From 03b4e9d6e1663f3c06649fcd80792482710ec19a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 9 Jan 2026 10:34:54 +0000
Subject: [PATCH 1/3] Initial plan


From 50f18f6743362692ccd172d5a5c497b3a2181053 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 9 Jan 2026 10:55:31 +0000
Subject: [PATCH 2/3] Initial plan: Fix relative URL in vignette

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>
---
 TreeTools-source | 1 +
 1 file changed, 1 insertion(+)
 create mode 160000 TreeTools-source

diff --git a/TreeTools-source b/TreeTools-source
new file mode 160000
index 000000000..cb8c32fd1
--- /dev/null
+++ b/TreeTools-source
@@ -0,0 +1 @@
+Subproject commit cb8c32fd1b3631ac4966e0377b884fb1e4a375c4

From 2c7ee14c37dbff94465bfd4b63d5a78dac412839 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 9 Jan 2026 10:56:51 +0000
Subject: [PATCH 3/3] Fix relative URL in vignette: use 00Index.html instead of
 index.html

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>
---
 vignettes/using-distances.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/using-distances.Rmd b/vignettes/using-distances.Rmd
index 7a8885cfe..e1e7b5940 100644
--- a/vignettes/using-distances.Rmd
+++ b/vignettes/using-distances.Rmd
@@ -28,7 +28,7 @@ Selecting an appropriate normalizing constant may require careful consideration
 of the purpose to which a tree distance metric is being put.
 
 The default normalization behaviour of each function when `normalize = TRUE` is
-listed in the [function reference](../reference/index.html), or can be viewed
+listed in the [function reference](../reference/00Index.html), or can be viewed
 by typing `?FunctionName` in the R terminal.
 
 ### Nye _et al._ tree similarity