[FIX] Update outdated docs links

README.md

@@ -25,10 +25,10 @@
 
 The annotation tool is a Vue application, developed in [JavaScript](https://www.javascript.com/) using a variety of tools including [Nuxt](https://nuxtjs.org/), [Cypress](https://www.cypress.io/), and [BootstrapVue](https://bootstrap-vue.org/docs).
 
-Please refer to our [**official documentation**](https://neurobagel.org/annotation_tool/) for more information on how to use the annotation tool.
+Please refer to our [**official documentation**](https://neurobagel.org/user_guide/annotation_tool/) for more information on how to use the annotation tool.
 
 [Quickstart](#quickstart) |
-[Documentation](https://neurobagel.org/annotation_tool/) |
+[Documentation](https://neurobagel.org/user_guide/annotation_tool/) |
 [Local Installation](#local-installation) |
 [Workflow](#workflow) |
 [Testing](#testing) |

pages/download.vue

@@ -32,7 +32,7 @@
 
                 <b-alert v-model="outputIsValid" variant="success" :show="dictionaryCollapsed">
                     <h1>🎉 Congratulations!</h1>
-                    You have successfully created an <a href="https://neurobagel.org/dictionaries/" target="_blank">neurobagel annotated .json data dictionary</a>.
+                    You have successfully created a <a href="https://neurobagel.org/data_models/dictionaries/" target="_blank">neurobagel annotated .json data dictionary</a>.
                 </b-alert>
 
                 <h3>Data Dictionary</h3>
@@ -50,7 +50,7 @@
                 </p>
                 <ul>
                     <li>Download the .json data dictionary to your local hard drive by clicking the green "Download" button.</li>
-                    <li>Use the .json data dictionary to <a href="https://neurobagel.org/cli/" target="_blank">create a harmonized view of your data</a></li>
+                    <li>Use the .json data dictionary to <a href="https://neurobagel.org/user_guide/cli/" target="_blank">create a harmonized view of your data</a></li>
                     <li>Learn more about <a href="https://neurobagel.org/" target="_blank">neurobagel</a> and how to use harmonized data for cross-dataset search.</li>
                 </ul>
             </b-col>
@@ -213,4 +213,4 @@ pre {
   max-height: 400px;
   overflow-y: auto;
 }
-</style>
+</style>

pages/home.vue

@@ -23,21 +23,21 @@
                 <b-collapse id="collapse-1">
                     <br />
                     <p>
-                        More details can be found <a href="https://neurobagel.org/annotation_tool/" target="_blank">in our documentation</a>.
+                        More details can be found <a href="https://neurobagel.org/user_guide/annotation_tool/" target="_blank">in our documentation</a>.
                     </p>
                     <ol>
-                        <li>Upload a TSV phenotypic file (<a href="https://neurobagel.org/data_prep/" target="_blank">see our docs for the TSV requirements</a>)</li>
+                        <li>Upload a TSV phenotypic file (<a href="https://neurobagel.org/user_guide/data_prep/" target="_blank">see our docs for the TSV requirements</a>)</li>
                         <li>Upload a <a href="https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file" target="_blank">BIDS-compatible JSON data dictionary</a> (optional)</li>
                         <li>Annotate any or all COLUMNS in your data table by telling us what kind of subject information they are "about"</li>
                         <li>
                             Annotate the unique VALUES in the columns you have annotated, by mapping them to controlled terms from
-                            <a href="https://neurobagel.org/term_naming_standards/#currently-used-namespaces" target="_blank">existing vocabularies</a>
+                            <a href="https://neurobagel.org/data_models/term_naming_standards/#currently-used-namespaces" target="_blank">existing vocabularies</a>
                         </li>
                         <li>Download your annotated JSON data dictionary</li>
                     </ol>
                     <b>What next?</b>
                     <p>
-                        You can now use the new data dictionary to <a href="https://neurobagel.org/cli/" target="_blank">create a harmonized representation of your subject-level data</a> (optional, uses other neurobagel tools).<br />
+                        You can now use the new data dictionary to <a href="https://neurobagel.org/user_guide/cli/" target="_blank">create a harmonized representation of your subject-level data</a> (optional, uses other neurobagel tools).<br />
                         To learn more about neurobagel, check out our website: <a href="https://neurobagel.org/" target="_blank">neurobagel.org</a>.
                     </p>
                 </b-collapse>
@@ -178,4 +178,4 @@
         }
     };
 
-</script>
+</script>