d5eb66bbcd1674..d817827693d30ddb699b4ef1c29612841c4c0717
--- 1/doc/admin/cheat_sheet.textile
--- 2/doc/admin/cheat_sheet.textile
+++ b/doc/admin/cheat_sheet.textile
@@@ -3,7 -3,7 +3,7 @@@ layout: defaul
  navsection: adminguide
  title: Cheat Sheet
  navorder: 1
 ----
 +...
  
  h1. Cheat Sheet
  
@@@ -41,7 -41,7 +41,7 @@@ read -rd $'\000' newlink <<EOF; arv lin
  {
  "tail_kind":"arvados#user",
  "tail_uuid":"$user_uuid",
- "head_kind":"arvados#virtual_machine",
+ "head_kind":"arvados#virtualMachine",
  "head_uuid":"$vm_uuid",
  "link_class":"permission",
  "name":"can_login",

diff --combined doc/api/resources.textile
index 7247096fc1ead451a21cfe7994e60b9babb8cd83,2783af695d907bd3eee2864a03b34db96060ddfc..8a54a142255a546160b9deaf1f2b9f7690be0454
--- 1/doc/api/resources.textile
--- 2/doc/api/resources.textile
+++ b/doc/api/resources.textile
@@@ -4,7 -4,7 +4,7 @@@ navsection: ap
  navmenu: Concepts
  title: Resources
  navorder: 4
 ----
 +...
  
  h1. Resources
  
@@@ -35,7 -35,7 +35,7 @@@ h2. Attributes of resource list
  
  table(table table-bordered table-condensed).
  |*Attribute*|*Type*|*Description*|*Example*|
- |kind|string|@arvados#{resource_type}_list@|@arvados#project_list@|
+ |kind|string|@arvados#{resource_type}List@|@arvados#projectList@|
  |etag|string|The ETag[1] of the resource list|@cd3o1wi9sf934saajykawrz2e@|
  |self_link|string|||
  |next_page_token|string|||

diff --combined doc/api/schema/Link.textile
index 117c10cb164e921e4d6065492a350f75e646481e,624bf53d9d657b0679137296ff26e07efe732a0d..952d6f04857ad2c58678771f8c32fffa173f0941
--- 1/doc/api/schema/Link.textile
--- 2/doc/api/schema/Link.textile
+++ b/doc/api/schema/Link.textile
@@@ -4,13 -4,13 +4,13 @@@ navsection: ap
  navmenu: Schema
  title: Link
  navorder: 12
 ----
 +...
  
  h1. Link
  
  **Links** describe relationships between Arvados objects, and from objects to primitives.
  
- Links are directional: each metadata object has a tail (subject), class, name, properties, and head (object or value).  A Link may describe a relationship between two objects in an Arvados database: e.g. a _permission_ link between a User and a Group defines the permissions that User has to read or modify the Group.  Other Links simply represent metadata for a single object, e.g. the _identifier_ Link, in which the _name_ property represents a human-readable identifier for the object at the link's head.
+ Links are directional: each metadata object has a tail (the "subject" being described), class, name, properties, and head (the "object" that describes the "subject").  A Link may describe a relationship between two objects in an Arvados database: e.g. a _permission_ link between a User and a Group defines the permissions that User has to read or modify the Group.  Other Links simply represent metadata for a single object, e.g. the _identifier_ Link, in which the _name_ property represents a human-readable identifier for the object at the link's head.
  
  For links that don't make sense to share between API clients, a _link_class_ that begins with @client@ (like @client.my_app_id@ or @client.my_app_id.anythinghere@) should be used.
  

diff --combined doc/user/tutorials/running-external-program.textile
index a1a7873a385a2ddd104d2b0ed9b640554f0a35cb,21b8c6f8d90897f98280245f97985de4925a1cc3..34cb71ab757b67ae3f639168c702b1135645703e
--- 1/doc/user/tutorials/running-external-program.textile
--- 2/doc/user/tutorials/running-external-program.textile
+++ b/doc/user/tutorials/running-external-program.textile
@@@ -4,7 -4,7 +4,7 @@@ navsection: userguid
  navmenu: Tutorials
  title: "Running external programs"
  navorder: 18
 ----
 +...
  
  h1. Running external programs
  
@@@ -12,14 -12,16 +12,16 @@@ This tutorial demonstrates how to use C
  
  *This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
  
+ In this tutorial, you will use the external program @md5sum@ to compute hashes instead of the built-in Python library used in earlier tutorials.
+ 
  Start by entering the @crunch_scripts@ directory of your git repository:
  
  <notextile>
  <pre><code>$ <span class="userinput">cd you/crunch_scripts</span>
  </code></pre>
  </notextile>
- 
- Next, using your favorite text editor, create a new file called @run-md5sum.py@ in the @crunch_scripts@ directory.  Add the following code to compute the md5 hash of each file in a collection:
+  
+ Next, using your favorite text editor, create a new file called @run-md5sum.py@ in the @crunch_scripts@ directory.  Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
  
  <pre><code class="userinput">{% include run-md5sum.py %}</code></pre>
  

diff --combined doc/user/tutorials/tutorial-firstscript.textile
index daa71fa68e0a3d04d338f86124ea1d81430d076a,08e63747c562ec3e50a1aabffbc90cd9ce1f4657..5cb8c26cb110207df65c1683a4451ba6bc803f3b
--- 1/doc/user/tutorials/tutorial-firstscript.textile
--- 2/doc/user/tutorials/tutorial-firstscript.textile
+++ b/doc/user/tutorials/tutorial-firstscript.textile
@@@ -4,7 -4,7 +4,7 @@@ navsection: userguid
  navmenu: Tutorials
  title: "Writing a Crunch script"
  navorder: 13
 ----
 +...
  
  h1. Writing a Crunch script
  
@@@ -30,7 -30,7 +30,7 @@@ On the Arvados Workbench, navigate to _
  Next, on the Arvados virtual machine, clone your git repository:
  
  <notextile>
- <pre><code>$ <span class="userinput">git clone git://git.{{ site.arvados_api_host }}:you.git</span>
+ <pre><code>$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:you.git</span>
  Cloning into 'you'...</code></pre>
  </notextile>