Fix/internal links

docs/user-guide/cadsr_users/1_building_templates.md

@@ -7,12 +7,12 @@ This page covers the basics of building templates in the {{ page.cedarw }}, with
 
 - [Introduction](#intro)
 - [Step-by-step guide: build a template](#step-by-step-guide)
-  - Step 1 - [Navigate to your workspace](#workspace)
-  - Step 2 - [Create a new template object](#create-template)
-  - Step 3 - [Add CDEs to your template](#add-cdes)
-  - Step 4 - [Configure CDE options](#configure-cdes)
-  - Step 5 - [Save your template](#save-template)
-  - Step 6 - [Share your template](#share-template)
+      - Step 1 - [Navigate to your workspace](#workspace)
+      - Step 2 - [Create a new template object](#create-template)
+      - Step 3 - [Add CDEs to your template](#add-cdes)
+      - Step 4 - [Configure CDE options](#configure-cdes)
+      - Step 5 - [Save your template](#save-template)
+      - Step 6 - [Share your template](#share-template)
 
 ***
 
@@ -75,7 +75,7 @@ A section with instructions for making copies of CDEs is included later in this
 
 This page describes the process of adding individual CDEs to templates. One advantage to this approach is that you are allowed to make edits to CDE's common options, as well as edits to all other field types from within a template container. The {{ page.cedarw }} offers the ability to group CDEs together into "elements" so that multiple CDEs can be added to a template at once. The tradeoff for this approach is that the CDEs and other fields contained in elements are unmodifiable once the element has been added to a template. 
 
-More detail and instructions for creating elements with multiple CDEs are given on a [separate page](../building_elements). Understanding how to build templates in the {{ page.cedarw }} is not a prerequisite for creating elements.
+More detail and instructions for creating elements with multiple CDEs are given on a [separate page](../3_building_elements). Understanding how to build templates in the {{ page.cedarw }} is not a prerequisite for creating elements.
 <br /><br />
 
 

docs/user-guide/cadsr_users/2_importing_templates.md

@@ -7,12 +7,12 @@ This page covers the basics of importing caDSR Form Builder forms into the {{ pa
 
 - [Introduction](#intro)
 - [Step-by-step guide: import a template](#step-by-step-guide)
-  - Step 1 - [Export form(s) to XML format](#export-forms)
-  - Step 2 - [Navigate to your workspace](#workspace)
-  - Step 3 - [Select XML files for import](#select-xml-files)
-  - Step 4 - [Perform an import](#import)
-  - Step 5 - [Look over the import report](#import-report)
-  - Step 6 - [View the imported template](#view-template)
+      - Step 1 - [Export form(s) to XML format](#export-forms)
+      - Step 2 - [Navigate to your workspace](#workspace)
+      - Step 3 - [Select XML files for import](#select-xml-files)
+      - Step 4 - [Perform an import](#import)
+      - Step 5 - [Look over the import report](#import-report)
+      - Step 6 - [View the imported template](#view-template)
 - [Editing imported templates](#edit-template)
 
 ---

docs/user-guide/cadsr_users/3_building_elements.md

@@ -7,16 +7,16 @@ This page covers the basics of building elements in the {{ page.cedarw }}, with
 
 - [Introduction](#intro)
 - [Step-by-step guide: build an element](#step-by-step-guide)
-  - Step 1 - [Navigate to your workspace](#workspace)
-  - Step 2 - [Create a new element](#create-element)
-  - Step 3 - [Add CDEs to your element](#add-cdes)
-  - Step 4 - [Configure CDE options](#configure-cdes)
-    - [Preferred labels](#opts-labels)
-    - [Cardinality](#opts-cardinality)
-    - [Required vs. optional](#opts-required)
-    - [Suggestions](#opts-suggest)
-    - [Hidden](#opts-hide)
-    - [Permissible values](#opts-values)
+    - Step 1 - [Navigate to your workspace](#workspace)
+    - Step 2 - [Create a new element](#create-element)
+    - Step 3 - [Add CDEs to your element](#add-cdes)
+    - Step 4 - [Configure CDE options](#configure-cdes)
+        - [Preferred labels](#opts-labels)
+        - [Cardinality](#opts-cardinality)
+        - [Required vs. optional](#opts-required)
+        - [Suggestions](#opts-suggest)
+        - [Hidden](#opts-hide)
+        - [Permissible values](#opts-values)
 - [Arranging CDEs in elements](#arrange-cdes)
 - [Deleteing CDEs from elements](#delete-cdes)
 - [Nesting elements](#nesting)
@@ -91,7 +91,7 @@ This will launch a modal dialog where you can use the search bar across the top
 
 You can select items in the list of search results to display a details pane on the right hand side of the dialog for viewing informaton such as the CDE owner, storage location, version number, etc.
 
-If you need more information about how to efficiently search for CDEs in the {{ page.cedarw }}, please refer to the ["Finding CDEs"](../finding_cdes) page.
+If you need more information about how to efficiently search for CDEs in the {{ page.cedarw }}, please refer to the ["Finding CDEs"](../4_finding_cdes) page.
 
 Once you locate the desired CDE, select it in the middle pane of the search dialog and click the "SELECT" button. This will insert the CDE into your element and return to the element designer.
 
@@ -146,7 +146,7 @@ The REQUIRED link allows you to specify whether or not the CDE needs to be fille
 ### Suggestions
 <a name="opts-suggest"></a>
 
-Setting SUGGESTIONS to YES enables the {{ page.cedarw }} intelligent authoring suggestion system for the field. For a detailed explanation of this functionality, see [Understanding the Suggestion System](../../sections/c4/understanding_the_suggestion_system/).
+Setting SUGGESTIONS to YES enables the {{ page.cedarw }} intelligent authoring suggestion system for the field. For a detailed explanation of this functionality, see [Understanding the Suggestion System](../../sections/c4/3_understanding_the_suggestion_system/).
 
 ### Hidden
 <a name="opts-hide"></a>

docs/user-guide/cadsr_users/4_finding_cdes.md

@@ -83,7 +83,7 @@ as the "Desktop". One way to make sure the Desktop view is displayed is to
 click on the Workspace link in the upper-left portion of the window. For a 
 more in-depth explanation of the Desktop and other components displayed in 
 the Workspace, refer to the section entitled 
-"[Your CEDAR Workspace](../../sections/a4/your_cedar_workspace)" in the 
+"[Your CEDAR Workspace](../../sections/a4/3_your_cedar_workspace)" in the 
 "[Desktop and Navigation](../../basic_topics/a4_desktop_and_navigation)" chapter.
 
 When CDEs are imported into the {{ page.cedarw }}, they are named by 

docs/user-guide/pages/cedar-for-cadsr.md

@@ -24,4 +24,4 @@ The {{ page.fb }} and {{ page.cedarw }} use different naming conventions to desc
 |module|element|
 |permissible values|values|
 
-To get started with any of the following topics, navigate to the [CEDAR Workbench](http://cedar.metadatacenter.org/){:target="_blank"} and log in to your account. If you need instructions for creating an account, please refer to the "[Accounts and Logging In](basic_topics/a1_accounts_and_logging_in "Accounts and Logging In")" section of the user guide.
+To get started with any of the following topics, navigate to the [CEDAR Workbench](http://cedar.metadatacenter.org/){:target="_blank"} and log in to your account. If you need instructions for creating an account, please refer to the "[Accounts and Logging In](../../basic_topics/a1_accounts_and_logging_in "Accounts and Logging In")" section of the user guide.

docs/user-guide/pages/faq.md

@@ -17,17 +17,17 @@ If you want to submit your metadata (even including data) to a particular domain
 **How do I get an account on CEDAR?**
 
 Detailed instructions are available in our 
-CEDAR User Manual's [Accounts and Logging In chapter](https://metadatacenter.github.io/cedar-manual/basic_topics/a1_accounts_and_logging_in/).
+CEDAR User Manual's [Accounts and Logging In chapter](../../basic_topics/a1_accounts_and_logging_in/).
 
 Just go to [the CEDAR application](https://cedar.metadatacenter.org), where you will see a login screen. You can register for the system using the Register link on that screen (just above the red Google icon), using your social media account or email address. That's it—you can start using CEDAR now!
 
 **I can't figure out what to do! How do I create a template or fill one out?**
 
-**[Quick reference for template creation](https://metadatacenter.github.io/cedar-manual/cedar_templates/c2_building_basic_templates/)**  If you want to create a template that people can then use, go to your home directory (using the Home button at upper left). To create a new template (or anything else) move the mouse pointer to the New button in the upper left, wait for the options to pop up, and select what you want to create.
+**[Quick reference for template creation](../../cedar_templates/c2_building_basic_templates/)**  If you want to create a template that people can then use, go to your home directory (using the Home button at upper left). To create a new template (or anything else) move the mouse pointer to the New button in the upper left, wait for the options to pop up, and select what you want to create.
 
-**[Quick reference for filling out metadata](https://metadatacenter.github.io/cedar-manual/basic_topics/a5_filling_out_creating_metadata/)**  To fill out some metadata for a template, you'll need to find the template you're providing metadata for (hint: you can [search for it](https://metadatacenter.github.io/cedar-manual/basic_topics/a2_finding_resources/)), then control-click or right-click on the template and select "Populate" to generate a form to fill out. (If someone else has given you a link to fill out a CEDAR template, just go to that link in your browser.) Once you're logged in you'll be in the Metadata Editor, ready to start filling out metadata.
+**[Quick reference for filling out metadata](../../basic_topics/a5_filling_out_creating_metadata/)**  To fill out some metadata for a template, you'll need to find the template you're providing metadata for (hint: you can [search for it](../../basic_topics/a2_finding_resources/)), then control-click or right-click on the template and select "Populate" to generate a form to fill out. (If someone else has given you a link to fill out a CEDAR template, just go to that link in your browser.) Once you're logged in you'll be in the Metadata Editor, ready to start filling out metadata.
 
-For more startup information, go to our [CEDAR User Manual](https://metadatacenter.github.io/cedar-manual/), or to our [CEDAR training page](https://more.metadatacenter.org/tools-training/training-cedar), 
+For more startup information, go to our [CEDAR User Manual](../../../user-overview/), or to our [CEDAR training page](https://more.metadatacenter.org/tools-training/training-cedar), 
 which each have a variety of introductory content.
 
 **What makes CEDAR forms so special? Google forms/SurveyMonkey surveys can do most of this.**
@@ -51,7 +51,7 @@ Over time CEDAR developers will be adding more time savers, like pulling in meta
 **What format is the metadata saved in? How can I access it?**
 
 We save the metadata as JSON-LD (in a Mongo database). We make it available (to those with access privileges) via the user interface, in both JSON-LD and the equivalent RDF. Click on the format (at the bottom of the screen) to choose how you want to view it 
-[detailed information in CEDAR's User Manual](https://metadatacenter.github.io/cedar-manual/sections/a3/4_viewing_resource_as_raw_metadata/)
+[detailed information in CEDAR's User Manual](../../sections/a3/4_viewing_resource_as_raw_json/)
 
 You can also access the metadata via the CEDAR API, in both of these formats, and in a "condensed JSON" format. That last format gets rid of lots of the links in the metadata 
 (including much of the rich semantics).
@@ -76,8 +76,8 @@ Our example repository on GitHub shows how to generate Java classes that produce
 
 **What is the 'link' field type for?**
 
-This is appropriate when you know the result has to be a URL, or some other type of IRI (the internationalized, generalized form of a URL). Unlike text fields, this field type validates the metadata entry to make sure it’s an IRI, and it produces appropriately typed RDF in the resulting metadata. Please reference the [Adding Fields section](https://metadatacenter.github.io/cedar-manual/sections/c2/2_adding_fields/)
-and the [Field Type Reference](https://metadatacenter.github.io/cedar-manual/sections/c2/field_type_reference/)
+This is appropriate when you know the result has to be a URL, or some other type of IRI (the internationalized, generalized form of a URL). Unlike text fields, this field type validates the metadata entry to make sure it’s an IRI, and it produces appropriately typed RDF in the resulting metadata. Please reference the [Adding Fields section](../../sections/c2/2_adding_fields/)
+and the [Field Type Reference](../../sections/c2/field_type_reference/)
 for more information on field types.
 
 **What do you use for your identifiers?**
@@ -90,14 +90,14 @@ you will see the first identifier string, like `https://repo.metadatacenter.net/
 
 Note that the template identifier will not (yet) resolve in your browser if you do not prefix it with the appropriate CEDAR context, e.g., in this case `https://cedar.metadatacenter.net/templates/edit/`.
 
-Detailed information on our identifiers is available at [How CEDAR Defines and Applies IRIs (URIs, URLs)](https://metadatacenter.github.io/cedar-manual/sections/c4/how_cedar_defines_and_accesses_identifiers/)
+Detailed information on our identifiers is available at [How CEDAR Defines and Applies IRIs (URIs, URLs)](../../sections/b1/3_how_cedar_defines_and_accesses_identifiers/)
 
 
 **How do I look up all instances of a template?**
 
 If you have read access to the template, 
 you can look in the metadata for the template to see all the instances
-to which you have read or write access. See [Viewing Resource Metadata](https://metadatacenter.github.io/cedar-manual/a3/5_viewing_resource_metadata/)
+to which you have read or write access. See [Viewing Resource Metadata](../../sections/a3/5_viewing_resource_metadata/)
 to learn how to find the metadata for an artifact in the CEDAR Desktop.
 
 Use the API search feature with the identifier of the template to find all the related instances. See the [API search documentation](https://resource.metadatacenter.org/api/#!/Template32Instances/get_search) for the details. 
@@ -113,7 +113,7 @@ Please tell us if there is a CEDAR field that does not handle them correctly.
 **Can I deploy CEDAR in my own computing environment?**
 
 Yes, though CEDAR has not been thoroughly tested in remote deployments. 
-We have [detailed instructions about deploying CEDAR](https://metadatacenter.readthedocs.io/en/latest/install-developer/intro.html).
+We have [detailed instructions about deploying CEDAR](../../../install-overview/).
 There are several caveats:
 * We don't have a good way to upgrade metadata instances to match a new metadata schema. (We do this manually when our schema has a breaking change.)
 * You will need to continue using BioPortal or another OntoPortal-based ontology repository for your vocabularies.

docs/user-guide/sections/a1/logging_in_with_cedar.md

@@ -6,6 +6,6 @@ status: Ready
 
 To log in, go to [https://cedar.metadatacenter.org](https://cedar.metadatacenter.org "CEDAR Workbench"), and enter the account name and your password as shown in the screenshot below. If you have forgotten your password, you can use the "Forgot Password?" link just below the Password line. Once you have logged in, you will see the CEDAR Workspace. 
 
-In the next section, we provide important information about the visibility of your account, your content, and your user information. Or if you prefer, you may skip to the CEDAR Workspace [Desktop and Navigation](https://metadatacenter.github.io/cedar-manual/basic_topics/a4_desktop_and_navigation/) section, or the [Finding Resources](https://metadatacenter.github.io/cedar-manual/basic_topics/a2_finding_resources/) section.
+In the next section, we provide important information about the visibility of your account, your content, and your user information. Or if you prefer, you may skip to the CEDAR Workspace [Desktop and Navigation](../../../basic_topics/a4_desktop_and_navigation/) section, or the [Finding Resources](../../../basic_topics/a2_finding_resources/) section.
 
 ![](../../../img/userguide/login.png){:width="50%" class="centered"}

docs/user-guide/sections/a2/1_simple_searching.md

@@ -4,7 +4,7 @@ status: Ready
 ---
 # Simple Searching
 
-*To learn about simple navigation in the Desktop, visit [Navigating Within CEDAR](https://metadatacenter.github.io/cedar-manual/sections/a4/navigating_within_cedar/).*
+*To learn about simple navigation in the Desktop, visit [Navigating Within CEDAR](../../a4/2_navigating_within_cedar/).*
 
 <h1>Searching use the search bar</h1>
 
@@ -19,7 +19,7 @@ The CEDAR Workbench organizes resources in three different categories, depending
 
 Searching for a resource in a particular set is very simple. Just click on the given set (e.g., "Shared with everybody") and input the search string as free text in the search bar, as described above. All the resources in the selected set that have the string  listed in their labels, version, or description are shown. 
 
-You can also constrain the resulting resources by their type, as described in [Constraining the Results by Type](https://metadatacenter.github.io/cedar-manual/sections/a2/3_constraining_the_results_by_type/).
+You can also constrain the resulting resources by their type, as described in [Constraining the Results by Type](../../a2/3_constraining_the_results_by_type/).
 
 The search results are illustrated in the Figure below. In later sections, we will demonstrate how to organize and constrain these search results, and perform advanced searches.