Update remaining tools/ references missed in rename commit

README.md, update-prerelease-reference.yml, typst.qmd, and
build-all.sh were edited but not staged by the original commit.
Also removes the orphaned freeze cache for typst.qmd.

Author: cderv

.github/workflows/update-prerelease-reference.yml

@@ -121,14 +121,14 @@ jobs:
 
       - name: Generate format/cell/project reference JSON
         run: |
-          quarto run tools/reference.ts
+          quarto run _tools/reference.ts
 
       - name: Generate CLI reference
         run: |
           # Generate CLI info JSON
           quarto dev-call cli-info > docs/cli/cli-info.json
           # Generate markdown from JSON
-          quarto run tools/reference-cli-generate-md.R
+          quarto run _tools/reference-cli-generate-md.R
 
       # --- Check for changes ---
 
@@ -188,8 +188,8 @@ jobs:
 
           ## Scripts run
 
-          - \`tools/reference.ts\` - format/cell/project reference JSON
-          - \`tools/reference-cli-generate-md.R\` - CLI reference markdown
+          - \`_tools/reference.ts\` - format/cell/project reference JSON
+          - \`_tools/reference-cli-generate-md.R\` - CLI reference markdown
           EOF
 
           if [ -n "$existing_pr_number" ]; then

README.md

@@ -100,7 +100,7 @@ Documents running python with the Knitr engine will go through **reticulate**. *
 The tablular data on options listed in the [Reference section](https://quarto.org/docs/reference/) are generated automatically by running:
 
 ```
-quarto run tools/reference.ts
+quarto run _tools/reference.ts
 ```
 
 This builds the `.json` files in `docs/references` based on the [Quarto CLI schema](https://github.com/quarto-dev/quarto-cli/tree/main/src/resources/schema). The script assumes you have `quarto-cli/` at the same level in your directory structure as `quarto-web/`.