From 758098789ebb57805f695460862566572c188958 Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:13:14 +1000
Subject: [PATCH 1/9] Update _config.yml

---
 _config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_config.yml b/_config.yml
index 6c3e49d..2262294 100755
--- a/_config.yml
+++ b/_config.yml
@@ -21,6 +21,7 @@ defaults:
       path: ""
       type: "pages"
     values:
+      permalink: /:basename
       layout: "page"
       sidebar: main
 

From b0cbccecefd3971e0d27515f61ae928513918ba1 Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:16:26 +1000
Subject: [PATCH 2/9] Update _config.yml

---
 _config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/_config.yml b/_config.yml
index 2262294..dcf9b65 100755
--- a/_config.yml
+++ b/_config.yml
@@ -3,7 +3,6 @@ title: ABLeS
 topnav_title: ABLeS
 description: ABLeS
 remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
-permalink: pretty
 gtag: G-T8GWK081T9
 
 theme_variables:

From 56e56caf0459c281d54d415ce8b6863fb1aaba94 Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:20:00 +1000
Subject: [PATCH 3/9] Update _config.yml

---
 _config.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/_config.yml b/_config.yml
index dcf9b65..f6ca574 100755
--- a/_config.yml
+++ b/_config.yml
@@ -16,9 +16,6 @@ theme_variables:
 
 defaults:
   -
-    scope:
-      path: ""
-      type: "pages"
     values:
       permalink: /:basename
       layout: "page"

From c8c2b3547b6164e8721cb4f42b0526aa11405b7d Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:22:58 +1000
Subject: [PATCH 4/9] Update _config.yml

---
 _config.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/_config.yml b/_config.yml
index f6ca574..062607d 100755
--- a/_config.yml
+++ b/_config.yml
@@ -44,4 +44,8 @@ defaults:
 #aux_links_new_tab: true
 
 plugins:
+  - jemoji
+  - jekyll-sitemap
+  - jekyll-github-metadata
+  - webrick
   - elixir-toolkit-theme-plugins

From bf2a8b1451ca15e474a0b02c687809504467b0c5 Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:29:41 +1000
Subject: [PATCH 5/9] Update _config.yml

---
 _config.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/_config.yml b/_config.yml
index 062607d..55090c7 100755
--- a/_config.yml
+++ b/_config.yml
@@ -14,6 +14,10 @@ theme_variables:
     brand_logo: assets/img/Australian-Biocommons-Logo-Horizontal-RGB.png
     github: true
 
+exclude:
+  - README.md
+  - vendor
+  
 defaults:
   -
     values:

From b459e30348cf14b886fa49c7f26e940e05568db0 Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:32:06 +1000
Subject: [PATCH 6/9] Update _config.yml

---
 _config.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/_config.yml b/_config.yml
index 55090c7..d4bdfc1 100755
--- a/_config.yml
+++ b/_config.yml
@@ -20,6 +20,9 @@ exclude:
   
 defaults:
   -
+    scope:
+      path: ""
+      type: "pages"
     values:
       permalink: /:basename
       layout: "page"

From 66291f77a9d93a409b47a4e5d9cdf083cdc04acb Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:36:45 +1000
Subject: [PATCH 7/9] Update _config.yml

---
 _config.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/_config.yml b/_config.yml
index d4bdfc1..921b418 100755
--- a/_config.yml
+++ b/_config.yml
@@ -51,8 +51,4 @@ defaults:
 #aux_links_new_tab: true
 
 plugins:
-  - jemoji
-  - jekyll-sitemap
-  - jekyll-github-metadata
-  - webrick
   - elixir-toolkit-theme-plugins

From b795cda62d11f7f254dcd3a8b8f16c00a7df4d91 Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:40:41 +1000
Subject: [PATCH 8/9] Update index.md

---
 index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/index.md b/index.md
index 77c9ccc..19ea5c8 100755
--- a/index.md
+++ b/index.md
@@ -13,7 +13,7 @@ toc: false
             <li>Support for adopting best practices and effectively sharing outputs</li>
             <li>A community-driven repository of bioinformatics software</li>
         </ul>
-    <a class="emphasis" href="/eligibility/">Start here!</a>
+    <a class="emphasis" href="eligibility">Start here!</a>
   </aside>
   
   <main class="index-panel index-right-panel">

From ba1e7eb2082e72eb81cbd6c7486c7de85c1691ff Mon Sep 17 00:00:00 2001
From: Ziad Al-Bkhetan <ziadbkh@users.noreply.github.com>
Date: Mon, 4 May 2026 10:44:32 +1000
Subject: [PATCH 9/9] Update if89.md

---
 if89.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/if89.md b/if89.md
index c2c9723..b45f1c4 100755
--- a/if89.md
+++ b/if89.md
@@ -48,7 +48,7 @@ The list of tools available through the Australian BioCommons Shared Tools and W
                 </h2>
                 <div id="collapse-if89-tool-3" class="accordion-collapse collapse" aria-labelledby="heading-if89-tool-3" data-bs-parent="#accordion-if89-tool">
                   <div class="accordion-body">
-                   Please see <a href="/if89-technical/">documentation</a> for more information.
+                   Please see <a href="if89-technical">documentation</a> for more information.
                   </div>
                 </div>
               </div>