Hmm, try using separate symlinks that aren't excluded from Jekyll to load the base repo stuff into the site? Might be more reliable

site/.dots/README.md

@@ -1 +0,0 @@
-../../README.md

site/.dots/local

@@ -1 +0,0 @@
-../../local

site/README.html

@@ -2,6 +2,6 @@
 layout: page
 permalink: /README
 ---
-{% capture readme_text %}{% include_relative .dots/README.md %}{% endcapture %}
+{% capture readme_text %}{% include_relative README.md %}{% endcapture %}
 {% assign readme_text = readme_text | newline_to_br | split: '<br />' | shift | shift | join %}
 {{ readme_text | markdownify }}

site/README.md

@@ -0,0 +1 @@
+../README.md

site/index.html

@@ -1,4 +1,4 @@
 ---
 ---
-{% include_relative .dots/local/bin/dots %}
+{% include_relative local/bin/dots %}
 # <style>body { white-space: pre-wrap; font-family: Monoid, Inconsolata, "Ubuntu Mono", Consolas, Menlo, monospace; } a { font-size: 1.3em; }</style>

site/local

@@ -0,0 +1 @@
+../local