Broken link corrections. Fixes: #207; thank you @saldang!

content/features.md

@@ -58,7 +58,7 @@ in CWL are not necessarily run in the order they are listed, instead the order
 is determined by the dependencies between steps. Workflow steps which do not
 depend on one another may run in parallel.
 
-Additionally, the **[scatter](https://www.commonwl.org/user_guide/23-scatter-workflow/index.html)** feature in CWL allows the repeated execution of a CWL step in parallel (depending on the resources available) over a list of inputs.  This can be done without requiring the modification of the underlying tool description.
+Additionally, the **[scatter](https://www.commonwl.org/user_guide/topics/workflows.html#scattering-steps)** feature in CWL allows the repeated execution of a CWL step in parallel (depending on the resources available) over a list of inputs.  This can be done without requiring the modification of the underlying tool description.
 
 By design, the CWL standards do not impose any technical limitations to the size of files processed or to the number of tasks run in parallel. The major scalability bottlenecks are hardware-related — not having enough machines with enough memory, compute or disk space to process more and more data at a larger scale. As these boundaries move in the future with technological advances, the CWL standards should be able to keep up and not be a cause of limitations.
 

content/getting-started.html

@@ -10,9 +10,9 @@
 
 Below are some useful resources to getting started.  Additionally, help is available through [community resources](/community) such as the [CWL Matrix channel](https://matrix.to/#/#common-workflow-language_common-workflow-language:gitter.im).
 
-* Learn to write CWL using the [CWL user guide](/user_guide/) which provides a gentle introduction to creating CWL command line tool and workflow descriptions.
+* Learn to write CWL using the [CWL user guide](https://www.commonwl.org/user_guide/) which provides a gentle introduction to creating CWL command line tool and workflow descriptions.
 * Browse [CWL Implementations](/implementations/) to find a software package that's right for you.
-* Follow [CWL Recommended Practices](http://www.commonwl.org/user_guide/rec-practices/) to make your CWL tools and workflows more efficient, reusable and transparent.
+* Follow [CWL Recommended Practices](https://www.commonwl.org/user_guide/topics/best-practices.html#best-practices) to make your CWL tools and workflows more efficient, reusable and transparent.
 * Read <a href="https://github.com/pitagora-galaxy/cwl/wiki/CWL-Start-Guide-JP" lang="ja" hreflang="ja">CWLの日本語での解説ドキュメント</a>  a 15 minute introduction to the CWL project in Japanese.
 * Watch a series of [video lessons about CWL](https://stepik.org/lesson/35918/step/1?unit=15070) in Russian as part of the <a href="https://stepik.org/course/1612/syllabus" lang="ru">Управление вычислениями</a> (Computation Management) free online course.
 * Find [CWL descriptions for life-science tools](https://github.com/common-workflow-library/bio-cwl-tools) to use directly or incorporate into your workflows.

content/tools.md

@@ -122,7 +122,7 @@ can be used to provide a programmatic API or user interface to orchestrate execu
 |--- |--- |
 |[CWLProv](https://github.com/common-workflow-language/cwlprov)|Profile of [Research Object](https://www.researchobject.org/) and [W3C PROV](https://www.w3.org/TR/prov-overview/) for provenance of a CWL workflow run|
 |[RO-Crate](https://w3id.org/ro/crate)|Research Object Crate, packaging research data with schema.org metadata. Profiles for [workflows](https://w3id.org/workflowhub/workflow-ro-crate/) and [workflow runs](https://www.researchobject.org/workflow-run-crate/)|
-|[EDAM](https://edamontology.org/)|Ontology for categorizing operations and formats, useful in [CWL metadata](https://www.commonwl.org/user_guide/17-metadata/). Primarily used in bioscientific domains.|
+|[EDAM](https://edamontology.org/)|Ontology for categorizing operations and formats, useful in [CWL metadata](https://www.commonwl.org/user_guide/topics/metadata-and-authorship.html#metadata-and-authorship). Primarily used in bioscientific domains.|
 |[schema.org](https://schema.org/)|Vocabulary typically used in Web markup and in [CWL metadata](https://www.commonwl.org/user_guide/17-metadata/)|
 |[bioschemas](https://bioschemas.org/)|[Profiles](https://bioschemas.org/profiles/) for annotating life science on the Web, including [ComputationalWorkflow](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE) and [ComputationalTool](https://bioschemas.org/profiles/ComputationalTool/1.0-RELEASE)|
 |[GA4GH TRS](https://github.com/ga4gh/tool-registry-service-schemas)|Tool Registry Service API specification for discovering tools/workflows. Used by [workflow registries](/repos/) incl. WorkflowHub and Dockstore |

site/cwlsite.cwl

@@ -106,7 +106,7 @@ steps:
           <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" integrity="sha384-604wwakM23pEysLJAhja8Lm42IIwYrJ0dEAqzFsj9pJ/P5buiujjywArgPCi8eoz" crossorigin="anonymous" />
           <link rel="stylesheet" href="/assets/styles-fix.css" />
           <link rel="shortcut icon"
-          href="https://www.commonwl.org/user_guide/assets/favicons/cwl/favicon-96x96.png" />
+          href="https://www.commonwl.org/user_guide/_static/images/favicons/cwl/favicon-96x96.png" />
           <link rel="cite-as" href="https://doi.org/10.6084/m9.figshare.3115156.v2" />
     out: [html, targetdir, extra_out]
     run: makedoc.cwl