diff --git a/packages/lix-docs/default.nix b/packages/lix-docs/default.nix
index 62b8495..2d8f709 100644
--- a/packages/lix-docs/default.nix
+++ b/packages/lix-docs/default.nix
@@ -38,6 +38,10 @@ stdenv.mkDerivation {
     mv advanced-topics Advanced-Topics
     mv architecture/architecture.md architecture/index.md
     mv command-ref Command-Reference
+    sed -i 's!^- \[\(.*\)\]!# \1 !g' glossary.md
+    sed -i 's/^\(.*\)\({#gloss-.*}\)\(.*\)/\1\3\2/g' glossary.md
+    sed -i 's/ ,/,/g' glossary.md
+    sed -i 's/\(\S\){/\1 {/g' glossary.md
     pushd Command-Reference
     mv command-ref.md index.md
     mv files.md files/index.md
@@ -65,7 +69,9 @@ stdenv.mkDerivation {
     pushd nix-env
     find . -type f -name "*.md" -exec bash -c 'defaultFix "$0"' {} \;
     sed -i 's!\./nix-env!\./!g' index.md
+    sed -i 's!../Command-Reference/!\./!g' index.md
     popd
+    bash -c defaultFix conf-file.md
     popd
 
     # Contributing directory
@@ -75,6 +81,13 @@ stdenv.mkDerivation {
     sed -i 's!^## \[\(.*\)\]!## \1 !g' experimental-features.md
     popd
 
+    pushd language
+      sed -i '3s/##/#/' values.md
+      sed -E -i 's/(.*)(#type-\w+)">(\w+)<\/a>/## \3 {\2}/' values.md
+      sed -i 's/## List/# List/' values.md
+      sed -i 's/## Attribute Set/# Attribute Set/' values.md
+    popd
+
     # Final directories
     mv installation/installation.md installation/index.md
     mv package-management/package-management.md package-management/index.md
@@ -83,26 +96,35 @@ stdenv.mkDerivation {
     mv release-notes/release-notes.md release-notes/index.md
 
     # Admonitions
-    find . -type f -name "*.md" -exec perl -pi -e 's/  <div class="warning">/!!! warning/g' {} \;
+    find . -type f -name "*.md" -exec perl -pi -e 's/\s*<div class="warning">/!!! warning/g' {} \;
     find . -type f -name "*.md" -exec sed -i '/<\/div>/d' {} \;
     find . -type f -name "*.md" -exec perl -pi -e 's/\n\n\n/placeholderstring123/g' -0 {} \;
     find . -type f -name "*.md" -exec sed -i '/^!!! warning/,/placeholderstring123/s/^/\ \ \ \ /' {} \;
     find . -type f -name "*.md" -exec perl -pi -e 's/placeholderstring123/\n\n\n/g' -0 {} \;
-    find . -type f -name "*.md" -exec perl -pi -e 's/  > \*\*Warning\*\*/!!! warning2/g' {} \;
+    find . -type f -name "*.md" -exec perl -pi -e 's/\s*> \*\*Warning\*\*/!!! warning2/g' {} \;
     find . -type f -name "*.md" -exec sed -i '/^!!! warning2/,/^$/s/  >/\ \ \ /' {} \;
     find . -type f -name "*.md" -exec sed -i 's/!!! warning2/!!! warning/' {} \;
     find . -type f -name "*.md" -exec sed -i 's/^\ \ \ \ !!! warning/!!! warning/' {} \;
     find . -type f -name "*.md" -exec perl -pi -e 's/!!! warning\n   \n/!!! warning\n/g' -0 {} \;
+    find . -type f -name "*.md" -exec perl -pi -e 's/\s*> \*\*Note\*\*\n.*/\n\n!!! note/g' -0 {} \;
+    find . -type f -name "*.md" -exec sed -i '/^!!! note/,/^[^!>]/s/^>/\ \ \ /' {} \;
 
     # Increase all headings past line 1 by one level
     # Lix docs all have level-1 headings, we need at least level 2
     find . -type f -name "*.md" -exec sed -i '2,$s/# [^#]*/#&/g' {} \;
 
     # Clean up some local links
+    find . -type f -name "*.md" -exec sed -i 's/advanced-topics/Advanced-Topics/g' {} \;
     find . -type f -name "*.md" -exec sed -i 's/command-ref/Command-Reference/g' {} \;
+    find . -type f -name "*.md" -exec sed -i 's/package-management/Package-Management/g' {} \;
     find . -type f -name "*.md" -exec sed -i 's/new-cli/New-CLI/g' {} \;
-    find . -type f -name "*.md" -exec sed -i 's/Command-Reference\.(?:html|md)//g' {} \;
-    find . -type f -name "*.md" -exec sed -i 's/conf-file\.(?:html|md)/conf-file/g' {} \;
-    find . -type f -name "*.md" -exec sed -i 's/values\.(?:html|md)/values/g' {} \;
+    find . -type f -name "*.md" -exec sed -i 's/Command-Reference\.html//g' {} \;
+    find . -type f -name "*.md" -exec sed -i 's/Command-Reference\.md//g' {} \;
+    find . -type f -name "*.md" -exec sed -i 's/conf-file\.html/conf-file\.md/g' {} \;
+    find . -type f -name "*.md" -exec sed -i 's/nix-env\.md/nix-env/g' {} \;
+    find . -type f -name "*.md" -exec sed -i 's/values\.html/values\.md/g' {} \;
+
+    # Final misc cleanups
+    find . -type f -name "*.md" -exec sed -i 's/[\]//g' {} \;
   '';
 }