diff --git a/ChapterMaster.yyp b/ChapterMaster.yyp
index 1599b11422..1fdacf59dc 100644
--- a/ChapterMaster.yyp
+++ b/ChapterMaster.yyp
@@ -737,7 +737,7 @@
     {"id":{"name":"__HTTPParent","path":"scripts/__HTTPParent/__HTTPParent.yy",},},
     {"id":{"name":"__StructToDSMap","path":"scripts/__StructToDSMap/__StructToDSMap.yy",},},
     {"id":{"name":"Armamentarium","path":"scripts/Armamentarium/Armamentarium.yy",},},
-    {"id":{"name":"artifact_functions","path":"scripts/artifact_functions/artifact_functions.yy",},},
+    {"id":{"name":"scr_artifact_functions","path":"scripts/scr_artifact_functions/scr_artifact_functions.yy",},},
     {"id":{"name":"ArtifactStruct","path":"scripts/ArtifactStruct/ArtifactStruct.yy",},},
     {"id":{"name":"AudioManager","path":"scripts/AudioManager/AudioManager.yy",},},
     {"id":{"name":"ColourItem","path":"scripts/ColourItem/ColourItem.yy",},},
@@ -767,7 +767,7 @@
     {"id":{"name":"HTTPGet","path":"scripts/HTTPGet/HTTPGet.yy",},},
     {"id":{"name":"HTTPGetFile","path":"scripts/HTTPGetFile/HTTPGetFile.yy",},},
     {"id":{"name":"HTTPRequest","path":"scripts/HTTPRequest/HTTPRequest.yy",},},
-    {"id":{"name":"instance_create","path":"scripts/instance_create/instance_create.yy",},},
+    {"id":{"name":"scr_instance_functions","path":"scripts/scr_instance_functions/scr_instance_functions.yy",},},
     {"id":{"name":"is_specialist","path":"scripts/is_specialist/is_specialist.yy",},},
     {"id":{"name":"JsonFileListLoader","path":"scripts/JsonFileListLoader/JsonFileListLoader.yy",},},
     {"id":{"name":"LocalizationManager","path":"scripts/LocalizationManager/LocalizationManager.yy",},},
diff --git a/objects/obj_fleet/Create_0.gml b/objects/obj_fleet/Create_0.gml
index 9beb450e3a..b6bb644746 100644
--- a/objects/obj_fleet/Create_0.gml
+++ b/objects/obj_fleet/Create_0.gml
@@ -51,11 +51,7 @@ pla_fleet = instance_nearest(x, y, obj_p_fleet);
 ene_fleet = instance_nearest(x, y, obj_en_fleet);
 victory = false;
 
-instance_deactivate_all(true);
-instance_activate_object(obj_controller);
-instance_activate_object(obj_ini);
-instance_activate_object(obj_cursor);
-instance_activate_object(obj_img);
+instance_deactivate_all_safe();
 
 column[0] = "";
 column_width[0] = 0; // This is determined at the pre-battle screen
diff --git a/objects/obj_popup/Alarm_0.gml b/objects/obj_popup/Alarm_0.gml
index f5fd2074f1..0e7178a9b1 100644
--- a/objects/obj_popup/Alarm_0.gml
+++ b/objects/obj_popup/Alarm_0.gml
@@ -21,9 +21,7 @@ if (battle_special == 3.1) {
     obj_ncombat.threat = 4;
     obj_ncombat.formation_set = 3;
 
-    instance_deactivate_all(true);
-    instance_activate_object(obj_ini);
-    instance_activate_object(obj_controller);
+    instance_deactivate_all_safe();
     instance_activate_object(obj_ncombat);
 
     _roster = new Roster();
diff --git a/objects/obj_popup/Destroy_0.gml b/objects/obj_popup/Destroy_0.gml
index 368b33e8b1..2dc93e5032 100644
--- a/objects/obj_popup/Destroy_0.gml
+++ b/objects/obj_popup/Destroy_0.gml
@@ -4,9 +4,7 @@ if ((image == "chaos_symbol") && (title == "Concealed Heresy") && instance_exist
         // ** Starts the battle **
         is_in_combat = true;
 
-        instance_deactivate_all(true);
-        instance_activate_object(obj_controller);
-        instance_activate_object(obj_ini);
+        instance_deactivate_all_safe();
         instance_activate_object(obj_drop_select);
 
         instance_create(0, 0, obj_ncombat);
@@ -97,9 +95,7 @@ if (instance_exists(obj_controller)) {
 
         scr_civil_roster(obj_ncombat.battle_loc, obj_ncombat.battle_id, true);
 
-        instance_deactivate_all(true);
-        instance_activate_object(obj_controller);
-        instance_activate_object(obj_ini);
+        instance_deactivate_all_safe();
         instance_activate_object(obj_temp_meeting);
         instance_activate_object(obj_ncombat);
         instance_activate_object(obj_centerline);
diff --git a/objects/obj_star_select/Mouse_50.gml b/objects/obj_star_select/Mouse_50.gml
index ee6a23ade0..c936e05ebb 100644
--- a/objects/obj_star_select/Mouse_50.gml
+++ b/objects/obj_star_select/Mouse_50.gml
@@ -175,9 +175,7 @@ if (!instance_exists(obj_saveload) && !instance_exists(obj_drop_select)) {
 
                     combating = 1;
 
-                    instance_deactivate_all(true);
-                    instance_activate_object(obj_controller);
-                    instance_activate_object(obj_ini);
+                    instance_deactivate_all_safe();
                     instance_activate_object(p_fleet);
                     instance_activate_object(obj_star);
 
diff --git a/objects/obj_turn_end/Mouse_56.gml b/objects/obj_turn_end/Mouse_56.gml
index 8fc167c5c4..a67db2d289 100644
--- a/objects/obj_turn_end/Mouse_56.gml
+++ b/objects/obj_turn_end/Mouse_56.gml
@@ -83,11 +83,8 @@ if (!instance_exists(obj_saveload) && !instance_exists(obj_popup) && !instance_e
 
             add_fleet_ships_to_combat(battle_pobject[current_battle], _battle_instance);
 
-            instance_deactivate_all(true);
-            instance_activate_object(obj_controller);
-            instance_activate_object(obj_ini);
+            instance_deactivate_all_safe();
             instance_activate_object(_battle_instance);
-            instance_activate_object(obj_cursor);
         }
     }
 
@@ -111,9 +108,7 @@ if (!instance_exists(obj_saveload) && !instance_exists(obj_popup) && !instance_e
 
             combating = 1;
 
-            instance_deactivate_all(true);
-            instance_activate_object(obj_controller);
-            instance_activate_object(obj_ini);
+            instance_deactivate_all_safe();
             instance_activate_object(battle_object[current_battle]);
 
             var _battle_obj = battle_object[current_battle];
diff --git a/scripts/GitHubOAuth/GitHubOAuth.gml b/scripts/GitHubOAuth/GitHubOAuth.gml
index e3750fb772..63cc0a5aaa 100644
--- a/scripts/GitHubOAuth/GitHubOAuth.gml
+++ b/scripts/GitHubOAuth/GitHubOAuth.gml
@@ -22,8 +22,8 @@ function GitHubOAuth(_clientID, _clientSecret = undefined) constructor {
             __GitHubError("requestAuthenticationViaWebPage: Web-flow authentication is only supported on desktop platforms, please use device-flow for non-desktop platforms");
         }
 
-        // Ensure server does not exist
-        if (__github_worker.__server != undefined || __GitHubSystem().__pollTimesource != undefined) {
+        // Ensure no active request (centralized check handles deactivated worker)
+        if (__GitHubHasActiveRequest()) {
             __GitHubWarn("requestAuthenticationViaWebPage: Request is already in progress, ensure there is not another authentication request in-progress.");
             return;
         }
@@ -49,8 +49,8 @@ function GitHubOAuth(_clientID, _clientSecret = undefined) constructor {
     /// @arg {Array.String} scope An array of authentication scopes.
     /// @returns {Struct.GitHubRequest}
     static requestAuthentication = function(_scope) {
-        // Ensure server does not exist
-        if (__GitHubSystem().__pollTimesource != undefined || __github_worker.__server != undefined) {
+        // Ensure no active request (centralized check handles deactivated worker)
+        if (__GitHubHasActiveRequest()) {
             __GitHubWarn("requestAuthentication: Request is already in progress, ensure there is not another authentication request in-progress.");
             return;
         }
@@ -134,7 +134,7 @@ function GitHubOAuth(_clientID, _clientSecret = undefined) constructor {
     /// @desc Returns if there is an active authentication request in-progress.
     /// @returns {Bool}
     static hasActiveRequest = function() {
-        return __GitHubSystem().__pollTimesource != undefined || __github_worker.__server != undefined;
+        return __GitHubHasActiveRequest();
     };
 
     /// @func setAuthenticationCallback(callback)
@@ -371,6 +371,13 @@ function GitHubOAuth(_clientID, _clientSecret = undefined) constructor {
     };
 }
 
+/// @ignore
+// Centralized active-request check - ensures worker is visible before checking __server (deactivated hides handle)
+function __GitHubHasActiveRequest() {
+    __GitHubEnsureInstance();
+    return __GitHubSystem().__pollTimesource != undefined || (__github_worker.__server != undefined);
+}
+
 /// Stops and destroys the device-flow polling timesource and clears the poll state.
 /// Shared by the timeout branch, terminal-error path, success callback, errorback
 /// and cancelAuthentication so lifecycle handling cannot diverge.
diff --git a/scripts/__GitHubRequestServerShutdown/__GitHubRequestServerShutdown.gml b/scripts/__GitHubRequestServerShutdown/__GitHubRequestServerShutdown.gml
index 977796c1b8..df81e9ff4c 100644
--- a/scripts/__GitHubRequestServerShutdown/__GitHubRequestServerShutdown.gml
+++ b/scripts/__GitHubRequestServerShutdown/__GitHubRequestServerShutdown.gml
@@ -3,6 +3,8 @@
 /// Request a server shutdown
 /// @ignore
 function __GitHubRequestServerShutdown() {
+    __GitHubEnsureInstance();
+
     // Only schedule a shutdown when a web-flow server exists. Starting the delayed shutdown
     // without a server would destroy a server created by a later request.
     if (__github_worker.__server == undefined) {
diff --git a/scripts/__GitHubServerShutdown/__GitHubServerShutdown.gml b/scripts/__GitHubServerShutdown/__GitHubServerShutdown.gml
index 7bcc19ccce..acc5e5d463 100644
--- a/scripts/__GitHubServerShutdown/__GitHubServerShutdown.gml
+++ b/scripts/__GitHubServerShutdown/__GitHubServerShutdown.gml
@@ -3,6 +3,8 @@
 /// Actual shutdown
 /// @ignore
 function __GitHubServerShutdown() {
+    __GitHubEnsureInstance();
+
     // Check server for an active web-flow authentication
     if (__github_worker.__server != undefined) {
         // Destroy the network
diff --git a/scripts/__GitHubTick/__GitHubTick.gml b/scripts/__GitHubTick/__GitHubTick.gml
index 0231ef4df5..a8c4e0ea38 100644
--- a/scripts/__GitHubTick/__GitHubTick.gml
+++ b/scripts/__GitHubTick/__GitHubTick.gml
@@ -3,17 +3,29 @@
 /// @ignore
 function __GitHubTick() {
     var _system = __GitHubSystem();
+    var _expire = _system.__authenticationExpireTime;
 
-    if (_system.__authenticationExpireTime != undefined && _system.__authenticationExpireTime > 0) {
+    if (_expire != undefined && _expire > 0) {
         _system.__authenticationExpireTime--;
-    } else if (_system.__authenticationExpireTime != undefined && _system.__authenticationExpireTime <= 0 && __github_worker.__server != undefined && !__GitHubServerShuttingDown()) {
-        // Always request the shutdown first so a throwing timeout callback
-        // cannot leave the authentication server active
-        __GitHubRequestServerShutdown();
+        return;
+    }
+
+    if (_expire == undefined || _expire > 0) {
+        return;
+    }
+
+    __GitHubEnsureInstance();
+
+    if (__github_worker.__server == undefined || __GitHubServerShuttingDown()) {
+        return;
+    }
+
+    // Always request the shutdown first so a throwing timeout callback
+    // cannot leave the authentication server active
+    __GitHubRequestServerShutdown();
 
-        // Fire the timeout callback only once per shutdown sequence.
-        if (is_callable(_system.__authenticationTimeoutCallback)) {
-            _system.__authenticationTimeoutCallback();
-        }
+    // Fire the timeout callback only once per shutdown sequence.
+    if (is_callable(_system.__authenticationTimeoutCallback)) {
+        _system.__authenticationTimeoutCallback();
     }
 }
diff --git a/scripts/__GitHubWarn/__GitHubWarn.gml b/scripts/__GitHubWarn/__GitHubWarn.gml
index 30dca1561f..7a34396f6e 100644
--- a/scripts/__GitHubWarn/__GitHubWarn.gml
+++ b/scripts/__GitHubWarn/__GitHubWarn.gml
@@ -2,9 +2,5 @@
 
 /// @ignore
 function __GitHubWarn(_string) {
-    if (GITHUB_GML_RUNNING_FROM_IDE) {
-        show_error($" \nGitHub.gml:\n{_string}\n ", true);
-    } else {
-        show_debug_message($"GitHub.gml: Warning! {_string}");
-    }
+    show_debug_message($"GitHub.gml: Warning! {_string}");
 }
diff --git a/scripts/instance_create/instance_create.yy b/scripts/instance_create/instance_create.yy
deleted file mode 100644
index 5ccf8ab83b..0000000000
--- a/scripts/instance_create/instance_create.yy
+++ /dev/null
@@ -1,13 +0,0 @@
-{
-  "$GMScript":"v1",
-  "%Name":"instance_create",
-  "isCompatibility":true,
-  "isDnD":false,
-  "name":"instance_create",
-  "parent":{
-    "name":"instance",
-    "path":"folders/Scripts/compatibility/instance.yy",
-  },
-  "resourceType":"GMScript",
-  "resourceVersion":"2.0",
-}
\ No newline at end of file
diff --git a/scripts/scr_ancient_ruins/scr_ancient_ruins.gml b/scripts/scr_ancient_ruins/scr_ancient_ruins.gml
index 479d61743d..76bc8a6a9b 100644
--- a/scripts/scr_ancient_ruins/scr_ancient_ruins.gml
+++ b/scripts/scr_ancient_ruins/scr_ancient_ruins.gml
@@ -18,9 +18,7 @@ function scr_ancient_ruins_setup() {
 /// @self Struct.PlanetData
 function scr_ruins_suprise_attack_player() {
     try {
-        instance_deactivate_all(true);
-        instance_activate_object(obj_controller);
-        instance_activate_object(obj_ini);
+        instance_deactivate_all_safe();
         instance_activate_object(obj_star_select);
         instance_activate_object(obj_star);
         instance_activate_object(obj_ground_mission);
@@ -342,7 +340,7 @@ function ruins_exploration_main_sequence() {
         add_option({
             str1: "To Battle",
             choice_func: function() {
-                instance_deactivate_all(true);
+                instance_deactivate_all_safe();
                 instance_activate_object(obj_ground_mission);
                 instance_activate_object(obj_popup);
                 var _explore_feature = obj_ground_mission.explore_feature;
diff --git a/scripts/artifact_functions/artifact_functions.gml b/scripts/scr_artifact_functions/scr_artifact_functions.gml
similarity index 100%
rename from scripts/artifact_functions/artifact_functions.gml
rename to scripts/scr_artifact_functions/scr_artifact_functions.gml
diff --git a/scripts/artifact_functions/artifact_functions.yy b/scripts/scr_artifact_functions/scr_artifact_functions.yy
similarity index 73%
rename from scripts/artifact_functions/artifact_functions.yy
rename to scripts/scr_artifact_functions/scr_artifact_functions.yy
index 4453233631..05f9f24d28 100644
--- a/scripts/artifact_functions/artifact_functions.yy
+++ b/scripts/scr_artifact_functions/scr_artifact_functions.yy
@@ -1,9 +1,9 @@
 {
   "$GMScript":"v1",
-  "%Name":"artifact_functions",
+  "%Name":"scr_artifact_functions",
   "isCompatibility":false,
   "isDnD":false,
-  "name":"artifact_functions",
+  "name":"scr_artifact_functions",
   "parent":{
     "name":"Scripts",
     "path":"folders/Scripts.yy",
diff --git a/scripts/scr_dialogue/scr_dialogue.gml b/scripts/scr_dialogue/scr_dialogue.gml
index afdb0a2c5e..ca9c4dfe58 100644
--- a/scripts/scr_dialogue/scr_dialogue.gml
+++ b/scripts/scr_dialogue/scr_dialogue.gml
@@ -452,9 +452,7 @@ function scr_dialogue(diplo_keyphrase, data = {}) {
                 }
                 scr_civil_roster(obj_ncombat.battle_loc, obj_ncombat.battle_id, true);
 
-                instance_deactivate_all(true);
-                instance_activate_object(obj_controller);
-                instance_activate_object(obj_ini);
+                instance_deactivate_all_safe();
                 instance_activate_object(obj_temp_meeting);
                 instance_activate_object(obj_ncombat);
                 instance_activate_object(obj_centerline);
diff --git a/scripts/scr_drop_select_function/scr_drop_select_function.gml b/scripts/scr_drop_select_function/scr_drop_select_function.gml
index bf88902bff..f68ce53f45 100644
--- a/scripts/scr_drop_select_function/scr_drop_select_function.gml
+++ b/scripts/scr_drop_select_function/scr_drop_select_function.gml
@@ -228,9 +228,7 @@ function drop_select_unit_selection() {
                 obj_controller.last_raid_form = formation_possible[formation_current];
             }
 
-            instance_deactivate_all(true);
-            instance_activate_object(obj_controller);
-            instance_activate_object(obj_ini);
+            instance_deactivate_all_safe();
             instance_activate_object(obj_drop_select);
 
             // 135 ; temporary balancing
diff --git a/scripts/scr_inquisition_mission/scr_inquisition_mission.gml b/scripts/scr_inquisition_mission/scr_inquisition_mission.gml
index 970edeae0c..8d265d0714 100644
--- a/scripts/scr_inquisition_mission/scr_inquisition_mission.gml
+++ b/scripts/scr_inquisition_mission/scr_inquisition_mission.gml
@@ -786,9 +786,7 @@ function necron_tomb_mission_sequence() {
     }
 
     if (battle > 0) {
-        instance_deactivate_all(true);
-        instance_activate_object(obj_controller);
-        instance_activate_object(obj_ini);
+        instance_deactivate_all_safe();
         instance_activate_object(obj_star);
 
         instance_create(0, 0, obj_ncombat);
diff --git a/scripts/instance_create/instance_create.gml b/scripts/scr_instance_functions/scr_instance_functions.gml
similarity index 64%
rename from scripts/instance_create/instance_create.gml
rename to scripts/scr_instance_functions/scr_instance_functions.gml
index 89d7c8b462..2aa77c974d 100644
--- a/scripts/instance_create/instance_create.gml
+++ b/scripts/scr_instance_functions/scr_instance_functions.gml
@@ -23,3 +23,16 @@ function instances_exist_any(instance_set = []) {
     }
     return _exists;
 }
+
+/// @desc Deactivates all instances but preserves critical infrastructure workers.
+function instance_deactivate_all_safe() {
+    instance_deactivate_all(true);
+    instance_activate_object(__github_worker);
+    instance_activate_object(obj_persistent);
+    instance_activate_object(obj_garbage_collector);
+    instance_activate_object(obj_img);
+    instance_activate_object(obj_controller);
+    instance_activate_object(obj_ini);
+    instance_activate_object(obj_cursor);
+    instance_activate_object(obj_timer);
+}
diff --git a/scripts/scr_instance_functions/scr_instance_functions.yy b/scripts/scr_instance_functions/scr_instance_functions.yy
new file mode 100644
index 0000000000..603bfd03b4
--- /dev/null
+++ b/scripts/scr_instance_functions/scr_instance_functions.yy
@@ -0,0 +1,13 @@
+{
+  "$GMScript":"v1",
+  "%Name":"scr_instance_functions",
+  "isCompatibility":false,
+  "isDnD":false,
+  "name":"scr_instance_functions",
+  "parent":{
+    "name":"Global Functions",
+    "path":"folders/Scripts/Global Functions.yy",
+  },
+  "resourceType":"GMScript",
+  "resourceVersion":"2.0",
+}
\ No newline at end of file
diff --git a/scripts/scr_purge_world/scr_purge_world.gml b/scripts/scr_purge_world/scr_purge_world.gml
index 698e58142b..d1f7bdeef7 100644
--- a/scripts/scr_purge_world/scr_purge_world.gml
+++ b/scripts/scr_purge_world/scr_purge_world.gml
@@ -178,9 +178,7 @@ function scr_purge_world(action_type, action_score) {
                 obj_controller.cooldown = 30;
                 combating = 1; // Start battle here
 
-                instance_deactivate_all(true);
-                instance_activate_object(obj_controller);
-                instance_activate_object(obj_ini);
+                instance_deactivate_all_safe();
                 instance_activate_object(obj_drop_select);
 
                 instance_create(0, 0, obj_ncombat);