DEBUG!!! clan-core-for-checks = self

This reverts commit 46f746d09c.

checks/flake-module.nix

@@ -2,7 +2,6 @@
   self,
   lib,
   inputs,
-  privateInputs ? { },
   ...
 }:
 let
@@ -129,7 +128,7 @@ in
         // flakeOutputs
         // {
           clan-core-for-checks = pkgs.runCommand "clan-core-for-checks" { } ''
-            cp -r ${privateInputs.clan-core-for-checks} $out
+            cp -r ${self} $out
             chmod -R +w $out
             cp ${../flake.lock} $out/flake.lock
 

clanServices/coredns/tests/vm/default.nix

@@ -50,13 +50,13 @@
     dns =
       { pkgs, ... }:
       {
-        environment.systemPackages = [ pkgs.net-tools ];
+        environment.systemPackages = [ pkgs.nettools ];
       };
 
     client =
       { pkgs, ... }:
       {
-        environment.systemPackages = [ pkgs.net-tools ];
+        environment.systemPackages = [ pkgs.nettools ];
       };
 
     server01 = {

clanServices/sshd/README.md

@@ -1,91 +1,39 @@
-# Clan service: sshd
+The `sshd` Clan service manages SSH to make it easy to securely access your
-What it does
+machines over the internet. The service uses `vars` to store the SSH host keys
-- Generates and persists SSH host keys via `vars`.
+for each machine to ensure they remain stable across deployments.
-- Optionally issues CA‑signed host certificates for servers.
-- Installs the `server` CA public key into `clients` `known_hosts` for TOFU‑less verification.
 
+`sshd` also generates SSH certificates for both servers and clients allowing for
+certificate-based authentication for SSH.
 
-When to use it
+The service also disables password-based authentication over SSH, to access your
-- Zero‑TOFU SSH for dynamic fleets: admins/CI can connect to frequently rebuilt hosts (e.g., server-1.example.com) without prompts or per‑host `known_hosts` churn.
+machines you'll need to use public key authentication or certificate-based
+authentication.
 
-Roles
+## Usage
-- Server: runs sshd, presents a CA‑signed host certificate for `<machine>.<domain>`.
-- Client: trusts the CA for the given domains to verify servers’ certificates.
-  Tip: assign both roles to a machine if it should both present a cert and verify others.
-
-Quick start (with host certificates)
-Useful if you never want to get a prompt about trusting the ssh fingerprint.
-```nix
-{
-  inventory.instances = {
-    sshd-with-certs = {
-      module = { name = "sshd"; input = "clan-core"; };
-      # Servers present certificates for <machine>.example.com
-      roles.server.tags.all = { };
-      roles.server.settings = {
-        certificate.searchDomains = [ "example.com" ];
-        # Optional: also add RSA host keys
-        # hostKeys.rsa.enable = true;
-      };
-      # Clients trust the CA for *.example.com
-      roles.client.tags.all = { };
-      roles.client.settings = {
-        certificate.searchDomains = [ "example.com" ];
-      };
-    };
-  };
-}
-```
-
-Basic: only add persistent host keys (ed25519), no certificates
-Useful if you want to get an ssh "trust this server" prompt once and then never again. 
 ```nix
 {
   inventory.instances = {
+    # By default this service only generates ed25519 host keys
     sshd-basic = {
       module = {
         name = "sshd";
         input = "clan-core";
       };
       roles.server.tags.all = { };
+      roles.client.tags.all = { };
     };
-  };
+    # Also generate RSA host keys for all servers
-}
+    sshd-with-rsa = {
-```
+      module = {
-
+        name = "sshd";
-Example: selective trust per environment
+        input = "clan-core";
-Admins should trust only production; CI should trust prod and staging. Servers are reachable under both domains.
+      };
-```nix
-{
-  inventory.instances = {
-    sshd-env-scoped = {
-      module = { name = "sshd"; input = "clan-core"; };
-
-      # Servers present certs for both prod and staging FQDNs
       roles.server.tags.all = { };
       roles.server.settings = {
-        certificate.searchDomains = [ "prod.example.com" "staging.example.com" ];
+        hostKeys.rsa.enable = true;
-      };
-
-      # Admin laptop: trust prod only
-      roles.client.machines."admin-laptop".settings = {
-        certificate.searchDomains = [ "prod.example.com" ];
-      };
-
-      # CI runner: trust prod and staging
-      roles.client.machines."ci-runner-1".settings = {
-        certificate.searchDomains = [ "prod.example.com" "staging.example.com" ];
       };
+      roles.client.tags.all = { };
     };
   };
 }
 ```
-- Admin -> server1.prod.example.com: zero‑TOFU (verified via cert).
-- Admin -> server1.staging.example.com: falls back to TOFU (or is blocked by policy).
-- CI -> either prod or staging: zero‑TOFU for both.
-Note: server and client searchDomains don’t have to be identical; they only need to overlap for the hostnames you actually use.
-
-Notes
-- Connect using a name that matches a cert principal (e.g., `server1.example.com`); wildcards are not allowed inside the certificate.
-- CA private key stays in `vars` (not deployed); only the CA public key is distributed.
-- Logins still require your user SSH keys on the server (passwords are disabled).

clanServices/syncthing/vars.nix

@@ -11,9 +11,7 @@
       pkgs.syncthing
     ];
     script = ''
-      export TMPDIR=/tmp
+      syncthing generate --config "$out"
-      TEMPORARY=$(mktemp -d)
-      syncthing generate --config "$out" --data "$TEMPORARY"
       mv "$out"/key.pem "$out"/key
       mv "$out"/cert.pem "$out"/cert
       cat "$out"/config.xml | grep -oP '(?<=<device id=")[^"]+' | uniq > "$out"/id

devFlake/flake.lock

@@ -3,16 +3,16 @@
     "clan-core-for-checks": {
       "flake": false,
       "locked": {
-        "lastModified": 1760213549,
+        "lastModified": 1760368011,
-        "narHash": "sha256-XosVRUEcdsoEdRtXyz9HrRc4Dt9Ke+viM5OVF7tLK50=",
+        "narHash": "sha256-mLK2nwbfklfOGIVAKVNDwGyYz8mPh4fzsAqSK3BlCiI=",
-        "ref": "main",
+        "ref": "clan-25.05",
-        "rev": "9c8797e77031d8d472d057894f18a53bdc9bbe1e",
+        "rev": "1b3c129aa9741d99b27810652ca888b3fbfc3a11",
         "shallow": true,
         "type": "git",
         "url": "https://git.clan.lol/clan/clan-core"
       },
       "original": {
-        "ref": "main",
+        "ref": "clan-25.05",
         "shallow": true,
         "type": "git",
         "url": "https://git.clan.lol/clan/clan-core"
@@ -105,16 +105,16 @@
     },
     "nixpkgs-dev": {
       "locked": {
-        "lastModified": 1760161054,
+        "lastModified": 1760309387,
-        "narHash": "sha256-PO3cKHFIQEPI0dr/SzcZwG50cHXfjoIqP2uS5W78OXg=",
+        "narHash": "sha256-e0lvQ7+B1Y8zjykYHAj9tBv10ggLqK0nmxwvMU3J0Eo=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "e18d8ec6fafaed55561b7a1b54eb1c1ce3ffa2c5",
+        "rev": "6cd95994a9c8f7c6f8c1f1161be94119afdcb305",
         "type": "github"
       },
       "original": {
         "owner": "NixOS",
-        "ref": "nixos-unstable-small",
+        "ref": "nixos-25.05-small",
         "repo": "nixpkgs",
         "type": "github"
       }

devFlake/flake.nix

@@ -2,7 +2,7 @@
   description = "private dev inputs";
 
   # Dev dependencies
-  inputs.nixpkgs-dev.url = "github:NixOS/nixpkgs/nixos-unstable-small";
+  inputs.nixpkgs-dev.url = "github:NixOS/nixpkgs/nixos-25.05-small";
 
   inputs.flake-utils.url = "github:numtide/flake-utils";
   inputs.flake-utils.inputs.systems.follows = "systems";
@@ -15,7 +15,7 @@
 
   inputs.systems.url = "github:nix-systems/default";
 
-  inputs.clan-core-for-checks.url = "git+https://git.clan.lol/clan/clan-core?ref=main&shallow=1";
+  inputs.clan-core-for-checks.url = "git+https://git.clan.lol/clan/clan-core?ref=clan-25.05&shallow=1";
   inputs.clan-core-for-checks.flake = false;
 
   inputs.test-fixtures.url = "git+https://git.clan.lol/clan/test-fixtures";

flake.lock

@@ -71,15 +71,16 @@
         ]
       },
       "locked": {
-        "lastModified": 1758805352,
+        "lastModified": 1759509947,
-        "narHash": "sha256-BHdc43Lkayd+72W/NXRKHzX5AZ+28F3xaUs3a88/Uew=",
+        "narHash": "sha256-4XifSIHfpJKcCf5bZZRhj8C4aCpjNBaE3kXr02s4rHU=",
         "owner": "nix-darwin",
         "repo": "nix-darwin",
-        "rev": "c48e963a5558eb1c3827d59d21c5193622a1477c",
+        "rev": "000eadb231812ad6ea6aebd7526974aaf4e79355",
         "type": "github"
       },
       "original": {
         "owner": "nix-darwin",
+        "ref": "nix-darwin-25.05",
         "repo": "nix-darwin",
         "type": "github"
       }
@@ -114,15 +115,15 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 315532800,
+        "lastModified": 1760324802,
-        "narHash": "sha256-1tUpklZsKzMGI3gjo/dWD+hS8cf+5Jji8TF5Cfz7i3I=",
+        "narHash": "sha256-VWlJtLQ5EQQj45Wj0yTExtSjwRyZ59/qMqEwus/Exlg=",
-        "rev": "08b8f92ac6354983f5382124fef6006cade4a1c1",
+        "rev": "7e297ddff44a3cc93673bb38d0374df8d0ad73e4",
         "type": "tarball",
-        "url": "https://releases.nixos.org/nixpkgs/nixpkgs-25.11pre862603.08b8f92ac635/nixexprs.tar.xz"
+        "url": "https://releases.nixos.org/nixos/25.05/nixos-25.05.811135.7e297ddff44a/nixexprs.tar.xz"
       },
       "original": {
         "type": "tarball",
-        "url": "https://nixos.org/channels/nixpkgs-unstable/nixexprs.tar.xz"
+        "url": "https://nixos.org/channels/nixos-25.05/nixexprs.tar.xz"
       }
     },
     "root": {

flake.nix

@@ -2,9 +2,9 @@
   description = "clan.lol base operating system";
 
   inputs = {
-    nixpkgs.url = "https://nixos.org/channels/nixpkgs-unstable/nixexprs.tar.xz";
+    nixpkgs.url = "https://nixos.org/channels/nixos-25.05/nixexprs.tar.xz";
 
-    nix-darwin.url = "github:nix-darwin/nix-darwin";
+    nix-darwin.url = "github:nix-darwin/nix-darwin/nix-darwin-25.05";
     nix-darwin.inputs.nixpkgs.follows = "nixpkgs";
 
     flake-parts.url = "github:hercules-ci/flake-parts";

formatter.nix

@@ -11,8 +11,6 @@
       treefmt.programs.nixfmt.enable = true;
       treefmt.programs.nixfmt.package = pkgs.nixfmt-rfc-style;
       treefmt.programs.deadnix.enable = true;
-      treefmt.programs.sizelint.enable = true;
-      treefmt.programs.sizelint.failOnWarn = true;
       treefmt.programs.clang-format.enable = true;
       treefmt.settings.global.excludes = [
         "*.png"

lib/default.nix

@@ -28,7 +28,6 @@ lib.fix (
       # Plain imports.
       introspection = import ./introspection { inherit lib; };
       jsonschema = import ./jsonschema { inherit lib; };
-      facts = import ./facts.nix { inherit lib; };
       docs = import ./docs.nix { inherit lib; };
 
       # flakes

lib/facts.nix

@@ -1,71 +0,0 @@
-{ lib, ... }:
-clanDir:
-let
-
-  allMachineNames = lib.mapAttrsToList (name: _: name) (builtins.readDir clanDir);
-
-  getFactPath = machine: fact: "${clanDir}/machines/${machine}/facts/${fact}";
-
-  readFact =
-    machine: fact:
-    let
-      path = getFactPath machine fact;
-    in
-    if builtins.pathExists path then builtins.readFile path else null;
-
-  # Example:
-  #
-  # readFactFromAllMachines zerotier-ip
-  # => {
-  #   machineA = "1.2.3.4";
-  #   machineB = "5.6.7.8";
-  # };
-  readFactFromAllMachines =
-    fact:
-    let
-      machines = allMachineNames;
-      facts = lib.genAttrs machines (machine: readFact machine fact);
-      filteredFacts = lib.filterAttrs (_machine: fact: fact != null) facts;
-    in
-    filteredFacts;
-
-  # all given facts are are set and factvalues are never null.
-  #
-  # Example:
-  #
-  # readFactsFromAllMachines [ "zerotier-ip" "syncthing.pub" ]
-  # => {
-  #   machineA =
-  #     {
-  #       "zerotier-ip" = "1.2.3.4";
-  #       "synching.pub" = "1234";
-  #     };
-  #   machineB =
-  #     {
-  #       "zerotier-ip" = "5.6.7.8";
-  #       "synching.pub" = "23456719";
-  #     };
-  # };
-  readFactsFromAllMachines =
-    facts:
-    let
-      # machine -> fact -> factvalue
-      machinesFactsAttrs = lib.genAttrs allMachineNames (
-        machine: lib.genAttrs facts (fact: readFact machine fact)
-      );
-      # remove all machines which don't have all facts set
-      filteredMachineFactAttrs = lib.filterAttrs (
-        _machine: values: builtins.all (fact: values.${fact} != null) facts
-      ) machinesFactsAttrs;
-    in
-    filteredMachineFactAttrs;
-in
-{
-  inherit
-    allMachineNames
-    getFactPath
-    readFact
-    readFactFromAllMachines
-    readFactsFromAllMachines
-    ;
-}

pkgs/clan-app/clan_app/api/api_bridge.py

@@ -41,7 +41,7 @@ class ApiBridge(Protocol):
 
     def process_request(self, request: BackendRequest) -> None:
         """Process an API request through the middleware chain."""
-        from clan_app.middleware.base import MiddlewareContext  # noqa: PLC0415
+        from clan_app.middleware.base import MiddlewareContext
 
         with ExitStack() as stack:
             # Capture the current call stack up to this point
@@ -62,7 +62,7 @@ class ApiBridge(Protocol):
                     )
                     middleware.process(context)
                 except Exception as e:
-                    from clan_app.middleware.base import (  # noqa: PLC0415
+                    from clan_app.middleware.base import (
                         MiddlewareError,
                     )
 

pkgs/clan-app/clan_app/backends/http/http_bridge.py

@@ -191,13 +191,13 @@ class HttpBridge(ApiBridge, BaseHTTPRequestHandler):
 
         return file_data
 
-    def do_OPTIONS(self) -> None:
+    def do_OPTIONS(self) -> None:  # noqa: N802
         """Handle CORS preflight requests."""
         self.send_response_only(200)
         self._send_cors_headers()
         self.end_headers()
 
-    def do_GET(self) -> None:
+    def do_GET(self) -> None:  # noqa: N802
         """Handle GET requests."""
         parsed_url = urlparse(self.path)
         path = parsed_url.path
@@ -211,7 +211,7 @@ class HttpBridge(ApiBridge, BaseHTTPRequestHandler):
         else:
             self.send_api_error_response("info", "Not Found", ["http_bridge", "GET"])
 
-    def do_POST(self) -> None:
+    def do_POST(self) -> None:  # noqa: N802
         """Handle POST requests."""
         parsed_url = urlparse(self.path)
         path = parsed_url.path

pkgs/clan-app/clan_app/backends/webview/webview_bridge.py

@@ -34,7 +34,7 @@ class WebviewBridge(ApiBridge):
 
         log.debug(f"Sending response: {serialized}")
         # Import FuncStatus locally to avoid circular import
-        from .webview import FuncStatus  # noqa: PLC0415
+        from .webview import FuncStatus
 
         self.webview.return_(response._op_key, FuncStatus.SUCCESS, serialized)  # noqa: SLF001
 

pkgs/clan-cli/api.py

@@ -9,7 +9,7 @@ def main() -> None:
     load_in_all_api_functions()
 
     # import lazily since we otherwise we do not have all api functions loaded according to Qubasa
-    from clan_lib.api import API  # noqa: PLC0415
+    from clan_lib.api import API
 
     schema = API.to_json_schema()
     print(f"""{json.dumps(schema, indent=2)}""")

pkgs/clan-cli/clan_cli/generate_test_vars/cli.py

@@ -102,7 +102,7 @@ class TestFlake(Flake):
         opts: "ListOptions | None" = None,  # noqa: ARG002
     ) -> "dict[str, MachineResponse]":
         """List machines of a clan"""
-        from clan_lib.machines.actions import (  # noqa: PLC0415
+        from clan_lib.machines.actions import (
             InventoryMachine,
             MachineResponse,
         )

pkgs/clan-cli/clan_cli/secrets/groups.py

@@ -231,7 +231,7 @@ def remove_machine_command(args: argparse.Namespace) -> None:
 
 
 def add_group_argument(parser: argparse.ArgumentParser) -> None:
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_groups,
     )
@@ -334,7 +334,7 @@ def register_groups_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the machines to add",
         type=machine_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
     )
@@ -353,7 +353,7 @@ def register_groups_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the machines to remove",
         type=machine_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
     )
@@ -369,7 +369,7 @@ def register_groups_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the user to add",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )
@@ -388,7 +388,7 @@ def register_groups_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the user to remove",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )
@@ -407,7 +407,7 @@ def register_groups_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the secret",
         type=secret_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_secrets,
     )
@@ -426,7 +426,7 @@ def register_groups_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the secret",
         type=secret_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_secrets,
     )

pkgs/clan-cli/clan_cli/secrets/import_sops.py

@@ -69,7 +69,7 @@ def register_import_sops_parser(parser: argparse.ArgumentParser) -> None:
         default=[],
         help="the group to import the secrets to",
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_groups,
     )
@@ -82,7 +82,7 @@ def register_import_sops_parser(parser: argparse.ArgumentParser) -> None:
         default=[],
         help="the machine to import the secrets to",
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
     )
@@ -95,7 +95,7 @@ def register_import_sops_parser(parser: argparse.ArgumentParser) -> None:
         default=[],
         help="the user to import the secrets to",
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )

pkgs/clan-cli/clan_cli/secrets/machines.py

@@ -172,7 +172,7 @@ def register_machines_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the machine",
         type=machine_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
     )
@@ -192,7 +192,7 @@ def register_machines_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the machine",
         type=machine_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
     )
@@ -207,7 +207,7 @@ def register_machines_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the machine",
         type=machine_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
     )
@@ -225,7 +225,7 @@ def register_machines_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the machine",
         type=machine_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
         complete_secrets,
@@ -250,7 +250,7 @@ def register_machines_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the machine",
         type=machine_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
         complete_secrets,

pkgs/clan-cli/clan_cli/secrets/secrets.py

@@ -255,7 +255,7 @@ def add_secret_argument(parser: argparse.ArgumentParser, autocomplete: bool) ->
         type=secret_name_type,
     )
     if autocomplete:
-        from clan_cli.completions import (  # noqa: PLC0415
+        from clan_cli.completions import (
             add_dynamic_completer,
             complete_secrets,
         )
@@ -467,7 +467,7 @@ def register_secrets_parser(subparser: argparse._SubParsersAction) -> None:
         default=[],
         help="the group to import the secrets to (can be repeated)",
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_groups,
     )
@@ -480,7 +480,7 @@ def register_secrets_parser(subparser: argparse._SubParsersAction) -> None:
         default=[],
         help="the machine to import the secrets to (can be repeated)",
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_machines,
     )
@@ -493,7 +493,7 @@ def register_secrets_parser(subparser: argparse._SubParsersAction) -> None:
         default=[],
         help="the user to import the secrets to (can be repeated)",
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )

pkgs/clan-cli/clan_cli/secrets/users.py

@@ -281,7 +281,7 @@ def register_users_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the user",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )
@@ -295,7 +295,7 @@ def register_users_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the user",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )
@@ -312,7 +312,7 @@ def register_users_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the user",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_secrets,
         complete_users,
@@ -336,7 +336,7 @@ def register_users_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the group",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_secrets,
         complete_users,
@@ -360,7 +360,7 @@ def register_users_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the user",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )
@@ -378,7 +378,7 @@ def register_users_parser(parser: argparse.ArgumentParser) -> None:
         help="the name of the user",
         type=user_name_type,
     )
-    from clan_cli.completions import (  # noqa: PLC0415
+    from clan_cli.completions import (
         add_dynamic_completer,
         complete_users,
     )

pkgs/clan-cli/clan_cli/tests/test_vars.py

@@ -1,5 +1,6 @@
 import json
 import logging
+import os
 import shutil
 import subprocess
 import time
@@ -429,9 +430,43 @@ def test_generated_shared_secret_sops(
     machine1 = Machine(name="machine1", flake=Flake(str(flake.path)))
     machine2 = Machine(name="machine2", flake=Flake(str(flake.path)))
     cli.run(["vars", "generate", "--flake", str(flake.path), "machine1"])
-    assert check_vars(machine1.name, machine1.flake)
+
+    # Get the initial state of the flake directory after generation
+    def get_file_mtimes(path: str) -> dict[str, float]:
+        """Get modification times of all files in a directory tree."""
+        mtimes = {}
+        for root, _dirs, files in os.walk(path):
+            # Skip .git directory
+            if ".git" in root:
+                continue
+            for file in files:
+                filepath = Path(root) / file
+                mtimes[str(filepath)] = filepath.stat().st_mtime
+        return mtimes
+
+    initial_mtimes = get_file_mtimes(str(flake.path))
+
+    # First check_vars should not write anything
+    assert check_vars(machine1.name, machine1.flake), (
+        "machine1 has already generated vars, so check_vars should return True\n"
+        f"Check result:\n{check_vars(machine1.name, machine1.flake)}"
+    )
+    # Verify no files were modified
+    after_check_mtimes = get_file_mtimes(str(flake.path))
+    assert initial_mtimes == after_check_mtimes, (
+        "check_vars should not modify any files when vars are already valid"
+    )
+
+    assert not check_vars(machine2.name, machine2.flake), (
+        "machine2 has not generated vars yet, so check_vars should return False"
+    )
+    # Verify no files were modified
+    after_check_mtimes_2 = get_file_mtimes(str(flake.path))
+    assert initial_mtimes == after_check_mtimes_2, (
+        "check_vars should not modify any files when vars are not valid"
+    )
+
     cli.run(["vars", "generate", "--flake", str(flake.path), "machine2"])
-    assert check_vars(machine2.name, machine2.flake)
     m1_sops_store = sops.SecretStore(machine1.flake)
     m2_sops_store = sops.SecretStore(machine2.flake)
     # Create generators with machine context for testing

pkgs/clan-cli/clan_cli/vars/_types.py

@@ -171,7 +171,7 @@ class StoreBase(ABC):
         if generator.share:
             log_info = log.info
         else:
-            from clan_lib.machines.machines import Machine  # noqa: PLC0415
+            from clan_lib.machines.machines import Machine
 
             machine_obj = Machine(name=generator.machines[0], flake=self.flake)
             log_info = machine_obj.info

pkgs/clan-cli/clan_cli/vars/check.py

@@ -3,6 +3,7 @@ import logging
 from typing import TYPE_CHECKING
 
 from clan_cli.completions import add_dynamic_completer, complete_machines
+from clan_cli.vars.secret_modules import sops
 from clan_lib.errors import ClanError
 from clan_lib.flake import Flake, require_flake
 from clan_lib.machines.machines import Machine
@@ -26,13 +27,33 @@ class VarStatus:
         self.unfixed_secret_vars = unfixed_secret_vars
         self.invalid_generators = invalid_generators
 
+    def text(self) -> str:
+        log = ""
+        if self.missing_secret_vars:
+            log += "Missing secret vars:\n"
+            for var in self.missing_secret_vars:
+                log += f"  - {var.id}\n"
+        if self.missing_public_vars:
+            log += "Missing public vars:\n"
+            for var in self.missing_public_vars:
+                log += f"  - {var.id}\n"
+        if self.unfixed_secret_vars:
+            log += "Unfixed secret vars:\n"
+            for var in self.unfixed_secret_vars:
+                log += f"  - {var.id}\n"
+        if self.invalid_generators:
+            log += "Invalid generators (outdated invalidation hash):\n"
+            for gen in self.invalid_generators:
+                log += f"  - {gen}\n"
+        return log if log else "All vars are present and valid."
+
 
 def vars_status(
     machine_name: str,
     flake: Flake,
     generator_name: None | str = None,
 ) -> VarStatus:
-    from clan_cli.vars.generator import Generator  # noqa: PLC0415
+    from clan_cli.vars.generator import Generator
 
     machine = Machine(name=machine_name, flake=flake)
     missing_secret_vars = []
@@ -66,15 +87,32 @@ def vars_status(
                         f"Secret var '{file.name}' for service '{generator.name}' in machine {machine.name} is missing.",
                     )
                     missing_secret_vars.append(file)
+                if (
+                    isinstance(machine.secret_vars_store, sops.SecretStore)
+                    and generator.share
+                    and file.exists
+                    and not machine.secret_vars_store.machine_has_access(
+                        generator=generator,
+                        secret_name=file.name,
+                        machine=machine.name,
+                    )
+                ):
+                    msg = (
+                        f"Secret var '{generator.name}/{file.name}' is marked for deployment to machine '{machine.name}', but the machine does not have access to it.\n"
+                        f"Run 'clan vars generate {machine.name}' to fix this.\n"
+                    )
+                    machine.info(msg)
+                    missing_secret_vars.append(file)
+
                 else:
-                    msg = machine.secret_vars_store.health_check(
+                    health_msg = machine.secret_vars_store.health_check(
                         machine=machine.name,
                         generators=[generator],
                         file_name=file.name,
                     )
-                    if msg:
+                    if health_msg is not None:
                         machine.info(
-                            f"Secret var '{file.name}' for service '{generator.name}' in machine {machine.name} needs update: {msg}",
+                            f"Secret var '{file.name}' for service '{generator.name}' in machine {machine.name} needs update: {health_msg}",
                         )
                         unfixed_secret_vars.append(file)
 
@@ -106,6 +144,7 @@ def check_vars(
     generator_name: None | str = None,
 ) -> bool:
     status = vars_status(machine_name, flake, generator_name=generator_name)
+    log.info(f"Check results for machine '{machine_name}': \n{status.text()}")
     return not (
         status.missing_secret_vars
         or status.missing_public_vars

pkgs/clan-cli/clan_cli/vars/generator.py

@@ -259,6 +259,10 @@ class Generator:
                     _secret_store=sec_store,
                 )
 
+                # link generator to its files
+                for file in files:
+                    file.generator(generator)
+
                 if share:
                     # For shared generators, check if we already created it
                     existing = next(
@@ -478,7 +482,7 @@ class Generator:
             if sys.platform == "linux" and bwrap.bubblewrap_works():
                 cmd = bubblewrap_cmd(str(final_script), tmpdir)
             elif sys.platform == "darwin":
-                from clan_lib.sandbox_exec import sandbox_exec_cmd  # noqa: PLC0415
+                from clan_lib.sandbox_exec import sandbox_exec_cmd
 
                 cmd = stack.enter_context(sandbox_exec_cmd(str(final_script), tmpdir))
             else:

pkgs/clan-cli/clan_cli/vars/secret_modules/sops.py

@@ -54,7 +54,7 @@ class SecretStore(StoreBase):
     def ensure_machine_key(self, machine: str) -> None:
         """Ensure machine has sops keys initialized."""
         # no need to generate keys if we don't manage secrets
-        from clan_cli.vars.generator import Generator  # noqa: PLC0415
+        from clan_cli.vars.generator import Generator
 
         vars_generators = Generator.get_machine_generators([machine], self.flake)
         if not vars_generators:
@@ -98,7 +98,8 @@ class SecretStore(StoreBase):
     def machine_has_access(
         self, generator: Generator, secret_name: str, machine: str
     ) -> bool:
-        self.ensure_machine_key(machine)
+        if not has_machine(self.flake.path, machine):
+            return False
         key_dir = sops_machines_folder(self.flake.path) / machine
         return self.key_has_access(key_dir, generator, secret_name)
 
@@ -142,7 +143,7 @@ class SecretStore(StoreBase):
 
         """
         if generators is None:
-            from clan_cli.vars.generator import Generator  # noqa: PLC0415
+            from clan_cli.vars.generator import Generator
 
             generators = Generator.get_machine_generators([machine], self.flake)
         file_found = False
@@ -156,8 +157,6 @@ class SecretStore(StoreBase):
                     else:
                         continue
                 if file.secret and self.exists(generator, file.name):
-                    if file.deploy:
-                        self.ensure_machine_has_access(generator, file.name, machine)
                     needs_update, msg = self.needs_fix(generator, file.name, machine)
                     if needs_update:
                         outdated.append((generator.name, file.name, msg))
@@ -219,7 +218,7 @@ class SecretStore(StoreBase):
         return [store_folder]
 
     def populate_dir(self, machine: str, output_dir: Path, phases: list[str]) -> None:
-        from clan_cli.vars.generator import Generator  # noqa: PLC0415
+        from clan_cli.vars.generator import Generator
 
         vars_generators = Generator.get_machine_generators([machine], self.flake)
         if "users" in phases or "services" in phases:
@@ -283,6 +282,7 @@ class SecretStore(StoreBase):
     ) -> None:
         if self.machine_has_access(generator, name, machine):
             return
+        self.ensure_machine_key(machine)
         secret_folder = self.secret_path(generator, name)
         add_secret(
             self.flake.path,
@@ -292,7 +292,7 @@ class SecretStore(StoreBase):
         )
 
     def collect_keys_for_secret(self, machine: str, path: Path) -> set[sops.SopsKey]:
-        from clan_cli.secrets.secrets import (  # noqa: PLC0415
+        from clan_cli.secrets.secrets import (
             collect_keys_for_path,
             collect_keys_for_type,
         )
@@ -354,10 +354,10 @@ class SecretStore(StoreBase):
             ClanError: If the specified file_name is not found
 
         """
-        from clan_cli.secrets.secrets import update_keys  # noqa: PLC0415
+        from clan_cli.secrets.secrets import update_keys
 
         if generators is None:
-            from clan_cli.vars.generator import Generator  # noqa: PLC0415
+            from clan_cli.vars.generator import Generator
 
             generators = Generator.get_machine_generators([machine], self.flake)
         file_found = False

pkgs/clan-cli/clan_lib/api/__init__.py

@@ -319,9 +319,9 @@ def load_in_all_api_functions() -> None:
     We have to make sure python loads every wrapped function at least once.
     This is done by importing all modules from the clan_lib and clan_cli packages.
     """
-    import clan_cli  # noqa: PLC0415 # Avoid circular imports - many modules import from clan_lib.api
+    import clan_cli  # Avoid circular imports - many modules import from clan_lib.api
 
-    import clan_lib  # noqa: PLC0415 # Avoid circular imports - many modules import from clan_lib.api
+    import clan_lib  # Avoid circular imports - many modules import from clan_lib.api
 
     import_all_modules_from_package(clan_lib)
     import_all_modules_from_package(clan_cli)

pkgs/clan-cli/clan_lib/api/directory.py

@@ -88,7 +88,7 @@ def list_system_storage_devices() -> Blockdevices:
         A list of detected block devices with metadata like size, path, type, etc.
 
     """
-    from clan_lib.nix import nix_shell  # noqa: PLC0415
+    from clan_lib.nix import nix_shell
 
     cmd = nix_shell(
         ["util-linux"],
@@ -124,7 +124,7 @@ def get_clan_directory_relative(flake: Flake) -> str:
         ClanError: If the flake evaluation fails or directories cannot be found
 
     """
-    from clan_lib.dirs import get_clan_directories  # noqa: PLC0415
+    from clan_lib.dirs import get_clan_directories
 
     _, relative_dir = get_clan_directories(flake)
     return relative_dir

pkgs/clan-cli/clan_lib/flake/flake.py

@@ -1162,7 +1162,7 @@ class Flake:
         opts: "ListOptions | None" = None,
     ) -> "dict[str, MachineResponse]":
         """List machines of a clan"""
-        from clan_lib.machines.actions import list_machines  # noqa: PLC0415
+        from clan_lib.machines.actions import list_machines
 
         return list_machines(self, opts)
 

pkgs/clan-cli/clan_lib/locked_open/__init__.py

@@ -18,14 +18,14 @@ def locked_open(filename: Path, mode: str = "r") -> Generator:
 
 
 def write_history_file(data: Any) -> None:
-    from clan_lib.dirs import user_history_file  # noqa: PLC0415
+    from clan_lib.dirs import user_history_file
 
     with locked_open(user_history_file(), "w+") as f:
         f.write(json.dumps(data, cls=ClanJSONEncoder, indent=4))
 
 
 def read_history_file() -> list[dict]:
-    from clan_lib.dirs import user_history_file  # noqa: PLC0415
+    from clan_lib.dirs import user_history_file
 
     with locked_open(user_history_file(), "r") as f:
         content: str = f.read()

pkgs/clan-cli/clan_lib/machines/machines.py

@@ -33,7 +33,7 @@ class Machine:
 
     def get_inv_machine(self) -> "InventoryMachine":
         # Import on demand to avoid circular imports
-        from clan_lib.machines.actions import get_machine  # noqa: PLC0415
+        from clan_lib.machines.actions import get_machine
 
         return get_machine(self.flake, self.name)
 
@@ -95,7 +95,7 @@ class Machine:
 
     @cached_property
     def secret_vars_store(self) -> StoreBase:
-        from clan_cli.vars.secret_modules import password_store  # noqa: PLC0415
+        from clan_cli.vars.secret_modules import password_store
 
         secret_module = self.select("config.clan.core.vars.settings.secretModule")
         module = importlib.import_module(secret_module)
@@ -126,7 +126,7 @@ class Machine:
         return self.flake.path
 
     def target_host(self) -> Remote:
-        from clan_lib.network.network import get_best_remote  # noqa: PLC0415
+        from clan_lib.network.network import get_best_remote
 
         with get_best_remote(self) as remote:
             return remote

pkgs/clan-cli/clan_lib/machines/suggestions.py

@@ -42,7 +42,7 @@ def _suggest_similar_names(
 
 
 def get_available_machines(flake: Flake) -> list[str]:
-    from clan_lib.machines.list import list_machines  # noqa: PLC0415
+    from clan_lib.machines.list import list_machines
 
     machines = list_machines(flake)
     return list(machines.keys())

pkgs/clan-cli/clan_lib/network/network.py

@@ -34,7 +34,7 @@ class Peer:
             _var: dict[str, str] = self._host["var"]
             machine_name = _var["machine"]
             generator = _var["generator"]
-            from clan_lib.machines.machines import Machine  # noqa: PLC0415
+            from clan_lib.machines.machines import Machine
 
             machine = Machine(name=machine_name, flake=self.flake)
             var = get_machine_var(

pkgs/clan-cli/clan_lib/nix/__init__.py

@@ -88,7 +88,7 @@ def nix_eval(flags: list[str]) -> list[str]:
         ],
     )
     if os.environ.get("IN_NIX_SANDBOX"):
-        from clan_lib.dirs import nixpkgs_source  # noqa: PLC0415
+        from clan_lib.dirs import nixpkgs_source
 
         return [
             *default_flags,
@@ -169,7 +169,7 @@ def nix_shell(packages: list[str], cmd: list[str]) -> list[str]:
     if not missing_packages:
         return cmd
 
-    from clan_lib.dirs import nixpkgs_flake  # noqa: PLC0415
+    from clan_lib.dirs import nixpkgs_flake
 
     return [
         *nix_command(["shell", "--inputs-from", f"{nixpkgs_flake()!s}"]),

pkgs/clan-cli/clan_lib/ssh/remote.py

@@ -464,12 +464,12 @@ class Remote:
         self,
         opts: "ConnectionOptions | None" = None,
     ) -> None:
-        from clan_lib.network.check import check_machine_ssh_reachable  # noqa: PLC0415
+        from clan_lib.network.check import check_machine_ssh_reachable
 
         return check_machine_ssh_reachable(self, opts)
 
     def check_machine_ssh_login(self) -> None:
-        from clan_lib.network.check import check_machine_ssh_login  # noqa: PLC0415
+        from clan_lib.network.check import check_machine_ssh_login
 
         return check_machine_ssh_login(self)
 

pkgs/clan-cli/clan_lib/vars/generate.py

@@ -5,6 +5,7 @@ from clan_cli.vars import graph
 from clan_cli.vars.generator import Generator
 from clan_cli.vars.graph import requested_closure
 from clan_cli.vars.migration import check_can_migrate, migrate_files
+from clan_cli.vars.secret_modules import sops
 
 from clan_lib.api import API
 from clan_lib.errors import ClanError
@@ -152,15 +153,15 @@ def run_generators(
     if not machines:
         msg = "At least one machine must be provided"
         raise ClanError(msg)
+    all_generators = get_generators(machines, full_closure=True)
     if isinstance(generators, list):
         # List of generator names - use them exactly as provided
         if len(generators) == 0:
             return
-        all_generators = get_generators(machines, full_closure=True)
+        generators_to_run = [g for g in all_generators if g.key.name in generators]
-        generator_objects = [g for g in all_generators if g.key.name in generators]
     else:
         # None or single string - use get_generators with closure parameter
-        generator_objects = get_generators(
+        generators_to_run = get_generators(
             machines,
             full_closure=full_closure,
             generator_name=generators,
@@ -170,13 +171,30 @@ def run_generators(
     # TODO: make this more lazy and ask for every generator on execution
     if callable(prompt_values):
         prompt_values = {
-            generator.name: prompt_values(generator) for generator in generator_objects
+            generator.name: prompt_values(generator) for generator in generators_to_run
         }
 
     # execute health check
     for machine in machines:
         _ensure_healthy(machine=machine)
 
+    # ensure all selected machines have access to all selected shared generators
+    for machine in machines:
+        # This is only relevant for the sops store
+        # TODO: improve store abstraction to use Protocols and introduce a proper SecretStore interface
+        if not isinstance(machine.secret_vars_store, sops.SecretStore):
+            continue
+        for generator in all_generators:
+            if generator.share:
+                for file in generator.files:
+                    if not file.secret or not file.exists:
+                        continue
+                    machine.secret_vars_store.ensure_machine_has_access(
+                        generator,
+                        file.name,
+                        machine.name,
+                    )
+
     # get the flake via any machine (they are all the same)
     flake = machines[0].flake
 
@@ -188,13 +206,13 @@ def run_generators(
 
     # preheat the select cache, to reduce repeated calls during execution
     selectors = []
-    for generator in generator_objects:
+    for generator in generators_to_run:
         machine = get_generator_machine(generator)
         selectors.append(generator.final_script_selector(machine.name))
     flake.precache(selectors)
 
     # execute generators
-    for generator in generator_objects:
+    for generator in generators_to_run:
         machine = get_generator_machine(generator)
         if check_can_migrate(machine, generator):
             migrate_files(machine, generator)

pkgs/clan-cli/docs.py

@@ -290,9 +290,7 @@ def collect_commands() -> list[Category]:
         # 3. sort by title alphabetically
         return (c.title.split(" ")[0], c.title, weight)
 
-    result = sorted(result, key=weight_cmd_groups)
+    return sorted(result, key=weight_cmd_groups)
-
-    return result
 
 
 def build_command_reference() -> None:

pkgs/clan-vm-manager/clan_vm_manager/components/executor.py

@@ -36,7 +36,7 @@ class MPProcess:
 def _set_proc_name(name: str) -> None:
     if sys.platform != "linux":
         return
-    import ctypes  # noqa: PLC0415
+    import ctypes
 
     # Define the prctl function with the appropriate arguments and return type
     libc = ctypes.CDLL("libc.so.6")

pkgs/clan-vm-manager/clan_vm_manager/components/trayicon.py

@@ -759,12 +759,12 @@ class Win32Implementation(BaseImplementation):
     SM_CXSMICON = 49
 
     if sys.platform == "win32":
-        from ctypes import Structure  # noqa: PLC0415
+        from ctypes import Structure
 
         class WNDCLASSW(Structure):
             """Windows class structure for window registration."""
 
-            from ctypes import CFUNCTYPE, wintypes  # noqa: PLC0415
+            from ctypes import CFUNCTYPE, wintypes
 
             LPFN_WND_PROC = CFUNCTYPE(
                 wintypes.INT,
@@ -789,7 +789,7 @@ class Win32Implementation(BaseImplementation):
         class MENUITEMINFOW(Structure):
             """Windows menu item information structure."""
 
-            from ctypes import wintypes  # noqa: PLC0415
+            from ctypes import wintypes
 
             _fields_: ClassVar = [
                 ("cb_size", wintypes.UINT),
@@ -809,7 +809,7 @@ class Win32Implementation(BaseImplementation):
         class NOTIFYICONDATAW(Structure):
             """Windows notification icon data structure."""
 
-            from ctypes import wintypes  # noqa: PLC0415
+            from ctypes import wintypes
 
             _fields_: ClassVar = [
                 ("cb_size", wintypes.DWORD),
@@ -1061,7 +1061,7 @@ class Win32Implementation(BaseImplementation):
         if sys.platform != "win32":
             return
 
-        from ctypes import wintypes  # noqa: PLC0415
+        from ctypes import wintypes
 
         if self._menu is None:
             self.update_menu()
@@ -1110,7 +1110,7 @@ class Win32Implementation(BaseImplementation):
         if sys.platform != "win32":
             return 0
 
-        from ctypes import wintypes  # noqa: PLC0415
+        from ctypes import wintypes
 
         if msg == self.WM_TRAYICON:
             if l_param == self.WM_RBUTTONUP: