Autoloads can be overridden in General tab of Project Settings causing duplicate nodes in the scene tree.

[matthew1006]

Godot version:
Godot 3.1 alpha 3

OS/device including version:
All

Issue description:
Setting an override for an autoload from the general tab of the project settings or in project.godot overrides the script used by the autoload (you are not supposed to be able to override autoloads) but also results in multiple nodes with the same script (the override script) being added to the scene tree at runtime.
This is a follow up from #24054, see there for more details.

Steps to reproduce:

1. Add an autoload
2. Go to General/Autoload (if the Autoload section isn't there then close and reopen the project settings)
3. Override the autoload (debug works best to demonstrate)
   
4. Run the game and look at the remote scene tree
   
5. Check the scripts on the nodes. The override works.

[akien-mga]

Confirmed in the current master branch.

Test project: autoload_override.zip

Moreover, the overridden autoload also appears in the script completion, even though it's not usable as it contains a dot:

[akien-mga]

Even though #24054 was closed with the conclusion that overridden autoloads should not be supported, this issue shows that they're (weirdly) functional already, so I had a quick look at what would be needed to make them work for real.

I haven't handled things like GDScript completion yet, but this seems to do the trick to solve the duplicate autoload and properly load the overridden script:

diff --git a/main/main.cpp b/main/main.cpp
index c29a5a0aa6..88b16a4e4e 100644
--- a/main/main.cpp
+++ b/main/main.cpp
@@ -1615,7 +1615,7 @@ bool Main::start() {
 		ResourceLoader::add_custom_loaders();
 		ResourceSaver::add_custom_savers();
 
-		if (!project_manager && !editor) { // game
+		if (!project_manager && !editor) { // Run the game.
 			if (game_path != "" || script != "") {
 				if (script_debugger && script_debugger->is_remote()) {
 					ScriptDebuggerRemote *remote_debugger = static_cast<ScriptDebuggerRemote *>(script_debugger);
@@ -1623,22 +1623,34 @@ bool Main::start() {
 					remote_debugger->set_scene_tree(sml);
 				}
 
-				//autoload
+				// Autoloads.
 				List<PropertyInfo> props;
 				ProjectSettings::get_singleton()->get_property_list(&props);
 
-				//first pass, add the constants so they exist before any script is loaded
+				// First pass, add the constants so they exist before any script is loaded.
+				// Also check for overridden autoloads.
+				Vector<String> overridden;
 				for (List<PropertyInfo>::Element *E = props.front(); E; E = E->next()) {
-
-					String s = E->get().name;
-					if (!s.begins_with("autoload/"))
+					const String s = E->get().name;
+					if (!s.begins_with("autoload/")) {
 						continue;
-					String name = s.get_slicec('/', 1);
-					String path = ProjectSettings::get_singleton()->get(s);
-					bool global_var = false;
-					if (path.begins_with("*")) {
-						global_var = true;
 					}
+					const String name = s.get_slicec('/', 1);
+
+					int dot_pos = name.find(".");
+					if (dot_pos != -1) { // Autoload override.
+						// Save non-overridden property name to know which one to skip in step 2,
+						// if they are meant to be active (has relevant feature).
+						const String base_autoload = name.left(dot_pos);
+						const String feature = name.right(dot_pos + 1);
+						if (OS::get_singleton()->has_feature(feature)) {
+							overridden.push_back(base_autoload);
+						}
+						continue; // Don't register it as global var.
+					}
+
+					String path = ProjectSettings::get_singleton()->get(s);
+					bool global_var = path.begins_with("*");
 
 					if (global_var) {
 						for (int i = 0; i < ScriptServer::get_language_count(); i++) {
@@ -1647,23 +1659,41 @@ bool Main::start() {
 					}
 				}
 
-				//second pass, load into global constants
+				// Second pass, load into global constants.
+				// If we have any overridden autoload found in the previous step, we don't load
+				// the original ones if the override is active.
 				List<Node *> to_add;
 				for (List<PropertyInfo>::Element *E = props.front(); E; E = E->next()) {
-
-					String s = E->get().name;
-					if (!s.begins_with("autoload/"))
+					const String s = E->get().name;
+					if (!s.begins_with("autoload/")) {
 						continue;
+					}
 					String name = s.get_slicec('/', 1);
+
+					// Handle possible overridden autoloads.
+					int dot_pos = name.find(".");
+					if (dot_pos != -1) { // Autoload override.
+						const String base_autoload = name.left(dot_pos);
+						const String feature = name.right(dot_pos + 1);
+						if (!OS::get_singleton()->has_feature(feature)) {
+							continue; // Not enabled, skip.
+						}
+						// Keep original name (but overridden path).
+						name = base_autoload;
+					} else if (overridden.find(name) != -1) {
+						// Original autoload with valid override, so we skip it.
+						continue;
+					}
+
 					String path = ProjectSettings::get_singleton()->get(s);
-					bool global_var = false;
-					if (path.begins_with("*")) {
-						global_var = true;
-						path = path.substr(1, path.length() - 1);
+					bool global_var = path.begins_with("*");
+					if (global_var) {
+						path = path.right(1);
 					}
 
 					RES res = ResourceLoader::load(path);
-					ERR_CONTINUE_MSG(res.is_null(), "Can't autoload: " + path);
+					ERR_CONTINUE_MSG(res.is_null(), vformat("Can't load AutoLoad '%s' from: %s.", name, path));
+
 					Node *n = NULL;
 					if (res->is_class("PackedScene")) {
 						Ref<PackedScene> ps = res;
@@ -1672,20 +1702,20 @@ bool Main::start() {
 						Ref<Script> script_res = res;
 						StringName ibt = script_res->get_instance_base_type();
 						bool valid_type = ClassDB::is_parent_class(ibt, "Node");
-						ERR_CONTINUE_MSG(!valid_type, "Script does not inherit a Node: " + path);
+						ERR_CONTINUE_MSG(!valid_type,
+								vformat("Script of base type '%s' does not inherit Node and can't be used for AutoLoad '%s': %s.", ibt, name, path));
 
 						Object *obj = ClassDB::instance(ibt);
-
-						ERR_CONTINUE_MSG(obj == NULL, "Cannot instance script for autoload, expected 'Node' inheritance, got: " + String(ibt));
+						ERR_CONTINUE_MSG(obj == NULL,
+								vformat("Cannot instantiate script of base type '%s' for AutoLoad '%s': %s.", ibt, name, path));
 
 						n = Object::cast_to<Node>(obj);
 						n->set_script(script_res.get_ref_ptr());
 					}
+					ERR_CONTINUE_MSG(!n, vformat("Given path for AutoLoad '%s' is neither a Node nor a Script: %s.", name, path));
 
-					ERR_CONTINUE_MSG(!n, "Path in autoload not a node or script: " + path);
 					n->set_name(name);
-
-					//defer so references are all valid on _ready()
+					// Defer so references are all valid on _ready().
 					to_add.push_back(n);
 
 					if (global_var) {
@@ -1695,8 +1725,8 @@ bool Main::start() {
 					}
 				}
 
+				// Third pass, actually add the autoloads to the tree.
 				for (List<Node *>::Element *E = to_add.front(); E; E = E->next()) {
-
 					sml->get_root()->add_child(E->get());
 				}
 			}