docs: add admonition for `deepExtract` deprecation (#13904)

docs/usage/config-presets.md

@@ -253,6 +253,8 @@ For example the result may be:
 
 ## npm-hosted presets
 
+<!-- prettier-ignore -->
+!!! warning
     Using npm-hosted presets is deprecated, we recommend you do not follow these instructions and instead use a `local` preset.
 
 If you manage multiple repositories using Renovate and want the same custom config across all or most of them, then you might want to consider publishing your own preset config so that you can "extend" it in every applicable repository.

docs/usage/configuration-options.md

@@ -353,6 +353,8 @@ Another example would be if you want to configure a DCO signoff to each commit.
 
 ## commitMessage
 
+<!-- prettier-ignore -->
+!!! warning
     Editing of `commitMessage` directly is now deprecated and not recommended.
     Please instead edit the fields such as `commitMessageAction`, `commitMessageExtra`, etc.
 

lib/manager/gradle/readme.md

 The `gradle` manager's default behavior uses a custom parser written in JavaScript, similar to many others managers.
 It was initially known as `gradle-lite` but is now integrated into the `gradle` manager and used as default.
 
-Note: the `deepExtract` configuration option is deprecated, and will be removed in a future Renovate release.
-
 If `deepExtract` is configured to `true`, Renovate instead extracts Gradle dependencies by calling a custom Gradle script.
 The `gradle` binary is then used to extract Maven-type dependencies.
+
+<!-- prettier-ignore -->
+!!! warning
+    The `deepExtract` configuration option is deprecated, and will be removed in a future Renovate release.