fix some links

Author: mr-c

_episodes/02-1st-example.md

@@ -19,7 +19,7 @@ CWL documents are written in [JSON][json] or [YAML][yaml-homepage], or a mix of
 We will use YAML throughout this guide.
 If you are not familiar with YAML,
 you may find it helpful to refer to
-[this quick tutorial for the subset of YAML used in CWL](/yaml).
+[this quick tutorial for the subset of YAML used in CWL]({{ page.root }}{% link _extras/yaml.md %}).
 
 First, create a file called `1st-tool.cwl`, containing the boxed text below. It will help you to use a text editor that can be
 specified to produce text in YAML or JSON. Whatever text editor you use, the indents you see should not be created using tabs.
@@ -86,7 +86,7 @@ inputs:
 
 The `inputs` section describes the inputs of the tool.
 This is a mapped list of input parameters
-(see the [YAML Guide](/yaml#mapped-objects) for more about the format)
+(see the [YAML Guide]({{ page.root }}{% link _extras/yaml.md %}#maps) for more about the format)
 and each parameter includes an identifier,
 a data type,
 and optionally an `inputBinding`.

_episodes/09-array-inputs.md

@@ -76,7 +76,7 @@ separator string.
 Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where
 array values that are not defined with an associated key is marked by a leading
 This will be demonstrated in the next lesson
-and is discussed in more detail in the [YAML Guide](/yaml#arrays).
+and is discussed in more detail in the [YAML Guide]({{ page.root }}{% link _extras/yaml.md %}#arrays).
 You can specify arrays of arrays, arrays of records, and other complex types.
 
 {% include links.md %}

_episodes/10-array-outputs.md

@@ -54,7 +54,7 @@ Final process status is success
 ~~~
 {: .output}
 
-As described in the [YAML Guide](/yaml#arrays),
+As described in the [YAML Guide]({{ page.root }}{% link _extras/yaml.md %}#arrays),
 the array of expected outputs is specified in `array-outputs-job.yml` with each
 entry marked by a leading `-`. This format can also be used in CWL descriptions
 to mark entries in arrays, as demonstrated in several of the upcoming sections.

_extras/yaml.md

@@ -14,11 +14,11 @@ relevant when writing CWL descriptions and input parameter files.
 
 ### Contents
 
-- [Key-Value Pairs](/yaml/#key-value-pairs)
-- [Comments](/yaml/#comments)
-- [Mapped Objects](/yaml/#mapped-objects)
-- [Arrays](/yaml/#arrays)
-- [JSON Style](/yaml/#json-style)
+- [Key-Value Pairs]({{ page.root }}{% link _extras/yaml.md %}#key-value-pairs)
+- [Comments]({{ page.root }}{% link _extras/yaml.md %}#comments)
+- [Maps]({{ page.root }}{% link _extras/yaml.md %}#maps)
+- [Arrays]({{ page.root }}{% link _extras/yaml.md %}#arrays)
+- [JSON Style]({{ page.root }}{% link _extras/yaml.md %}#json-style)
 
 ### Key-Value Pairs