diff --git a/lib/modules.nix b/lib/modules.nix
index 2468b6fbdd22f..ee1aa16dbb04e 100644
--- a/lib/modules.nix
+++ b/lib/modules.nix
@@ -101,9 +101,31 @@ rec {
                   check ? true
                 }:
     let
+      withWarnings = x:
+        lib.warnIf (evalModulesArgs?args) "The args argument to evalModules is deprecated. Please set config._module.args instead."
+        lib.warnIf (evalModulesArgs?check) "The check argument to evalModules is deprecated. Please set config._module.check instead."
+        x;
+
+      legacyModules =
+        optional (evalModulesArgs?args) {
+          config = {
+            _module.args = args;
+          };
+        }
+        ++ optional (evalModulesArgs?check) {
+          config = {
+            _module.check = mkDefault check;
+          };
+        };
+      regularModules = modules ++ legacyModules;
+
       # This internal module declare internal options under the `_module'
       # attribute.  These options are fragile, as they are used by the
       # module system to change the interpretation of modules.
+      #
+      # When extended with extendModules or moduleType, a fresh instance of
+      # this module is used, to avoid conflicts and allow chaining of
+      # extendModules.
       internalModule = rec {
         _file = ./modules.nix;
 
@@ -125,7 +147,7 @@ rec {
           _module.check = mkOption {
             type = types.bool;
             internal = true;
-            default = check;
+            default = true;
             description = "Whether to check whether all option definitions have matching declarations.";
           };
 
@@ -151,14 +173,14 @@ rec {
           _module.args = {
             inherit extendModules;
             moduleType = type;
-          } // args;
+          };
         };
       };
 
       merged =
         let collected = collectModules
           (specialArgs.modulesPath or "")
-          (modules ++ [ internalModule ])
+          (regularModules ++ [ internalModule ])
           ({ inherit lib options config specialArgs; } // specialArgs);
         in mergeModules prefix (reverseList collected);
 
@@ -222,7 +244,7 @@ rec {
         prefix ? [],
         }:
           evalModules (evalModulesArgs // {
-            modules = evalModulesArgs.modules ++ modules;
+            modules = regularModules ++ modules;
             specialArgs = evalModulesArgs.specialArgs or {} // specialArgs;
             prefix = extendArgs.prefix or evalModulesArgs.prefix;
           });
@@ -231,7 +253,7 @@ rec {
         inherit modules specialArgs;
       };
 
-      result = {
+      result = withWarnings {
         options = checked options;
         config = checked (removeAttrs config [ "_module" ]);
         _module = checked (config._module);
diff --git a/nixos/lib/eval-config.nix b/nixos/lib/eval-config.nix
index 74b52daa3c8eb..d4567409f4015 100644
--- a/nixos/lib/eval-config.nix
+++ b/nixos/lib/eval-config.nix
@@ -8,6 +8,7 @@
 # as subcomponents (e.g. the container feature, or nixops if network
 # expressions are ever made modular at the top level) can just use
 # types.submodule instead of using eval-config.nix
+evalConfigArgs@
 { # !!! system can be set modularly, would be nice to remove
   system ? builtins.currentSystem
 , # !!! is this argument needed any more? The pkgs argument can
@@ -28,7 +29,7 @@
                  in if e == "" then [] else [(import e)]
 }:
 
-let extraArgs_ = extraArgs; pkgs_ = pkgs;
+let pkgs_ = pkgs;
 in
 
 let
@@ -51,28 +52,49 @@ let
     };
   };
 
-  noUserModules = lib.evalModules {
-    inherit prefix check;
-    modules = baseModules ++ extraModules ++ [ pkgsModule ];
-    args = extraArgs;
+  withWarnings = x:
+    lib.warnIf (evalConfigArgs?args) "The extraArgs argument to eval-config.nix is deprecated. Please set config._module.args instead."
+    lib.warnIf (evalConfigArgs?check) "The check argument to eval-config.nix is deprecated. Please set config._module.check instead."
+    x;
+
+  legacyModules =
+    lib.optional (evalConfigArgs?args) {
+      config = {
+        _module.args = extraArgs;
+      };
+    }
+    ++ lib.optional (evalConfigArgs?check) {
+      config = {
+        _module.check = lib.mkDefault check;
+      };
+    };
+  allUserModules = modules ++ legacyModules;
+
+  noUserModules = lib.evalModules ({
+    inherit prefix;
+    modules = baseModules ++ extraModules ++ [ pkgsModule modulesModule ];
     specialArgs =
       { modulesPath = builtins.toString ../modules; } // specialArgs;
-  };
+  });
 
-  # These are the extra arguments passed to every module.  In
-  # particular, Nixpkgs is passed through the "pkgs" argument.
-  extraArgs = extraArgs_ // {
-    inherit noUserModules baseModules extraModules modules;
+  # Extra arguments that are useful for constructing a similar configuration.
+  modulesModule = {
+    config = {
+      _module.args = {
+        inherit noUserModules baseModules extraModules modules;
+      };
+    };
   };
 
-in rec {
+  nixosWithUserModules = noUserModules.extendModules { modules = allUserModules; };
+
+in withWarnings {
 
   # Merge the option definitions in all modules, forming the full
   # system configuration.
-  inherit (noUserModules.extendModules { inherit modules; })
-    config options _module type;
+  inherit (nixosWithUserModules) config options _module type;
 
   inherit extraArgs;
 
-  inherit (_module.args) pkgs;
+  inherit (nixosWithUserModules._module.args) pkgs;
 }
diff --git a/nixos/modules/misc/documentation.nix b/nixos/modules/misc/documentation.nix
index 1f837f9efa22d..64b1c15086fc8 100644
--- a/nixos/modules/misc/documentation.nix
+++ b/nixos/modules/misc/documentation.nix
@@ -1,4 +1,4 @@
-{ config, lib, pkgs, baseModules, extraModules, modules, modulesPath, ... }:
+{ config, lib, pkgs, extendModules, noUserModules, ... }:
 
 with lib;
 
@@ -6,11 +6,8 @@ let
 
   cfg = config.documentation;
 
-  manualModules =
-    baseModules
-    # Modules for which to show options even when not imported
-    ++ [ ../virtualisation/qemu-vm.nix ]
-    ++ optionals cfg.nixos.includeAllModules (extraModules ++ modules);
+  /* Modules for which to show options even when not imported. */
+  extraDocModules = [ ../virtualisation/qemu-vm.nix ];
 
   /* For the purpose of generating docs, evaluate options with each derivation
     in `pkgs` (recursively) replaced by a fake with path "\${pkgs.attribute.path}".
@@ -24,13 +21,10 @@ let
     extraSources = cfg.nixos.extraModuleSources;
     options =
       let
-        scrubbedEval = evalModules {
-          modules = [ { nixpkgs.localSystem = config.nixpkgs.localSystem; } ] ++ manualModules;
-          args = (config._module.args) // { modules = [ ]; };
-          specialArgs = {
-            pkgs = scrubDerivations "pkgs" pkgs;
-            inherit modulesPath;
-          };
+        extendNixOS = if cfg.nixos.includeAllModules then extendModules else noUserModules.extendModules;
+        scrubbedEval = extendNixOS {
+          modules = extraDocModules;
+          specialArgs.pkgs = scrubDerivations "pkgs" pkgs;
         };
         scrubDerivations = namePrefix: pkgSet: mapAttrs
           (name: value: