Tidy up CLI reference generation flow (#3226)

# Description of Changes

Some minor cleanups in the flow for regenerating the CLI reference.

# API and ABI breaking changes

None

# Expected complexity level and risk

1

# Testing

- [x] Existing CI passes

Co-authored-by: Zeke Foppa <bfops@users.noreply.github.com>

Author: bfops

docs/README.md

@@ -37,13 +37,8 @@ git push -u origin a-branch-name-that-describes-my-change
 > NOTE! If you make a change to `nav.ts` you will have to run `npm run build` to generate a new `docs/nav.js` file.
 
 #### CLI Reference Section
-1. Run `cargo run --features markdown-docs -p spacetimedb-cli > cli-reference.md`
-
-We currently don't properly render markdown backticks and bolding that are inside of headers, so do these two manual replacements to make them look okay (these have only been tested on Linux):
-```bash
-sed -i'' -E 's!^(##) `(.*)`$!\1 \2!' docs/cli-reference.md
-sed -i'' -E 's!^(######) \*\*(.*)\*\*$!\1 <b>\2</b>!' docs/cli-reference.md
-```
+1. Run `cargo run --features markdown-docs -p spacetimedb-cli > docs/cli-reference.md`
+2. Run `pnpm format`
 
 ### Checking Links
 

docs/package.json

@@ -18,7 +18,7 @@
   },
   "scripts": {
     "build": "tsc --project ./tsconfig.json && pnpm fix-markdown && prettier --write docs/nav.js",
-    "fix-markdown": "tools/markdown-fix.mjs docs/cli-reference.md",
+    "fix-markdown": "scripts/markdown-fix.mjs docs/cli-reference.md",
     "format": "pnpm fix-markdown && prettier --write .",
     "lint": "prettier . --check --verbose",
     "check-links": "tsx scripts/checkLinks.ts"