wrapPackage: move "$@" from template into default args

Instead of hardcoding "$@" in the wrapper template, include it in the
default args list. The template no longer appends "$@" on its own.

This means passing explicit args to wrapPackage gives full control
over whether "$@" is included. The default args (from flags) still
append "$@" for backward compatibility.

Removes the custom wrapper function override from wrapper.nix since
wrapPackage's template no longer conflicts with the module's "$@"
injection.

Add CHANGELOG documenting breaking changes.

Author: Lassulus

CHANGELOG.md

@@ -0,0 +1,28 @@
+# Changelog
+
+## Unreleased
+
+### Breaking changes
+
+- `wrapPackage`: when passing explicit `args`, `"$@"` is no longer
+  appended automatically by the wrapper template. If you pass custom
+  `args` and want passthrough, include `"$@"` in your args list.
+  The default `args` (generated from `flags`) still includes `"$@"`.
+
+- `flagSeparator` default changed from `" "` to `null`. The old `" "`
+  default was misleading: it produced separate argv entries, not a
+  space-joined arg. `null` now means separate argv entries. If you
+  were explicitly passing `flagSeparator = " "` to get separate args,
+  remove it (or change to `null`).
+
+### Added
+
+- `lib/modules/command.nix`: base module with shared command spec
+  (args, env, hooks, exePath) used by both wrapper and systemd outputs.
+- `lib/modules/flags.nix`: flags module with per-flag ordering via
+  `{ value, order }` submodules. Default order is 1000. Reading
+  `config.flags` returns clean values (order is transparent).
+- `wrapper.nix` injects `"$@"` into args at order 1001, controllable
+  via the ordering system.
+- `outputs.wrapper` as the canonical output path (config.wrapper is
+  a backward-compatible alias).

lib/default.nix

@@ -451,7 +451,7 @@ let
       flags ? { },
       flagSeparator ? null,
       # null for "--flag" "value" (separate args) or "=" for "--flag=value"
-      args ? generateArgsFromFlags flags flagSeparator,
+      args ? generateArgsFromFlags flags flagSeparator ++ [ "$@" ],
       preHook ? "",
       postHook ? "",
       passthru ? { },
@@ -473,7 +473,7 @@ let
         ''
           ${envString}
           ${preHook}
-          ${lib.optionalString (postHook == "") "exec"} ${exePath}${flagsString} "$@"
+          ${lib.optionalString (postHook == "") "exec"} ${exePath}${flagsString}
           ${postHook}
         ''
       ),

lib/modules/wrapper.nix

@@ -65,22 +65,6 @@
         configuration = config;
       }
       // config.passthru;
-      # Custom wrapper function: "$@" is already in args, so don't add it again
-      wrapper =
-        {
-          exePath,
-          flagsString,
-          envString,
-          preHook,
-          postHook,
-          ...
-        }:
-        ''
-          ${envString}
-          ${preHook}
-          ${lib.optionalString (postHook == "") "exec"} ${exePath}${flagsString}
-          ${postHook}
-        '';
     };
   };
   options.wrapper = lib.mkOption {