docs: Update application.yaml (#14742)

Signed-off-by: Michael Crenshaw <350466+crenshaw-dev@users.noreply.github.com>

docs/operator-manual/application.yaml

@@ -188,6 +188,7 @@ spec:
     - CreateNamespace=true # Namespace Auto-Creation ensures that namespace specified as the application destination exists in the destination cluster.
     - PrunePropagationPolicy=foreground # Supported policies are background, foreground and orphan.
     - PruneLast=true # Allow the ability for resource pruning to happen as a final, implicit wave of a sync operation
+    - RespectIgnoreDifferences=true # When syncing changes, respect fields ignored by the ignoreDifferences configuration
     managedNamespaceMetadata: # Sets the metadata for the application namespace. Only valid if CreateNamespace=true (see above), otherwise it's a no-op.
       labels: # The labels to set on the application namespace
         any: label
@@ -206,7 +207,7 @@ spec:
         maxDuration: 3m # the maximum amount of time allowed for the backoff strategy
 
   # Will ignore differences between live and desired states during the diff. Note that these configurations are not
-  # used during the sync process.
+  # used during the sync process unless the `RespectIgnoreDifferences=true` sync option is enabled.
   ignoreDifferences:
   # for the specified json pointers
   - group: apps