Mark protobuf module as deprecated (#1778)

This moves the protobuf module from experimental to deprecated

Rationale:

* This is very seldom used, if used at all
* Not fully fleshed out (this really should be paired with a protoc-gen-pkl, which doesn't exist)
* There is a ProtoJSON wire format that we can already render to

pkl-commons-cli/src/main/kotlin/org/pkl/commons/cli/commands/BaseOptions.kt

@@ -102,17 +102,7 @@ class BaseOptions : OptionGroup() {
   private val defaults = CliBaseOptions()
 
   private val output =
-    arrayOf(
-      "json",
-      "jsonnet",
-      "pcf",
-      "properties",
-      "plist",
-      "textproto",
-      "xml",
-      "yaml",
-      "pkl-binary",
-    )
+    arrayOf("json", "jsonnet", "pcf", "properties", "plist", "xml", "yaml", "pkl-binary")
 
   val allowedModules: List<Pattern> by
     option(