Add docs for packages mode options locations

Resolves #2828

Author: Gerrit0

site/options.md

@@ -8,6 +8,7 @@ children:
     - options/organization.md
     - options/validation.md
     - options/other.md
+    - options/package-options.md
 ---
 
 Any command line arguments that are passed without a flag will be parsed as entry points.

site/options/input.md

@@ -68,7 +68,13 @@ sub-projects will _not_ be loaded. See
 [Gerrit0/typedoc-packages-example](https://github.com/Gerrit0/typedoc-packages-example)
 for an example monorepo which uses this option.
 
-Configuration specified in the root level project will _not_ be copied to child projects.
+> [!warning] When running in packages mode, options must be specified in the
+> correct location. As TypeDoc effectively runs with a clean options object for
+> each directory, options which take effect during conversion must be set within
+> [packageOptions](#packageoptions) or directly within configuration for each
+> project. Configuration specified in the root level project will _not_ be
+> copied to child projects. See the [package options](package-options.md) page
+> for documentation about where each option should be set.
 
 ### merge