fix: JSX transforms issue with favicon links

## Context
We do several [transformations](https://github.com/redwoodjs/sdk/blob/b839158d5f89eee392a4ab39041e7ebfb0b5eb49/docs/architecture/documentTransforms.md) to the jsx for `Document`s , using ts-morph.

## Problem
We had some transformation being done for nodes already removed from the ast, causing ts-morph to throw an error.

## Solution
Do several passes: first collect all the info we need, then do the modifications after. By not mixing collection and modification, we avoid ending up accessing removed nodes.

Author: justinvdm

pnpm-lock.yaml

@@ -154,10 +154,10 @@
     "wrangler": "^4.20.5"
   },
   "peerDependencies": {
-    "vite": "^6.2.6",
     "react": ">=19.2.0-0 <20",
     "react-dom": ">=19.2.0-0 <20",
-    "react-server-dom-webpack": ">=19.2.0-0 <20"
+    "react-server-dom-webpack": ">=19.2.0-0 <20",
+    "vite": "^6.2.6"
   },
   "optionalDependencies": {
     "react": "19.2.0-canary-39cad7af-20250411",
@@ -178,9 +178,11 @@
   "packageManager": "pnpm@9.14.4+sha512.c8180b3fbe4e4bca02c94234717896b5529740a6cbadf19fa78254270403ea2f27d4e1d46a08a0f56c89b63dc8ebfd3ee53326da720273794e6200fcf0d184ab",
   "devDependencies": {
     "@types/debug": "^4.1.12",
+    "@types/js-beautify": "^1.14.3",
     "@types/lodash": "^4.17.16",
     "@types/node": "^22.14.0",
     "@types/proper-lockfile": "^4.1.4",
+    "js-beautify": "^1.15.4",
     "semver": "^7.7.1",
     "tsx": "^4.19.4",
     "typescript": "^5.8.3",