diff --git a/README.md b/README.md
index 4ff6e55..0848373 100644
--- a/README.md
+++ b/README.md
@@ -102,7 +102,7 @@ Then import your module in your main source file.
 import decman
 from syncthing import Syncthing
 
-decman.modules |= {Syncthing()}
+decman.modules += [Syncthing()]
 ```
 
 Then run decman.
diff --git a/docs/README.md b/docs/README.md
index 024e1b8..062dd97 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -7,6 +7,8 @@ This contains the documentation for decman. Each plugin has its own documentatio
 - [aur](/docs/aur.md)
 - [flatpak](/docs/flatpak.md)
 
+Check out [extras](docs/extras.md) for documentation for built-in modules.
+
 ## Quick notes
 
 "Decman source" or "source" refers to your system configuration. It is set using the `--source` command line argument with decman.
@@ -210,11 +212,11 @@ A **Module** is the primary unit for grouping related files, directories, packag
 
 Each module is uniquely identified by its `name`.
 
-Remember to add modules to decman.
+Remember to add modules to decman. Modules are added to a list to preserve deterministic execution order for hooks.
 
 ```py
 import decman
-decman.modules |= {MyModule()}
+decman.modules += [MyModule()]
 ```
 
 ### Basic Structure
@@ -418,7 +420,7 @@ This method only gathers information. It doesn't apply it.
 ```py
 from decman import Store, Module
 
-def process_modules(self, store: Store, modules: set[Module]):
+def process_modules(self, store: Store, modules: list[Module]):
     ...
 
     # Toy example for setting modules as changed
diff --git a/docs/aur.md b/docs/aur.md
index aa2d069..2ba3da8 100644
--- a/docs/aur.md
+++ b/docs/aur.md
@@ -79,6 +79,11 @@ class MyModule(decman.Module):
 
 If these sets change, this plugin will flag the module as changed. The module's `on_change` method will be executed.
 
+## Keys used in the decman store
+
+- `aur_packages_for_module`
+- `custom_packages_for_module`
+
 ## Configuration
 
 This module has partially the same configuration with pacman. You'll have to define pacman output keywords and database options again.
diff --git a/docs/flatpak.md b/docs/flatpak.md
index 331c688..25f621f 100644
--- a/docs/flatpak.md
+++ b/docs/flatpak.md
@@ -47,6 +47,11 @@ class MyModule(decman.Module):
 
 If packages or user packages change, this plugin will flag the module as changed. The module's `on_change` method will be executed.
 
+## Keys used in the decman store
+
+- `flatpaks_for_module`
+- `user_flatpaks_for_module`
+
 ## Configuration
 
 It's possible to override the commands this plugin uses. Create your own `FlatpakCommands` class and override methods returning commands. These are the defaults.
diff --git a/docs/migrate-to-v1.md b/docs/migrate-to-v1.md
index ebbec13..5df6625 100644
--- a/docs/migrate-to-v1.md
+++ b/docs/migrate-to-v1.md
@@ -232,8 +232,6 @@ class MyModule(Module):
 
 #### New
 
-`decman.modules` is now a set instead of a list. If you wish to have multiple instances of the same module class, just name them differently. Name needs to be unique accross modules.
-
 Modules no longer have `version`s or `enabled` values. A module is enabled when it gets added to `decman.modules` and disabled when it gets removed from `decman.modules`. Versions are no longer needed because `after_version_change` has been removed and `on_change` has been added. `on_change` is executed automatically after the content of the module changes. `on_disable` will be executed automatically when the module is removed from `decman.modules`. It is no longer a instance method. Instead it must be a self-contained method with no references outside it. Not even imports.
 
 Module methods will get a `Store` instance passed to them as an argument. It can be used to store key-value pairs between decman runs.
@@ -245,7 +243,7 @@ import decman
 from decman import Module, Store, prg, sh
 from decman.plugins import pacman, aur, systemd, flatpak
 
-decman.modules |= {MyModule()}
+decman.modules += [MyModule()]
 
 class MyModule(Module):
     def __init__(self):
diff --git a/docs/pacman.md b/docs/pacman.md
index 4a57905..9a81017 100644
--- a/docs/pacman.md
+++ b/docs/pacman.md
@@ -42,6 +42,10 @@ class MyModule(decman.Module):
 
 If this set changes, this plugin will flag the module as changed. The module's `on_change` method will be executed.
 
+## Keys used in the decman store
+
+- `packages_for_module`
+
 ## Configuration
 
 This plugin has a pacman output highlight function. If pacman output contains some keywords, it will be highlighted. You can disable this feature or set the keywords.
diff --git a/docs/systemd.md b/docs/systemd.md
index 6234a5f..d945cf3 100644
--- a/docs/systemd.md
+++ b/docs/systemd.md
@@ -45,6 +45,11 @@ class MyModule(decman.Module):
 
 If units or user units change, this plugin will flag the module as changed. The module's `on_change` method will be executed.
 
+## Keys used in the decman store
+
+- `systemd_units_for_module`
+- `systemd_user_units_for_module`
+
 ## Configuration
 
 It's possible to override the commands this plugin uses. Create your own `SystemdCommands` class and override methods returning commands. These are the defaults.
diff --git a/example/README.md b/example/README.md
index 80be67c..c837d2d 100644
--- a/example/README.md
+++ b/example/README.md
@@ -85,7 +85,7 @@ import decman
 from base import BaseModule
 
 decman.pacman.packages |= {"openssh", "qemu-guest-agent", "sudo", "vim"}
-decman.modules |= {BaseModule()}
+decman.modules += [BaseModule()]
 ```
 
 This config is already enough to run decman for the first time.
@@ -162,7 +162,7 @@ from kde import KDE
 
 ...
 
-decman.modules |= {BaseModule(), KDE()}
+decman.modules += [BaseModule(), KDE()]
 ```
 
 I'll run decman once again. I'll also start SDDM manually, since decman can't autostart it.
diff --git a/example/plugin/decman_plugin_example.py b/example/plugin/decman_plugin_example.py
index 2381664..cf39aac 100644
--- a/example/plugin/decman_plugin_example.py
+++ b/example/plugin/decman_plugin_example.py
@@ -9,7 +9,7 @@ class Example(decman.Plugin):
     def available(self) -> bool:
         return os.path.exists("/tmp/example_plugin_available")
 
-    def process_modules(self, store: decman.Store, modules: set[decman.Module]):
+    def process_modules(self, store: decman.Store, modules: list[decman.Module]):
         # Toy example for setting modules as changed
         for module in modules:
             module._changed = True
diff --git a/example/source.py b/example/source.py
index 049e185..70a79b4 100644
--- a/example/source.py
+++ b/example/source.py
@@ -5,7 +5,7 @@ import decman
 
 decman.pacman.packages |= {"openssh", "qemu-guest-agent", "sudo", "vim"}
 
-decman.modules |= {BaseModule(), KDE()}
+decman.modules += [BaseModule(), KDE()]
 
 decman.files["/home/arch/.vimrc"] = decman.File(
     source_file="./files/vimrc", owner="arch", permissions=0o600
diff --git a/plugins/decman-flatpak/src/decman/plugins/flatpak.py b/plugins/decman-flatpak/src/decman/plugins/flatpak.py
index 0bfa0b8..1a9fa01 100644
--- a/plugins/decman-flatpak/src/decman/plugins/flatpak.py
+++ b/plugins/decman-flatpak/src/decman/plugins/flatpak.py
@@ -46,7 +46,7 @@ class Flatpak(plugins.Plugin):
     def available(self) -> bool:
         return shutil.which("flatpak") is not None
 
-    def process_modules(self, store: _store.Store, modules: set[module.Module]):
+    def process_modules(self, store: _store.Store, modules: list[module.Module]):
         # These store keys are used to track changes in modules.
         # This way when these change, module can be marked as changed
         store.ensure("flatpaks_for_module", {})
diff --git a/plugins/decman-pacman/src/decman/plugins/aur/__init__.py b/plugins/decman-pacman/src/decman/plugins/aur/__init__.py
index 9f04737..848529a 100644
--- a/plugins/decman-pacman/src/decman/plugins/aur/__init__.py
+++ b/plugins/decman-pacman/src/decman/plugins/aur/__init__.py
@@ -90,7 +90,7 @@ class AUR(plugins.Plugin):
             and shutil.which("mkarchroot") is not None
         )
 
-    def process_modules(self, store: _store.Store, modules: set[module.Module]):
+    def process_modules(self, store: _store.Store, modules: list[module.Module]):
         # This is used to track changes in modules.
         store.ensure("aur_packages_for_module", {})
         store.ensure("custom_packages_for_module", {})
diff --git a/plugins/decman-pacman/src/decman/plugins/pacman.py b/plugins/decman-pacman/src/decman/plugins/pacman.py
index 0ec77bd..894ec73 100644
--- a/plugins/decman-pacman/src/decman/plugins/pacman.py
+++ b/plugins/decman-pacman/src/decman/plugins/pacman.py
@@ -58,7 +58,7 @@ class Pacman(plugins.Plugin):
     def available(self) -> bool:
         return shutil.which("pacman") is not None
 
-    def process_modules(self, store: _store.Store, modules: set[module.Module]):
+    def process_modules(self, store: _store.Store, modules: list[module.Module]):
         # This is used to track changes in modules.
         store.ensure("packages_for_module", {})
 
diff --git a/plugins/decman-systemd/src/decman/plugins/systemd.py b/plugins/decman-systemd/src/decman/plugins/systemd.py
index 143a406..bad2351 100644
--- a/plugins/decman-systemd/src/decman/plugins/systemd.py
+++ b/plugins/decman-systemd/src/decman/plugins/systemd.py
@@ -83,7 +83,7 @@ class Systemd(plugins.Plugin):
     def available(self) -> bool:
         return shutil.which("systemctl") is not None
 
-    def process_modules(self, store: _store.Store, modules: set[module.Module]):
+    def process_modules(self, store: _store.Store, modules: list[module.Module]):
         # These store keys are used to track changes in modules.
         # This way when these change, module can be marked as changed
         store.ensure("systemd_units_for_module", {})
diff --git a/src/decman/__init__.py b/src/decman/__init__.py
index bebb7b0..db70810 100644
--- a/src/decman/__init__.py
+++ b/src/decman/__init__.py
@@ -63,7 +63,7 @@ __all__ = [
 # -----------------------------------------
 files: dict[str, File] = {}
 directories: dict[str, Directory] = {}
-modules: set[Module] = set()
+modules: list[Module] = []
 execution_order: list[str] = [
     "files",
     "pacman",
diff --git a/src/decman/core/file_manager.py b/src/decman/core/file_manager.py
index 0241f0a..9d5bd99 100644
--- a/src/decman/core/file_manager.py
+++ b/src/decman/core/file_manager.py
@@ -10,7 +10,7 @@ import decman.core.store as _store
 
 def update_files(
     store: _store.Store,
-    modules: set[module.Module],
+    modules: list[module.Module],
     files: dict[str, fs.File],
     directories: dict[str, fs.Directory],
     dry_run: bool = False,
diff --git a/src/decman/core/store.py b/src/decman/core/store.py
index 4ab0b77..58e4aeb 100644
--- a/src/decman/core/store.py
+++ b/src/decman/core/store.py
@@ -74,5 +74,14 @@ class _SetJSONEncoder(json.JSONEncoder):
 
 def _decode_sets(obj: typing.Any) -> typing.Any:
     if isinstance(obj, dict) and obj.get("__type__") == "set" and "items" in obj:
-        return set(obj["items"])
+        # decode lists inside sets as tuples
+        norm = []
+
+        for item in obj["items"]:
+            if isinstance(item, list):
+                norm.append(tuple(item))
+            else:
+                norm.append(item)
+
+        return set(norm)
     return obj
diff --git a/src/decman/plugins/__init__.py b/src/decman/plugins/__init__.py
index e264087..bdfb1cc 100644
--- a/src/decman/plugins/__init__.py
+++ b/src/decman/plugins/__init__.py
@@ -40,7 +40,7 @@ class Plugin:
         """
         return True
 
-    def process_modules(self, store: _store.Store, modules: set[module.Module]):
+    def process_modules(self, store: _store.Store, modules: list[module.Module]):
         """
         Processes a module.
         """