don't enable ssh askpass for now if we have a build_host set

Reviewed-on: https://git.clan.lol/clan/clan-core/pulls/4242

clanModules/borgbackup/roles/client.nix

@@ -196,7 +196,7 @@ in
         pkgs.xkcdpass
       ];
       script = ''
-        ssh-keygen -t ed25519 -N "" -f "$out"/borgbackup.ssh
+        ssh-keygen -t ed25519 -N "" -C "" -f "$out"/borgbackup.ssh
         xkcdpass -n 4 -d - > "$out"/borgbackup.repokey
       '';
     };

clanModules/importer/README.md

@@ -7,7 +7,7 @@ The importer module allows users to configure importing modules in a flexible an
 
 It exposes the `extraModules` functionality of the inventory, without any added configuration.
 
-## Usage:
+## Usage
 
 ```nix
 inventory.services = {

clanModules/sshd/roles/server.nix

@@ -54,7 +54,7 @@ in
         pkgs.openssh
       ];
       script = ''
-        ssh-keygen -t ed25519 -N "" -f "$out"/ssh.id_ed25519
+        ssh-keygen -t ed25519 -N "" -C "" -f "$out"/ssh.id_ed25519
       '';
     };
 
@@ -74,7 +74,7 @@ in
         pkgs.openssh
       ];
       script = ''
-        ssh-keygen -t rsa -b 4096 -N "" -f "$out"/ssh.id_rsa
+        ssh-keygen -t rsa -b 4096 -N "" -C "" -f "$out"/ssh.id_rsa
       '';
     };
 

clanModules/sshd/shared.nix

@@ -36,7 +36,7 @@
             pkgs.openssh
           ];
           script = ''
-            ssh-keygen -t ed25519 -N "" -f "$out"/id_ed25519
+            ssh-keygen -t ed25519 -N "" -C "" -f "$out"/id_ed25519
           '';
         };
 

clanServices/borgbackup/default.nix

@@ -256,7 +256,7 @@
                     pkgs.xkcdpass
                   ];
                   script = ''
-                    ssh-keygen -t ed25519 -N "" -f "$out"/borgbackup.ssh
+                    ssh-keygen -t ed25519 -N "" -C "" -f "$out"/borgbackup.ssh
                     xkcdpass -n 4 -d - > "$out"/borgbackup.repokey
                   '';
                 };

clanServices/importer/README.md

@@ -1,7 +1,7 @@
 The importer module allows users to configure importing modules in a flexible and structured way.
 It exposes the `extraModules` functionality of the inventory, without any added configuration.
 
-## Usage:
+## Usage
 
 ```nix
 inventory.instances = {

clanServices/sshd/README.md

@@ -0,0 +1,36 @@
+The `sshd` Clan service manages SSH to make it easy to securely access your machines over the internet. The service uses `vars` to store the SSH host keys for each machine to ensure they remain stable across deployments.
+
+`sshd` also generates SSH certificates for both servers and clients allowing for certificate-based authentication for SSH.
+
+The service also disables password-based authentication over SSH, to access your machines you'll need to use public key authentication or certificate-based authentication.
+
+## Usage
+
+```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";
+        input = "clan-core";
+      };
+      roles.server.tags.all = { };
+      roles.server.settings = {
+        hostKeys.rsa.enable = true;
+      };
+      roles.client.tags.all = { };
+    };
+  };
+}
+```

clanServices/sshd/default.nix

@@ -2,7 +2,7 @@
 {
   _class = "clan.service";
   manifest.name = "clan-core/sshd";
-  manifest.description = "Enables secure remote access to the machine over ssh.";
+  manifest.description = "Enables secure remote access to the machine over SSH";
   manifest.categories = [
     "System"
     "Network"
@@ -49,7 +49,7 @@
                 pkgs.openssh
               ];
               script = ''
-                ssh-keygen -t ed25519 -N "" -f "$out"/id_ed25519
+                ssh-keygen -t ed25519 -N "" -C "" -f "$out"/id_ed25519
               '';
             };
 
@@ -109,7 +109,7 @@
                   pkgs.openssh
                 ];
                 script = ''
-                  ssh-keygen -t ed25519 -N "" -f "$out"/id_ed25519
+                  ssh-keygen -t ed25519 -N "" -C "" -f "$out"/id_ed25519
                 '';
               };
 
@@ -151,7 +151,7 @@
                   pkgs.openssh
                 ];
                 script = ''
-                  ssh-keygen -t rsa -b 4096 -N "" -f "$out"/ssh.id_rsa
+                  ssh-keygen -t rsa -b 4096 -N "" -C "" -f "$out"/ssh.id_rsa
                 '';
               };
 
@@ -164,7 +164,7 @@
                   pkgs.openssh
                 ];
                 script = ''
-                  ssh-keygen -t ed25519 -N "" -f "$out"/ssh.id_ed25519
+                  ssh-keygen -t ed25519 -N "" -C "" -f "$out"/ssh.id_ed25519
                 '';
               };
             };

clanServices/users/README.md

@@ -1,30 +1,31 @@
 ## Usage
 
-```
-inventory.instances = {
-
-  # Deploy user alice on all machines. Don't prompt for password (will be
-  # auto-generated).
-
-  user-alice = {
-    module = {
-      name = "users";
-      input = "clan";
+```nix
+{
+  inventory.instances = {
+    # Deploy user alice on all machines. Don't prompt for password (will be
+    # auto-generated).
+    user-alice = {
+      module = {
+        name = "users";
+        input = "clan";
+      };
+      roles.default.tags.all = { };
+      roles.default.settings = {
+        user = "alice";
+        prompt = false;
+      };
     };
-    roles.default.tags.all = { };
-    roles.default.settings = {
-      user = "alice";
-      prompt = false;
+
+    # Deploy user bob only on his laptop. Prompt for a password.
+    user-bob = {
+      module = {
+        name = "users";
+        input = "clan";
+      };
+      roles.default.machines.bobs-laptop = { };
+      roles.default.settings.user = "bob";
     };
   };
-
-  # Deploy user bob only on his laptop. Prompt for a password.
-  user-bob = {
-    module = {
-      name = "users";
-      input = "clan";
-    };
-    roles.default.machines.bobs-laptop = { };
-    roles.default.settings.user = "bob";
-  };
+}
 ```

docs/mkdocs.yml

@@ -62,6 +62,7 @@ nav:
       - Vars Backend: guides/vars-backend.md
       - Facts Backend: guides/secrets.md
       - Adding more machines: guides/more-machines.md
+      - Target Host: guides/target-host.md
       - Inventory:
           - Inventory: guides/inventory.md
       - Secure Boot: guides/secure-boot.md
@@ -154,6 +155,7 @@ nav:
           - reference/cli/show.md
           - reference/cli/ssh.md
           - reference/cli/state.md
+          - reference/cli/templates.md
           - reference/cli/vars.md
           - reference/cli/vms.md
       - NixOS Modules:

docs/site/decisions/04-fetching-nix-from-python.md

@@ -28,7 +28,7 @@ Benefits:
 * Caching mechanism is very simple.
 
 
-### Method 2: Direct access:
+### Method 2: Direct access
 
 Directly calling the evaluator / build sandbox via `nix build` and `nix eval`within the Python code
 

docs/site/guides/disk-encryption.md

@@ -122,8 +122,8 @@ CTRL+D
 4. Locally generate ssh host keys. You only need to generate ones for the algorithms you're using in `authorizedKeys`.
 
 ```bash
-ssh-keygen -q -N "" -t ed25519 -f ./initrd_host_ed25519_key
-ssh-keygen -q -N "" -t rsa -b 4096 -f ./initrd_host_rsa_key
+ssh-keygen -q -N "" -C "" -t ed25519 -f ./initrd_host_ed25519_key
+ssh-keygen -q -N "" -C "" -t rsa -b 4096 -f ./initrd_host_rsa_key
 ```
 
 5. Securely copy your local initrd ssh host keys to the installer's `/mnt` directory:

docs/site/guides/target-host.md

@@ -0,0 +1,82 @@
+# How to Set `targetHost` for a Machine
+
+The `targetHost` defines where the machine can be reached for operations like SSH or deployment. You can set it in two ways, depending on your use case.
+
+---
+
+## ✅ Option 1: Use the Inventory (Recommended for Static Hosts)
+
+If the hostname is **static**, like `server.example.com`, set it in the **inventory**:
+
+```{.nix title="flake.nix" hl_lines="8"}
+{
+  # edlided
+  outputs =
+    { self, clan-core, ... }:
+    let
+      clan = clan-core.lib.clan {
+        inventory.machines.jon = {
+            deploy.targetHost = "root@server.example.com";
+        };
+      };
+    in
+    {
+      inherit (clan.config) nixosConfigurations nixosModules clanInternals;
+      # elided
+    };
+}
+```
+
+This is fast, simple and explicit, and doesn’t require evaluating the NixOS config. We can also displayed it in the clan-cli or clan-app.
+
+---
+
+## ✅ Option 2: Use NixOS (Only for Dynamic Hosts)
+
+If your target host depends on a **dynamic expression** (like using the machine’s evaluated FQDN), set it inside the NixOS module:
+
+```{.nix title="flake.nix" hl_lines="8"}
+{
+  # edlided
+  outputs =
+    { self, clan-core, ... }:
+    let
+      clan = clan-core.lib.clan {
+        machines.jon = {config, ...}: {
+            clan.core.networking.targetHost = "jon@${config.networking.fqdn}";
+        };
+      };
+    in
+    {
+      inherit (clan.config) nixosConfigurations nixosModules clanInternals;
+      # elided
+    };
+}
+```
+
+Use this **only if the value cannot be made static**, because it’s slower and won't be displayed in the clan-cli or clan-app yet.
+
+---
+
+## 📝 TL;DR
+
+| Use Case                  | Use Inventory? | Example                          |
+| ------------------------- | -------------- | -------------------------------- |
+| Static hostname           | ✅ Yes          | `root@server.example.com`        |
+| Dynamic config expression | ❌ No           | `jon@${config.networking.fqdn}` |
+
+---
+
+## 🚀 Coming Soon: Unified Networking Module
+
+We’re working on a new networking module that will automatically do all of this for you.
+
+- Easier to use
+- Sane defaults: You’ll always be able to reach the machine — no need to worry about hostnames.
+- ✨ Migration from **either method** will be supported and simple.
+
+## Summary
+
+- Ask: *Does this hostname dynamically change based on NixOS config?*
+- If **no**, use the inventory.
+- If **yes**, then use NixOS config.

flake.lock

@@ -16,11 +16,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1751413887,
-        "narHash": "sha256-+ut7DrSwamExIvaCFdiTYD88NTSYJFG2CEOvCha59vI=",
-        "rev": "246f0d66547d073af6249e4f7852466197e871ed",
+        "lastModified": 1751846468,
+        "narHash": "sha256-h0mpWZIOIAKj4fmLNyI2HDG+c0YOkbYmyJXSj/bQ9s0=",
+        "rev": "a2166c13b0cb3febdaf36391cd2019aa2ccf4366",
         "type": "tarball",
-        "url": "https://git.clan.lol/api/v1/repos/clan/data-mesher/archive/246f0d66547d073af6249e4f7852466197e871ed.tar.gz"
+        "url": "https://git.clan.lol/api/v1/repos/clan/data-mesher/archive/a2166c13b0cb3febdaf36391cd2019aa2ccf4366.tar.gz"
       },
       "original": {
         "type": "tarball",
@@ -34,11 +34,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1751607816,
-        "narHash": "sha256-5PtrwjqCIJ4DKQhzYdm8RFePBuwb+yTzjV52wWoGSt4=",
+        "lastModified": 1751854533,
+        "narHash": "sha256-U/OQFplExOR1jazZY4KkaQkJqOl59xlh21HP9mI79Vc=",
         "owner": "nix-community",
         "repo": "disko",
-        "rev": "da6109c917b48abc1f76dd5c9bf3901c8c80f662",
+        "rev": "16b74a1e304197248a1bc663280f2548dbfcae3c",
         "type": "github"
       },
       "original": {
@@ -164,10 +164,10 @@
     "nixpkgs": {
       "locked": {
         "lastModified": 315532800,
-        "narHash": "sha256-0HRxGUoOMtOYnwlMWY0AkuU88WHaI3Q5GEILmsWpI8U=",
-        "rev": "a48741b083d4f36dd79abd9f760c84da6b4dc0e5",
+        "narHash": "sha256-mUlYenGbsUFP0A3EhfKJXmUl5+MQGJLhoEop2t3g5p4=",
+        "rev": "ceb24d94c6feaa4e8737a8e2bd3cf71c3a7eaaa0",
         "type": "tarball",
-        "url": "https://releases.nixos.org/nixpkgs/nixpkgs-25.11pre823094.a48741b083d4/nixexprs.tar.xz"
+        "url": "https://releases.nixos.org/nixpkgs/nixpkgs-25.11pre826033.ceb24d94c6fe/nixexprs.tar.xz"
       },
       "original": {
         "type": "tarball",

lib/modules/clan/module.nix

@@ -229,8 +229,6 @@ in
     clanInternals = {
       inventoryClass =
         let
-          localModuleSet =
-            lib.filterAttrs (n: _: !inventory._legacyModules ? ${n}) inventory.modules // config.modules;
           flakeInputs = config.self.inputs;
         in
         {
@@ -240,7 +238,7 @@ in
           imports = [
             ../inventoryClass/builder/default.nix
             (lib.modules.importApply ../inventoryClass/service-list-from-inputs.nix {
-              inherit flakeInputs clanLib localModuleSet;
+              inherit flakeInputs clanLib;
             })
             {
               inherit inventory directory;

lib/modules/inventoryClass/service-list-from-inputs.nix

@@ -1,12 +1,9 @@
 {
   flakeInputs,
   clanLib,
-  localModuleSet,
 }:
 { lib, config, ... }:
-
 let
-
   inspectModule =
     inputName: moduleName: module:
     let
@@ -28,16 +25,30 @@ in
 {
   options.modulesPerSource = lib.mkOption {
     # { sourceName :: { moduleName :: {} }}
+    readOnly = true;
+    type = lib.types.raw;
     default =
       let
         inputsWithModules = lib.filterAttrs (_inputName: v: v ? clan.modules) flakeInputs;
-
       in
       lib.mapAttrs (
         inputName: v: lib.mapAttrs (inspectModule inputName) v.clan.modules
       ) inputsWithModules;
   };
   options.localModules = lib.mkOption {
-    default = lib.mapAttrs (inspectModule "self") localModuleSet;
+    readOnly = true;
+    type = lib.types.raw;
+    default = config.modulesPerSource.self;
+  };
+  options.templatesPerSource = lib.mkOption {
+    # { sourceName :: { moduleName :: {} }}
+    readOnly = true;
+    type = lib.types.raw;
+    default =
+      let
+        inputsWithTemplates = lib.filterAttrs (_inputName: v: v ? clan.templates) flakeInputs;
+      in
+      lib.mapAttrs (_inputName: v: lib.mapAttrs (_n: t: t) v.clan.templates) inputsWithTemplates;
+
   };
 }

nixosModules/clanCore/vars/default.nix

@@ -40,6 +40,18 @@ in
   };
 
   config = {
+    # Check for removed passBackend option usage
+    assertions = [
+      {
+        assertion = config.clan.core.vars.settings.passBackend == null;
+        message = ''
+          The option `clan.core.vars.settings.passBackend' has been removed.
+          Use clan.core.vars.password-store.passPackage instead.
+          Set it to pkgs.pass for GPG or pkgs.passage for age encryption.
+        '';
+      }
+    ];
+
     # check all that all non-secret files have no owner/group/mode set
     warnings = lib.foldl' (
       warnings: generator:

nixosModules/clanCore/vars/secret/password-store.nix

@@ -54,7 +54,7 @@ in
 {
   _class = "nixos";
 
-  options.clan.vars.password-store = {
+  options.clan.core.vars.password-store = {
     secretLocation = lib.mkOption {
       type = lib.types.path;
       default = "/etc/secret-vars";
@@ -62,6 +62,13 @@ in
         location where the tarball with the password-store secrets will be uploaded to and the manifest
       '';
     };
+    passPackage = lib.mkOption {
+      type = lib.types.package;
+      default = pkgs.pass;
+      description = ''
+        Password store package to use. Can be pkgs.pass for GPG-based storage or pkgs.passage for age-based storage.
+      '';
+    };
   };
   config = {
     clan.core.vars.settings =
@@ -76,7 +83,7 @@ in
                 else if file.config.neededFor == "services" then
                   "/run/secrets/${file.config.generatorName}/${file.config.name}"
                 else if file.config.neededFor == "activation" then
-                  "${config.clan.password-store.secretLocation}/activation/${file.config.generatorName}/${file.config.name}"
+                  "${config.clan.core.vars.password-store.secretLocation}/activation/${file.config.generatorName}/${file.config.name}"
                 else if file.config.neededFor == "partitioning" then
                   "/run/partitioning-secrets/${file.config.generatorName}/${file.config.name}"
                 else
@@ -95,7 +102,7 @@ in
               ]
               ''
                 [ -e /run/current-system ] || echo setting up secrets...
-                ${installSecretTarball}/bin/install-secret-tarball ${config.clan.vars.password-store.secretLocation}/secrets_for_users.tar.gz /run/user-secrets
+                ${installSecretTarball}/bin/install-secret-tarball ${config.clan.core.vars.password-store.secretLocation}/secrets_for_users.tar.gz /run/user-secrets
               ''
             // lib.optionalAttrs (config.system ? dryActivationScript) {
               supportsDryActivation = true;
@@ -111,7 +118,7 @@ in
               ]
               ''
                 [ -e /run/current-system ] || echo setting up secrets...
-                ${installSecretTarball}/bin/install-secret-tarball ${config.clan.vars.password-store.secretLocation}/secrets.tar.gz /run/secrets
+                ${installSecretTarball}/bin/install-secret-tarball ${config.clan.core.vars.password-store.secretLocation}/secrets.tar.gz /run/secrets
               ''
             // lib.optionalAttrs (config.system ? dryActivationScript) {
               supportsDryActivation = true;
@@ -129,7 +136,7 @@ in
             serviceConfig = {
               Type = "oneshot";
               ExecStart = [
-                "${installSecretTarball}/bin/install-secret-tarball ${config.clan.vars.password-store.secretLocation}/secrets_for_users.tar.gz /run/user-secrets"
+                "${installSecretTarball}/bin/install-secret-tarball ${config.clan.core.vars.password-store.secretLocation}/secrets_for_users.tar.gz /run/user-secrets"
               ];
               RemainAfterExit = true;
             };
@@ -142,7 +149,7 @@ in
             serviceConfig = {
               Type = "oneshot";
               ExecStart = [
-                "${installSecretTarball}/bin/install-secret-tarball ${config.clan.vars.password-store.secretLocation}/secrets.tar.gz /run/secrets"
+                "${installSecretTarball}/bin/install-secret-tarball ${config.clan.core.vars.password-store.secretLocation}/secrets.tar.gz /run/secrets"
               ];
               RemainAfterExit = true;
             };

nixosModules/clanCore/vars/settings-opts.nix

@@ -15,17 +15,6 @@
     '';
   };
 
-  passBackend = lib.mkOption {
-    type = lib.types.enum [
-      "passage"
-      "pass"
-    ];
-    default = "pass";
-    description = ''
-      password-store backend to use. Valid options are `pass` and `passage`
-    '';
-  };
-
   secretModule = lib.mkOption {
     type = lib.types.str;
     internal = true;
@@ -65,4 +54,15 @@
       the python import path to the public module
     '';
   };
+
+  # Legacy option that guides migration
+  passBackend = lib.mkOption {
+    type = lib.types.nullOr lib.types.str;
+    default = null;
+    visible = false;
+    description = ''
+      DEPRECATED: This option has been removed. Use clan.vars.password-store.passPackage instead.
+      Set it to pkgs.pass for GPG or pkgs.passage for age encryption.
+    '';
+  };
 }

pkgs/clan-app/ui-2d/src/api/index.tsx

@@ -90,7 +90,7 @@ const handleCancel = async <K extends OperationNames>(
   orig_task: Promise<BackendReturnType<K>>,
 ) => {
   console.log("Canceling operation: ", ops_key);
-  const { promise, op_key } = _callApi("cancel_task", { task_id: ops_key });
+  const { promise, op_key } = _callApi("delete_task", { task_id: ops_key });
   promise.catch((error) => {
     toast.custom(
       (t) => (

pkgs/clan-app/ui-2d/src/components/machine-list-item/index.tsx

@@ -75,7 +75,7 @@ export const MachineListItem = (props: MachineListItemProps) => {
     }
 
     setInstalling(true);
-    await callApi("install_machine", {
+    await callApi("run_machine_install", {
       opts: {
         machine: {
           name: name,
@@ -163,7 +163,7 @@ export const MachineListItem = (props: MachineListItemProps) => {
     }
 
     await callApi(
-      "deploy_machine",
+      "run_machine_deploy",
       {
         machine: {
           name: name,

pkgs/clan-app/ui-2d/src/queries/clan-meta.ts

@@ -13,7 +13,7 @@ export const clanMetaQuery = (uri: string | undefined = undefined) =>
       queryFn: async () => {
         console.log("fetching clan meta", clanURI);
 
-        const result = await callApi("show_clan_meta", {
+        const result = await callApi("get_clan_details", {
           flake: { identifier: clanURI! },
         }).promise;
 

pkgs/clan-app/ui-2d/src/queries/index.ts

@@ -33,27 +33,6 @@ export const createModulesQuery = (
     },
   }));
 
-export const tagsQuery = (uri: string | undefined) =>
-  useQuery<string[]>(() => ({
-    queryKey: [uri, "tags"],
-    placeholderData: [],
-    queryFn: async () => {
-      if (!uri) return [];
-
-      const response = await callApi("get_inventory", {
-        flake: { identifier: uri },
-      }).promise;
-      if (response.status === "error") {
-        console.error("Failed to fetch data");
-      } else {
-        const machines = response.data.machines || {};
-        const tags = Object.values(machines).flatMap((m) => m.tags || []);
-        return tags;
-      }
-      return [];
-    },
-  }));
-
 export const machinesQuery = (uri: string | undefined) =>
   useQuery<string[]>(() => ({
     queryKey: [uri, "machines"],
@@ -61,7 +40,7 @@ export const machinesQuery = (uri: string | undefined) =>
     queryFn: async () => {
       if (!uri) return [];
 
-      const response = await callApi("get_inventory", {
+      const response = await callApi("list_machines", {
         flake: { identifier: uri },
       }).promise;
       if (response.status === "error") {

pkgs/clan-app/ui-2d/src/routes/clans/create.tsx

@@ -66,7 +66,7 @@ export const CreateClan = () => {
     }
 
     // Will generate a key if it doesn't exist, and add a user to the clan
-    const k = await callApi("keygen", {
+    const k = await callApi("create_secrets_user", {
       flake_dir: target_dir[0],
     }).promise;
 
@@ -203,6 +203,6 @@ export const CreateClan = () => {
 };
 
 type Meta = Extract<
-  OperationResponse<"show_clan_meta">,
+  OperationResponse<"get_clan_details">,
   { status: "success" }
 >["data"];

pkgs/clan-app/ui-2d/src/routes/clans/details.tsx

@@ -23,7 +23,7 @@ const EditClanForm = (props: EditClanFormProps) => {
   const handleSubmit: SubmitHandler<GeneralData> = async (values, event) => {
     await toast.promise(
       (async () => {
-        await callApi("update_clan_meta", {
+        await callApi("set_clan_details", {
           options: {
             flake: { identifier: props.directory },
             meta: values,
@@ -128,7 +128,7 @@ const EditClanForm = (props: EditClanFormProps) => {
   );
 };
 
-type GeneralData = SuccessQuery<"show_clan_meta">["data"];
+type GeneralData = SuccessQuery<"get_clan_details">["data"];
 
 export const ClanDetails = () => {
   const params = useParams();

pkgs/clan-app/ui-2d/src/routes/flash/view.tsx

@@ -100,7 +100,7 @@ export const Flash = () => {
   const deviceQuery = createQuery(() => ({
     queryKey: ["block_devices"],
     queryFn: async () => {
-      const result = await callApi("show_block_devices", {}).promise;
+      const result = await callApi("list_block_devices", {}).promise;
       if (result.status === "error") throw new Error("Failed to fetch data");
       return result.data;
     },
@@ -110,7 +110,7 @@ export const Flash = () => {
   const keymapQuery = createQuery(() => ({
     queryKey: ["list_keymaps"],
     queryFn: async () => {
-      const result = await callApi("list_possible_keymaps", {}).promise;
+      const result = await callApi("list_keymaps", {}).promise;
       if (result.status === "error") throw new Error("Failed to fetch data");
       return result.data;
     },
@@ -120,7 +120,7 @@ export const Flash = () => {
   const langQuery = createQuery(() => ({
     queryKey: ["list_languages"],
     queryFn: async () => {
-      const result = await callApi("list_possible_languages", {}).promise;
+      const result = await callApi("list_languages", {}).promise;
       if (result.status === "error") throw new Error("Failed to fetch data");
       return result.data;
     },
@@ -157,7 +157,7 @@ export const Flash = () => {
     console.log("Confirmed flash:", values);
     try {
       await toast.promise(
-        callApi("flash_machine", {
+        callApi("run_machine_flash", {
           machine: {
             name: values.machine.devicePath,
             flake: {

pkgs/clan-app/ui-2d/src/routes/hosts/view.tsx

@@ -4,7 +4,7 @@ import { Button } from "../../components/Button/Button";
 import Icon from "@/src/components/icon";
 
 type ServiceModel = Extract<
-  OperationResponse<"show_mdns">,
+  OperationResponse<"list_mdns_services">,
   { status: "success" }
 >["data"]["services"];
 
@@ -16,7 +16,7 @@ export const HostList: Component = () => {
       <div class="" data-tip="Refresh install targets">
         <Button
           variant="light"
-          onClick={() => callApi("show_mdns", {})}
+          onClick={() => callApi("list_mdns_services", {})}
           startIcon={<Icon icon="Update" />}
         ></Button>
       </div>

pkgs/clan-app/ui-2d/src/routes/machines/components/InstallMachine.tsx

@@ -120,7 +120,7 @@ export function InstallMachine(props: InstallMachineProps) {
         throw new Error("No target host found for the machine");
       }
 
-      const installPromise = callApi("install_machine", {
+      const installPromise = callApi("run_machine_install", {
         opts: {
           machine: {
             name: props.name,

pkgs/clan-app/ui-2d/src/routes/machines/components/MachineForm.tsx

@@ -149,7 +149,7 @@ export function MachineForm(props: MachineFormProps) {
 
     setIsUpdating(true);
     const r = await callApi(
-      "deploy_machine",
+      "run_machine_deploy",
       {
         machine: {
           name: machine,

pkgs/clan-app/ui-2d/src/routes/machines/install/hardware-step.tsx

@@ -71,7 +71,7 @@ export const HWStep = (props: StepProps<HardwareValues>) => {
   const hwReportQuery = useQuery(() => ({
     queryKey: [props.dir, props.machine_id, "hw_report"],
     queryFn: async () => {
-      const result = await callApi("show_machine_hardware_config", {
+      const result = await callApi("get_machine_hardware_summary", {
         machine: {
           flake: {
             identifier: props.dir,
@@ -127,7 +127,7 @@ export const HWStep = (props: StepProps<HardwareValues>) => {
       return;
     }
 
-    const r = await callApi("generate_machine_hardware_info", {
+    const r = await callApi("run_machine_hardware_info", {
       opts: {
         machine: {
           name: props.machine_id,

pkgs/clan-app/ui-2d/src/routes/machines/install/vars-step.tsx

@@ -173,7 +173,7 @@ export const VarsStep = (props: VarsStepProps) => {
       toast.error("Error fetching data");
       return;
     }
-    const result = await callApi("generate_vars_for_machine", {
+    const result = await callApi("run_generators", {
       machine_name: props.machine_id,
       base_dir: props.dir,
       generators: generatorsQuery.data.map((generator) => generator.name),

pkgs/clan-app/ui-2d/src/routes/modules/add.tsx

@@ -1,5 +1,5 @@
 import { BackButton } from "@/src/components/BackButton";
-import { createModulesQuery, machinesQuery, tagsQuery } from "@/src/queries";
+import { createModulesQuery, machinesQuery } from "@/src/queries";
 import { useParams } from "@solidjs/router";
 import { For, Match, Switch } from "solid-js";
 import { ModuleInfo } from "./list";
@@ -34,28 +34,11 @@ interface AddModuleProps {
 
 const AddModule = (props: AddModuleProps) => {
   const { activeClanURI } = useClanContext();
-  const tags = tagsQuery(activeClanURI());
   const machines = machinesQuery(activeClanURI());
   return (
     <div>
       <div>Add to your clan</div>
-      <Switch fallback="loading">
-        <Match when={tags.data}>
-          {(tags) => (
-            <For each={Object.keys(props.data.roles)}>
-              {(role) => (
-                <>
-                  <div class="text-neutral-600">{role}s</div>
-                  <RoleForm
-                    avilableTags={tags()}
-                    availableMachines={machines.data || []}
-                  />
-                </>
-              )}
-            </For>
-          )}
-        </Match>
-      </Switch>
+      <Switch fallback="loading">Removed</Switch>
     </div>
   );
 };

pkgs/clan-app/ui-2d/src/routes/modules/details.tsx

@@ -62,7 +62,6 @@ const Details = (props: DetailsProps) => {
     navigate(`/modules/add/${props.id}`);
     // const uri = activeURI();
     // if (!uri) return;
-    // const res = await callApi("get_inventory", { base_path: uri });
     // if (res.status === "error") {
     //   toast.error("Failed to fetch inventory");
     //   return;

pkgs/clan-app/ui/src/api/index.tsx

@@ -90,7 +90,7 @@ const handleCancel = async <K extends OperationNames>(
   orig_task: Promise<BackendReturnType<K>>,
 ) => {
   console.log("Canceling operation: ", ops_key);
-  const { promise, op_key } = _callApi("cancel_task", { task_id: ops_key });
+  const { promise, op_key } = _callApi("delete_task", { task_id: ops_key });
   promise.catch((error) => {
     toast.custom(
       (t) => (

pkgs/clan-app/ui/src/components/v2/Alert/Alert.css

@@ -0,0 +1,39 @@
+div.alert {
+  @apply flex gap-2.5 px-6 py-4 size-full rounded-md items-start;
+
+  &.has-icon {
+    @apply pl-4;
+
+    svg.icon {
+      @apply relative top-0.5;
+    }
+  }
+
+  &.has-dismiss {
+    @apply pr-4;
+  }
+
+  & > div.content {
+    @apply flex flex-col gap-2 size-full;
+  }
+
+  &.info {
+    @apply bg-semantic-info-1 border border-semantic-info-3 fg-semantic-info-3;
+  }
+
+  &.error {
+    @apply bg-semantic-error-2 border border-semantic-error-3 fg-semantic-error-3;
+  }
+
+  &.warning {
+    @apply bg-semantic-warning-2 border border-semantic-warning-3 fg-semantic-warning-3;
+  }
+
+  &.success {
+    @apply bg-semantic-success-1 border border-semantic-success-3 fg-semantic-success-3;
+  }
+
+  & > button.dismiss-trigger {
+    @apply relative top-0.5;
+  }
+}

pkgs/clan-app/ui/src/components/v2/Alert/Alert.stories.tsx

@@ -0,0 +1,138 @@
+import type { Meta, StoryObj } from "@kachurun/storybook-solid";
+import { Alert, AlertProps } from "@/src/components/v2/Alert/Alert";
+import { expect, fn } from "storybook/test";
+import { StoryContext } from "@kachurun/storybook-solid-vite";
+
+const meta: Meta<AlertProps> = {
+  title: "Components/Alert",
+  component: Alert,
+  decorators: [
+    (Story: StoryObj) => (
+      <div class="w-72">
+        <Story />
+      </div>
+    ),
+  ],
+};
+
+export default meta;
+
+type Story = StoryObj<AlertProps>;
+
+export const Info: Story = {
+  args: {
+    type: "info",
+    title: "Headline",
+    description:
+      "Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.",
+  },
+};
+
+export const Error: Story = {
+  args: {
+    ...Info.args,
+    type: "error",
+  },
+};
+
+export const Warning: Story = {
+  args: {
+    ...Info.args,
+    type: "warning",
+  },
+};
+
+export const Success: Story = {
+  args: {
+    ...Info.args,
+    type: "success",
+  },
+};
+
+export const InfoIcon: Story = {
+  args: {
+    ...Info.args,
+    icon: "Info",
+  },
+};
+
+export const ErrorIcon: Story = {
+  args: {
+    ...Error.args,
+    icon: "WarningFilled",
+  },
+};
+
+export const WarningIcon: Story = {
+  args: {
+    ...Warning.args,
+    icon: "WarningFilled",
+  },
+};
+
+export const SuccessIcon: Story = {
+  args: {
+    ...Success.args,
+    icon: "Checkmark",
+  },
+};
+
+export const InfoDismiss: Story = {
+  args: {
+    ...Info.args,
+    onDismiss: fn(),
+    play: async ({ canvas, step, userEvent, args }: StoryContext) => {
+      await userEvent.click(canvas.getByRole("button"));
+      await expect(args.onDismiss).toHaveBeenCalled();
+    },
+  },
+};
+
+export const ErrorDismiss: Story = {
+  args: {
+    ...InfoDismiss.args,
+    type: "error",
+  },
+};
+
+export const WarningDismiss: Story = {
+  args: {
+    ...InfoDismiss.args,
+    type: "warning",
+  },
+};
+
+export const SuccessDismiss: Story = {
+  args: {
+    ...InfoDismiss.args,
+    type: "success",
+  },
+};
+
+export const InfoIconDismiss: Story = {
+  args: {
+    ...InfoDismiss.args,
+    icon: "Info",
+  },
+};
+
+export const ErrorIconDismiss: Story = {
+  args: {
+    ...ErrorDismiss.args,
+    icon: "WarningFilled",
+  },
+};
+
+export const WarningIconDismiss: Story = {
+  args: {
+    ...WarningDismiss.args,
+    icon: "WarningFilled",
+  },
+};
+
+export const SuccessIconDismiss: Story = {
+  args: {
+    ...SuccessDismiss.args,
+    icon: "Checkmark",
+  },
+};

pkgs/clan-app/ui/src/components/v2/Alert/Alert.tsx

@@ -0,0 +1,43 @@
+import "./Alert.css";
+import cx from "classnames";
+import Icon, { IconVariant } from "@/src/components/v2/Icon/Icon";
+import { Typography } from "@/src/components/v2/Typography/Typography";
+import { Button } from "@kobalte/core/button";
+import { Alert as KAlert } from "@kobalte/core/alert";
+
+export interface AlertProps {
+  type: "success" | "error" | "warning" | "info";
+  title: string;
+  description: string;
+  icon?: IconVariant;
+  onDismiss?: () => void;
+}
+
+export const Alert = (props: AlertProps) => (
+  <KAlert
+    class={cx("alert", props.type, {
+      "has-icon": props.icon,
+      "has-dismiss": props.onDismiss,
+    })}
+  >
+    {props.icon && <Icon icon={props.icon} color="inherit" size="1rem" />}
+    <div class="content">
+      <Typography hierarchy="body" size="default" weight="bold" color="inherit">
+        {props.title}
+      </Typography>
+      <Typography hierarchy="body" size="xs" color="inherit">
+        {props.description}
+      </Typography>
+    </div>
+    {props.onDismiss && (
+      <Button
+        name="dismiss-alert"
+        class="dismiss-trigger"
+        onClick={props.onDismiss}
+        aria-label={`Dismiss ${props.type} alert`}
+      >
+        <Icon icon="Close" color="primary" size="0.75rem" />
+      </Button>
+    )}
+  </KAlert>
+);

pkgs/clan-app/ui/src/queries/clan-meta.ts

@@ -13,7 +13,7 @@ export const clanMetaQuery = (uri: string | undefined = undefined) =>
       queryFn: async () => {
         console.log("fetching clan meta", clanURI);
 
-        const result = await callApi("show_clan_meta", {
+        const result = await callApi("get_clan_details", {
           flake: { identifier: clanURI! },
         }).promise;
 

pkgs/clan-app/ui/src/routes/clans/create.tsx

@@ -49,7 +49,7 @@ export const CreateClan = () => {
     const r = await callApi("create_clan", {
       opts: {
         dest: target_dir[0],
-        template_name: template,
+        template: template,
         initial: {
           meta,
           services: {},
@@ -65,7 +65,7 @@ export const CreateClan = () => {
     }
 
     // Will generate a key if it doesn't exist, and add a user to the clan
-    const k = await callApi("keygen", {
+    const k = await callApi("create_secrets_user", {
       flake_dir: target_dir[0],
     }).promise;
 
@@ -202,6 +202,6 @@ export const CreateClan = () => {
 };
 
 type Meta = Extract<
-  OperationResponse<"show_clan_meta">,
+  OperationResponse<"get_clan_details">,
   { status: "success" }
 >["data"];

pkgs/clan-app/ui/src/routes/clans/details.tsx

@@ -23,7 +23,7 @@ const EditClanForm = (props: EditClanFormProps) => {
   const handleSubmit: SubmitHandler<GeneralData> = async (values, event) => {
     await toast.promise(
       (async () => {
-        await callApi("update_clan_meta", {
+        await callApi("set_clan_details", {
           options: {
             flake: { identifier: props.directory },
             meta: values,
@@ -128,7 +128,7 @@ const EditClanForm = (props: EditClanFormProps) => {
   );
 };
 
-type GeneralData = SuccessQuery<"show_clan_meta">["data"];
+type GeneralData = SuccessQuery<"get_clan_details">["data"];
 
 export const ClanDetails = () => {
   const params = useParams();

pkgs/clan-app/ui/src/routes/hosts/view.tsx

@@ -4,7 +4,7 @@ import { Button } from "../../components/Button/Button";
 import Icon from "@/src/components/icon";
 
 type ServiceModel = Extract<
-  OperationResponse<"show_mdns">,
+  OperationResponse<"list_mdns_services">,
   { status: "success" }
 >["data"]["services"];
 
@@ -16,7 +16,7 @@ export const HostList: Component = () => {
       <div class="" data-tip="Refresh install targets">
         <Button
           variant="light"
-          onClick={() => callApi("show_mdns", {})}
+          onClick={() => callApi("list_mdns_services", {})}
           startIcon={<Icon icon="Update" />}
         ></Button>
       </div>

pkgs/clan-cli/clan_cli/__init__.py

@@ -15,6 +15,7 @@ from . import (
     clan,
     secrets,
     select,
+    templates,
     state,
     vms,
 )
@@ -195,6 +196,13 @@ For more detailed information, visit: {help_hyperlink("getting-started", "https:
 
     clan.register_parser(parser_flake)
 
+    parser_templates = subparsers.add_parser(
+        "templates",
+        help="Subcommands to interact with templates",
+        formatter_class=argparse.RawTextHelpFormatter,
+    )
+    templates.register_parser(parser_templates)
+
     parser_flash = subparsers.add_parser(
         "flash",
         help="Flashes your machine to an USB drive",

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

@@ -4,7 +4,6 @@ import argparse
 from clan_cli.clan.inspect import register_inspect_parser
 
 from .create import register_create_parser
-from .list import register_list_parser
 
 
 # takes a (sub)parser and configures it
@@ -19,5 +18,3 @@ def register_parser(parser: argparse.ArgumentParser) -> None:
     register_create_parser(create_parser)
     inspect_parser = subparser.add_parser("inspect", help="Inspect a clan ")
     register_inspect_parser(inspect_parser)
-    list_parser = subparser.add_parser("list", help="List clan templates")
-    register_list_parser(list_parser)

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

@@ -4,36 +4,17 @@ import logging
 from pathlib import Path
 
 from clan_lib.clan.create import CreateOptions, create_clan
-from clan_lib.templates import (
-    InputPrio,
-)
 
 log = logging.getLogger(__name__)
 
 
 def register_create_parser(parser: argparse.ArgumentParser) -> None:
-    parser.add_argument(
-        "--input",
-        type=str,
-        help="""Flake input name to use as template source
-        can be specified multiple times, inputs are tried in order of definition
-        Example: --input clan --input clan-core
-        """,
-        action="append",
-        default=[],
-    )
-
-    parser.add_argument(
-        "--no-self",
-        help="Do not look into own flake for templates",
-        action="store_true",
-        default=False,
-    )
-
     parser.add_argument(
         "--template",
         type=str,
-        help="Clan template name",
+        help="""Reference to the template to use for the clan. default="default". In the format '<flake_ref>#template_name' Where <flake_ref> is a flake reference (e.g. github:org/repo) or a local path (e.g. '.' ).
+        Omitting '<flake_ref>#' will use the builtin templates (e.g. just 'default' from clan-core ).
+        """,
         default="default",
     )
 
@@ -59,19 +40,10 @@ def register_create_parser(parser: argparse.ArgumentParser) -> None:
     )
 
     def create_flake_command(args: argparse.Namespace) -> None:
-        if len(args.input) == 0:
-            args.input = ["clan", "clan-core"]
-
-        if args.no_self:
-            input_prio = InputPrio.try_inputs(tuple(args.input))
-        else:
-            input_prio = InputPrio.try_self_then_inputs(tuple(args.input))
-
         create_clan(
             CreateOptions(
-                input_prio=input_prio,
                 dest=args.path,
-                template_name=args.template,
+                template=args.template,
                 setup_git=not args.no_git,
                 src_flake=args.flake,
                 update_clan=not args.no_update,

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

@@ -1,24 +0,0 @@
-import argparse
-import logging
-
-from clan_lib.templates import list_templates
-
-log = logging.getLogger(__name__)
-
-
-def list_command(args: argparse.Namespace) -> None:
-    template_list = list_templates("clan", args.flake)
-
-    print("Available local templates:")
-    for name, template in template_list.self.items():
-        print(f"  {name}: {template['description']}")
-
-    print("Available templates from inputs:")
-    for input_name, input_templates in template_list.inputs.items():
-        print(f"  {input_name}:")
-        for name, template in input_templates.items():
-            print(f"    {name}: {template['description']}")
-
-
-def register_list_parser(parser: argparse.ArgumentParser) -> None:
-    parser.set_defaults(func=list_command)

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

@@ -1,14 +1,14 @@
 import argparse
 import logging
 
-from clan_lib.clan.get import show_clan_meta
+from clan_lib.clan.get import get_clan_details
 
 log = logging.getLogger(__name__)
 
 
 def show_command(args: argparse.Namespace) -> None:
     flake_path = args.flake.path
-    meta = show_clan_meta(flake_path)
+    meta = get_clan_details(flake_path)
 
     print(f"Name: {meta.get('name')}")
     print(f"Description: {meta.get('description', '-')}")

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

@@ -17,7 +17,7 @@ from clan_cli.vars.generate import generate_vars
 from clan_cli.vars.upload import populate_secret_vars
 
 from .automount import pause_automounting
-from .list import list_possible_keymaps, list_possible_languages
+from .list import list_keymaps, list_languages
 
 log = logging.getLogger(__name__)
 
@@ -37,7 +37,7 @@ class Disk:
 
 # TODO: unify this with machine install
 @API.register
-def flash_machine(
+def run_machine_flash(
     machine: Machine,
     *,
     mode: str,
@@ -59,7 +59,7 @@ def flash_machine(
         generate_vars([machine])
 
         if system_config.language:
-            if system_config.language not in list_possible_languages():
+            if system_config.language not in list_languages():
                 msg = (
                     f"Language '{system_config.language}' is not a valid language. "
                     f"Run 'clan flash list languages' to see a list of possible languages."
@@ -68,7 +68,7 @@ def flash_machine(
             system_config_nix["i18n"] = {"defaultLocale": system_config.language}
 
         if system_config.keymap:
-            if system_config.keymap not in list_possible_keymaps():
+            if system_config.keymap not in list_keymaps():
                 msg = (
                     f"Keymap '{system_config.keymap}' is not a valid keymap. "
                     f"Run 'clan flash list keymaps' to see a list of possible keymaps."

pkgs/clan-cli/clan_cli/flash/flash_cmd.py

@@ -11,7 +11,7 @@ from clan_lib.machines.machines import Machine
 
 from clan_cli.completions import add_dynamic_completer, complete_machines
 
-from .flash import Disk, SystemConfig, flash_machine
+from .flash import Disk, SystemConfig, run_machine_flash
 
 log = logging.getLogger(__name__)
 
@@ -84,7 +84,7 @@ def flash_command(args: argparse.Namespace) -> None:
         if ask != "y":
             return
 
-    flash_machine(
+    run_machine_flash(
         machine,
         mode=opts.mode,
         disks=opts.disks,

pkgs/clan-cli/clan_cli/flash/list.py

@@ -2,6 +2,7 @@ import argparse
 import logging
 import os
 from pathlib import Path
+from typing import TypedDict
 
 from clan_lib.api import API
 from clan_lib.cmd import Log, RunOpts, run
@@ -11,8 +12,17 @@ from clan_lib.nix import nix_build
 log = logging.getLogger(__name__)
 
 
+class FlashOptions(TypedDict):
+    languages: list[str]
+    keymaps: list[str]
+
+
 @API.register
-def list_possible_languages() -> list[str]:
+def get_flash_options() -> FlashOptions:
+    return {"languages": list_languages(), "keymaps": list_keymaps()}
+
+
+def list_languages() -> list[str]:
     cmd = nix_build(["nixpkgs#glibcLocales"])
     result = run(cmd, RunOpts(log=Log.STDERR, error_msg="Failed to find glibc locales"))
     locale_file = Path(result.stdout.strip()) / "share" / "i18n" / "SUPPORTED"
@@ -37,8 +47,7 @@ def list_possible_languages() -> list[str]:
     return languages
 
 
-@API.register
-def list_possible_keymaps() -> list[str]:
+def list_keymaps() -> list[str]:
     cmd = nix_build(["nixpkgs#kbd"])
     result = run(cmd, RunOpts(log=Log.STDERR, error_msg="Failed to find kbdinfo"))
     keymaps_dir = Path(result.stdout.strip()) / "share" / "keymaps"
@@ -61,11 +70,11 @@ def list_possible_keymaps() -> list[str]:
 
 def list_command(args: argparse.Namespace) -> None:
     if args.cmd == "languages":
-        languages = list_possible_languages()
+        languages = list_languages()
         for language in languages:
             print(language)
     elif args.cmd == "keymaps":
-        keymaps = list_possible_keymaps()
+        keymaps = list_keymaps()
         for keymap in keymaps:
             print(keymap)
 

pkgs/clan-cli/clan_cli/host_key_check.py

@@ -1,28 +0,0 @@
-"""Common argument types and utilities for host key checking in clan CLI commands."""
-
-import argparse
-
-from clan_lib.ssh.host_key import HostKeyCheck
-
-
-def host_key_check_type(value: str) -> HostKeyCheck:
-    """
-    Argparse type converter for HostKeyCheck enum.
-    """
-    try:
-        return HostKeyCheck(value)
-    except ValueError:
-        valid_values = [e.value for e in HostKeyCheck]
-        msg = f"Invalid host key check mode: {value}. Valid options: {', '.join(valid_values)}"
-        raise argparse.ArgumentTypeError(msg) from None
-
-
-def add_host_key_check_arg(
-    parser: argparse.ArgumentParser, default: HostKeyCheck = HostKeyCheck.ASK
-) -> None:
-    parser.add_argument(
-        "--host-key-check",
-        type=host_key_check_type,
-        default=default,
-        help=f"Host key (.ssh/known_hosts) check mode. Options: {', '.join([e.value for e in HostKeyCheck])}",
-    )

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

@@ -34,7 +34,7 @@ Examples:
   $ clan machines update [MACHINES]
   Will update the specified machines [MACHINES], if [MACHINES] is omitted, the command
   will attempt to update every configured machine.
-  To exclude machines being updated `clan.deployment.requireExplicitUpdate = true;`
+  To exclude machines being updated `clan.core.deployment.requireExplicitUpdate = true;`
   can be set in the machine config.
 
   $ clan machines update --tags [TAGS..]

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

@@ -5,14 +5,13 @@ from pathlib import Path
 from clan_lib.machines.hardware import (
     HardwareConfig,
     HardwareGenerateOptions,
-    generate_machine_hardware_info,
+    run_machine_hardware_info,
 )
 from clan_lib.machines.machines import Machine
 from clan_lib.machines.suggestions import validate_machine_names
 from clan_lib.ssh.remote import Remote
 
 from clan_cli.completions import add_dynamic_completer, complete_machines
-from clan_cli.host_key_check import add_host_key_check_arg
 
 from .types import machine_name_type
 
@@ -39,7 +38,7 @@ def update_hardware_config_command(args: argparse.Namespace) -> None:
         host_key_check=args.host_key_check, private_key=args.identity_file
     )
 
-    generate_machine_hardware_info(opts, target_host)
+    run_machine_hardware_info(opts, target_host)
 
 
 def register_update_hardware_config(parser: argparse.ArgumentParser) -> None:
@@ -56,7 +55,12 @@ def register_update_hardware_config(parser: argparse.ArgumentParser) -> None:
         nargs="?",
         help="ssh address to install to in the form of user@host:2222",
     )
-    add_host_key_check_arg(parser)
+    parser.add_argument(
+        "--host-key-check",
+        choices=["strict", "ask", "tofu", "none"],
+        default="ask",
+        help="Host key (.ssh/known_hosts) check mode.",
+    )
     parser.add_argument(
         "--password",
         help="Pre-provided password the cli will prompt otherwise if needed.",

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

@@ -4,7 +4,7 @@ import sys
 from pathlib import Path
 
 from clan_lib.errors import ClanError
-from clan_lib.machines.install import BuildOn, InstallOptions, install_machine
+from clan_lib.machines.install import BuildOn, InstallOptions, run_machine_install
 from clan_lib.machines.machines import Machine
 from clan_lib.ssh.remote import Remote
 
@@ -13,7 +13,6 @@ from clan_cli.completions import (
     complete_machines,
     complete_target_host,
 )
-from clan_cli.host_key_check import add_host_key_check_arg
 from clan_cli.machines.hardware import HardwareConfig
 from clan_cli.ssh.deploy_info import DeployInfo, find_reachable_host, ssh_command_parse
 
@@ -66,7 +65,7 @@ def install_command(args: argparse.Namespace) -> None:
             if ask != "y":
                 return None
 
-        return install_machine(
+        return run_machine_install(
             InstallOptions(
                 machine=machine,
                 kexec=args.kexec,
@@ -98,7 +97,12 @@ def register_install_parser(parser: argparse.ArgumentParser) -> None:
         help="do not reboot after installation (deprecated)",
         default=False,
     )
-    add_host_key_check_arg(parser)
+    parser.add_argument(
+        "--host-key-check",
+        choices=["strict", "ask", "tofu", "none"],
+        default="ask",
+        help="Host key (.ssh/known_hosts) check mode.",
+    )
     parser.add_argument(
         "--build-on",
         choices=[x.value for x in BuildOn],

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

@@ -4,10 +4,12 @@ import sys
 
 from clan_lib.async_run import AsyncContext, AsyncOpts, AsyncRuntime
 from clan_lib.errors import ClanError
-from clan_lib.machines.list import list_full_machines, query_machines_by_tags
+from clan_lib.flake.flake import Flake
+from clan_lib.machines.actions import list_machines
+from clan_lib.machines.list import instantiate_inventory_to_machines
 from clan_lib.machines.machines import Machine
 from clan_lib.machines.suggestions import validate_machine_names
-from clan_lib.machines.update import deploy_machine
+from clan_lib.machines.update import run_machine_deploy
 from clan_lib.nix import nix_config
 from clan_lib.ssh.remote import Remote
 
@@ -16,129 +18,139 @@ from clan_cli.completions import (
     complete_machines,
     complete_tags,
 )
-from clan_cli.host_key_check import add_host_key_check_arg
 
 log = logging.getLogger(__name__)
 
 
+def requires_explicit_update(m: Machine) -> bool:
+    try:
+        if m.select("config.clan.deployment.requireExplicitUpdate"):
+            return False
+    except Exception:
+        pass
+
+    try:
+        # check if the machine has a target host set
+        m.target_host  # noqa: B018
+    except ClanError:
+        return False
+
+    return True
+
+
+def get_machines_for_update(
+    flake: Flake,
+    explicit_names: list[str],
+    filter_tags: list[str],
+) -> list[Machine]:
+    all_machines = list_machines(flake)
+    machines_with_tags = list_machines(flake, {"filter": {"tags": filter_tags}})
+
+    if filter_tags and not machines_with_tags:
+        msg = f"No machines found with tags: {' AND '.join(filter_tags)}"
+        raise ClanError(msg)
+
+    # Implicit update all machines / with tags
+    # Using tags is not an explizit update
+    if not explicit_names:
+        machines_to_update = list(
+            filter(
+                requires_explicit_update,
+                instantiate_inventory_to_machines(flake, machines_with_tags).values(),
+            )
+        )
+        # all machines that are in the clan but not included in the update list
+        machine_names_to_update = [m.name for m in machines_to_update]
+        ignored_machines = {
+            m_name for m_name in all_machines if m_name not in machine_names_to_update
+        }
+
+        if not machines_to_update and ignored_machines:
+            print(
+                "WARNING: No machines to update.\n"
+                "The following defined machines were ignored because they\n"
+                "- Require explicit update (see 'requireExplicitUpdate')\n",
+                file=sys.stderr,
+            )
+            for m in ignored_machines:
+                print(m, file=sys.stderr)
+
+        return machines_to_update
+
+    # Else: Explicit update
+    machines_to_update = []
+    valid_names = validate_machine_names(explicit_names, flake)
+    for name in valid_names:
+        inventory_machine = machines_with_tags.get(name)
+        if not inventory_machine:
+            msg = "This is an internal bug"
+            raise ClanError(msg)
+
+        machines_to_update.append(
+            Machine.from_inventory(name, flake, inventory_machine)
+        )
+
+    return machines_to_update
+
+
 def update_command(args: argparse.Namespace) -> None:
     try:
         if args.flake is None:
             msg = "Could not find clan flake toplevel directory"
             raise ClanError(msg)
 
-        all_machines: list[Machine] = []
-        if args.tags:
-            tag_filtered_machines = query_machines_by_tags(args.flake, args.tags)
-            if args.machines:
-                selected_machines = [
-                    name for name in args.machines if name in tag_filtered_machines
-                ]
-            else:
-                selected_machines = list(tag_filtered_machines.keys())
-        else:
-            selected_machines = (
-                args.machines
-                if args.machines
-                else list(list_full_machines(args.flake).keys())
-            )
+        machines_to_update = get_machines_for_update(
+            args.flake, args.machines, args.tags
+        )
 
-        if args.tags and not selected_machines:
-            msg = f"No machines found with tags: {', '.join(args.tags)}"
-            raise ClanError(msg)
-
-        if args.machines:
-            validate_machine_names(args.machines, args.flake)
-
-        for machine_name in selected_machines:
-            machine = Machine(name=machine_name, flake=args.flake)
-            all_machines.append(machine)
-
-        if args.target_host is not None and len(all_machines) > 1:
+        if args.target_host is not None and len(machines_to_update) > 1:
             msg = "Target Host can only be set for one machines"
             raise ClanError(msg)
 
-        def filter_machine(m: Machine) -> bool:
-            try:
-                if m.select("config.clan.deployment.requireExplicitUpdate"):
-                    return False
-            except Exception:
-                pass
+        # Prepopulate the cache
+        config = nix_config()
+        system = config["system"]
+        machine_names = [machine.name for machine in machines_to_update]
+        args.flake.precache(
+            [
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.validationHash",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.deployment.requireExplicitUpdate",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.system.clan.deployment.nixosMobileWorkaround",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.secretModule",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.publicModule",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.settings.secretModule",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.settings.publicModule",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.services",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.{{share,dependencies,migrateFact,prompts}}",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.files.*.{{secret,deploy,owner,group,mode,neededFor}}",
+                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.secretUploadDirectory",
+            ]
+        )
 
-            try:
-                # check if the machine has a target host set
-                m.target_host  # noqa: B018
-            except ClanError:
-                return False
-
-            return True
-
-        machines_to_update = all_machines
-        implicit_all: bool = len(args.machines) == 0 and not args.tags
-        if implicit_all:
-            machines_to_update = list(filter(filter_machine, all_machines))
-
-        # machines that are in the list but not included in the update list
-        ignored_machines = {m.name for m in all_machines if m not in machines_to_update}
-
-        if not machines_to_update and ignored_machines:
-            print(
-                "WARNING: No machines to update.\n"
-                "The following defined machines were ignored because they\n"
-                "- Require explicit update (see 'requireExplicitUpdate')\n",
-                "- Might not have the `clan.core.networking.targetHost` nixos option set:\n",
-                file=sys.stderr,
-            )
-            for m in ignored_machines:
-                print(m, file=sys.stderr)
-
-        if machines_to_update:
-            # Prepopulate the cache
-            config = nix_config()
-            system = config["system"]
-            machine_names = [machine.name for machine in machines_to_update]
-            args.flake.precache(
-                [
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.validationHash",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.deployment.requireExplicitUpdate",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.system.clan.deployment.nixosMobileWorkaround",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.secretModule",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.publicModule",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.settings.secretModule",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.settings.publicModule",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.services",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.{{share,dependencies,migrateFact,prompts}}",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.files.*.{{secret,deploy,owner,group,mode,neededFor}}",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.secretUploadDirectory",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.vars.password-store.secretLocation",
-                    f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.settings.passBackend",
-                ]
-            )
-
-            host_key_check = args.host_key_check
-            with AsyncRuntime() as runtime:
-                for machine in machines_to_update:
-                    if args.target_host:
-                        target_host = Remote.from_ssh_uri(
-                            machine_name=machine.name,
-                            address=args.target_host,
-                        ).override(host_key_check=host_key_check)
-                    else:
-                        target_host = machine.target_host().override(
-                            host_key_check=host_key_check
-                        )
-                    runtime.async_run(
-                        AsyncOpts(
-                            tid=machine.name,
-                            async_ctx=AsyncContext(prefix=machine.name),
-                        ),
-                        deploy_machine,
-                        machine=machine,
-                        target_host=target_host,
-                        build_host=machine.build_host(),
+        host_key_check = args.host_key_check
+        with AsyncRuntime() as runtime:
+            for machine in machines_to_update:
+                if args.target_host:
+                    target_host = Remote.from_ssh_uri(
+                        machine_name=machine.name,
+                        address=args.target_host,
+                    ).override(host_key_check=host_key_check)
+                else:
+                    target_host = machine.target_host().override(
+                        host_key_check=host_key_check
                     )
-                runtime.join_all()
-                runtime.check_all()
+                runtime.async_run(
+                    AsyncOpts(
+                        tid=machine.name,
+                        async_ctx=AsyncContext(prefix=machine.name),
+                    ),
+                    run_machine_deploy,
+                    machine=machine,
+                    target_host=target_host,
+                    build_host=machine.build_host(),
+                )
+            runtime.join_all()
+            runtime.check_all()
 
     except KeyboardInterrupt:
         log.warning("Interrupted by user")
@@ -164,7 +176,12 @@ def register_update_parser(parser: argparse.ArgumentParser) -> None:
     )
     add_dynamic_completer(tag_parser, complete_tags)
 
-    add_host_key_check_arg(parser)
+    parser.add_argument(
+        "--host-key-check",
+        choices=["strict", "ask", "tofu", "none"],
+        default="ask",
+        help="Host key (.ssh/known_hosts) check mode.",
+    )
     parser.add_argument(
         "--target-host",
         type=str,

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

@@ -0,0 +1,162 @@
+import pytest
+from clan_lib.flake import Flake
+
+from clan_cli.machines.update import get_machines_for_update
+
+# Functions to test
+from clan_cli.tests.fixtures_flakes import FlakeForTest
+
+
+@pytest.mark.parametrize(
+    ("test_flake_with_core", "explicit_names", "filter_tags", "expected_names"),
+    [
+        (
+            {
+                "inventory_expr": r"""{
+                    machines.jon = { tags = [ "foo" "bar" ]; };
+                    machines.sara = { tags = [ "foo" "baz" ]; };
+                }"""
+            },
+            ["jon"],  # explizit names
+            [],  # filter tags
+            ["jon"],  # expected
+        )
+    ],
+    # Important!
+    # tells pytest to pass these values to the fixture
+    # So we can write it to the flake fixtures
+    indirect=["test_flake_with_core"],
+)
+@pytest.mark.with_core
+def test_get_machines_for_update_single_name(
+    test_flake_with_core: FlakeForTest,
+    explicit_names: list[str],
+    filter_tags: list[str],
+    expected_names: list[str],
+) -> None:
+    selected_for_update = get_machines_for_update(
+        Flake(str(test_flake_with_core.path)),
+        explicit_names=explicit_names,
+        filter_tags=filter_tags,
+    )
+    names = [m.name for m in selected_for_update]
+
+    print(explicit_names, filter_tags)
+    assert names == expected_names
+
+
+@pytest.mark.parametrize(
+    ("test_flake_with_core", "explicit_names", "filter_tags", "expected_names"),
+    [
+        (
+            {
+                "inventory_expr": r"""{
+                    machines.jon = { tags = [ "foo" "bar" ]; };
+                    machines.sara = { tags = [ "foo" "baz" ]; };
+                }"""
+            },
+            [],  # explizit names
+            ["foo"],  # filter tags
+            ["jon", "sara"],  # expected
+        )
+    ],
+    # Important!
+    # tells pytest to pass these values to the fixture
+    # So we can write it to the flake fixtures
+    indirect=["test_flake_with_core"],
+)
+@pytest.mark.with_core
+def test_get_machines_for_update_tags(
+    test_flake_with_core: FlakeForTest,
+    explicit_names: list[str],
+    filter_tags: list[str],
+    expected_names: list[str],
+) -> None:
+    selected_for_update = get_machines_for_update(
+        Flake(str(test_flake_with_core.path)),
+        explicit_names=explicit_names,
+        filter_tags=filter_tags,
+    )
+    names = [m.name for m in selected_for_update]
+
+    print(explicit_names, filter_tags)
+    assert names == expected_names
+
+
+@pytest.mark.parametrize(
+    ("test_flake_with_core", "explicit_names", "filter_tags", "expected_names"),
+    [
+        (
+            {
+                "inventory_expr": r"""{
+                    machines.jon = { tags = [ "foo" "bar" ]; };
+                    machines.sara = { tags = [ "foo" "baz" ]; };
+                }"""
+            },
+            ["sara"],  # explizit names
+            ["foo"],  # filter tags
+            ["sara"],  # expected
+        )
+    ],
+    # Important!
+    # tells pytest to pass these values to the fixture
+    # So we can write it to the flake fixtures
+    indirect=["test_flake_with_core"],
+)
+@pytest.mark.with_core
+def test_get_machines_for_update_tags_and_name(
+    test_flake_with_core: FlakeForTest,
+    explicit_names: list[str],
+    filter_tags: list[str],
+    expected_names: list[str],
+) -> None:
+    selected_for_update = get_machines_for_update(
+        Flake(str(test_flake_with_core.path)),
+        explicit_names=explicit_names,
+        filter_tags=filter_tags,
+    )
+    names = [m.name for m in selected_for_update]
+
+    print(explicit_names, filter_tags)
+    assert names == expected_names
+
+
+@pytest.mark.parametrize(
+    ("test_flake_with_core", "explicit_names", "filter_tags", "expected_names"),
+    [
+        (
+            {
+                "inventory_expr": r"""{
+                    machines.jon = { tags = [ "foo" "bar" ]; };
+                    machines.sara = { tags = [ "foo" "baz" ]; };
+                }"""
+            },
+            [],  # no explizit names
+            [],  # no filter tags
+            ["jon", "sara", "vm1", "vm2"],  # all machines
+        ),
+    ],
+    # Important!
+    # tells pytest to pass these values to the fixture
+    # So we can write it to the flake fixtures
+    indirect=["test_flake_with_core"],
+)
+@pytest.mark.with_core
+def test_get_machines_for_update_implicit_all(
+    test_flake_with_core: FlakeForTest,
+    explicit_names: list[str],
+    filter_tags: list[str],
+    expected_names: list[str],
+) -> None:
+    selected_for_update = get_machines_for_update(
+        Flake(str(test_flake_with_core.path)),
+        explicit_names=explicit_names,
+        filter_tags=filter_tags,
+    )
+    names = [m.name for m in selected_for_update]
+
+    print(explicit_names, filter_tags)
+    assert names == expected_names
+
+
+# TODO: Add more tests for requireExplicitUpdate

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

@@ -13,7 +13,6 @@ from pathlib import Path
 from tempfile import NamedTemporaryFile
 from typing import IO, Any
 
-from clan_lib.api import API
 from clan_lib.cmd import Log, RunOpts, run
 from clan_lib.dirs import user_config_dir
 from clan_lib.errors import ClanError
@@ -62,7 +61,7 @@ class KeyType(enum.Enum):
 
                     try:
                         for public_key in get_public_age_keys(content):
-                            log.info(
+                            log.debug(
                                 f"Found age public key from a private key "
                                 f"in {key_path}: {public_key}"
                             )
@@ -85,7 +84,7 @@ class KeyType(enum.Enum):
 
                 try:
                     for public_key in get_public_age_keys(content):
-                        log.info(
+                        log.debug(
                             f"Found age public key from a private key "
                             f"in the environment (SOPS_AGE_KEY): {public_key}"
                         )
@@ -107,7 +106,7 @@ class KeyType(enum.Enum):
             if pgp_fingerprints := os.environ.get("SOPS_PGP_FP"):
                 for fp in pgp_fingerprints.strip().split(","):
                     msg = f"Found PGP public key in the environment (SOPS_PGP_FP): {fp}"
-                    log.info(msg)
+                    log.debug(msg)
                     keyring.append(fp)
             return keyring
 
@@ -398,7 +397,6 @@ def default_admin_private_key_path() -> Path:
     return user_config_dir() / "sops" / "age" / "keys.txt"
 
 
-@API.register
 def maybe_get_admin_public_keys() -> list[SopsKey] | None:
     keyring = SopsKey.collect_public_keys()
 

pkgs/clan-cli/clan_cli/ssh/deploy_info.py

@@ -8,14 +8,12 @@ from typing import Any
 from clan_lib.cmd import run
 from clan_lib.errors import ClanError
 from clan_lib.nix import nix_shell
-from clan_lib.ssh.host_key import HostKeyCheck
-from clan_lib.ssh.remote import Remote
+from clan_lib.ssh.remote import HostKeyCheck, Remote
 
 from clan_cli.completions import (
     add_dynamic_completer,
     complete_machines,
 )
-from clan_cli.host_key_check import add_host_key_check_arg
 from clan_cli.ssh.tor import TorTarget, spawn_tor, ssh_tor_reachable
 
 log = logging.getLogger(__name__)
@@ -100,7 +98,7 @@ def find_reachable_host(deploy_info: DeployInfo) -> Remote | None:
         return deploy_info.addrs[0]
 
     for addr in deploy_info.addrs:
-        if addr.is_ssh_reachable():
+        if addr.check_machine_ssh_reachable():
             return addr
     return None
 
@@ -183,5 +181,10 @@ def register_parser(parser: argparse.ArgumentParser) -> None:
         "--png",
         help="specify the json file for ssh data as the qrcode image (generated by starting the clan installer)",
     )
-    add_host_key_check_arg(parser, default=HostKeyCheck.TOFU)
+    parser.add_argument(
+        "--host-key-check",
+        choices=["strict", "ask", "tofu", "none"],
+        default="tofu",
+        help="Host key (.ssh/known_hosts) check mode.",
+    )
     parser.set_defaults(func=ssh_command)

pkgs/clan-cli/clan_cli/ssh/test_deploy_info.py

@@ -4,7 +4,6 @@ from pathlib import Path
 import pytest
 from clan_lib.cmd import RunOpts, run
 from clan_lib.nix import nix_shell
-from clan_lib.ssh.host_key import HostKeyCheck
 from clan_lib.ssh.remote import Remote
 
 from clan_cli.ssh.deploy_info import DeployInfo, find_reachable_host
@@ -24,7 +23,7 @@ def test_qrcode_scan(temp_dir: Path) -> None:
     run(cmd, RunOpts(input=data.encode()))
 
     # Call the qrcode_scan function
-    deploy_info = DeployInfo.from_qr_code(img_path, HostKeyCheck.NONE)
+    deploy_info = DeployInfo.from_qr_code(img_path, "none")
 
     host = deploy_info.addrs[0]
     assert host.address == "192.168.122.86"
@@ -47,7 +46,7 @@ def test_qrcode_scan(temp_dir: Path) -> None:
 
 def test_from_json() -> None:
     data = '{"pass":"scabbed-defender-headlock","tor":"qjeerm4r6t55hcfum4pinnvscn5njlw2g3k7ilqfuu7cdt3ahaxhsbid.onion","addrs":["192.168.122.86"]}'
-    deploy_info = DeployInfo.from_json(json.loads(data), HostKeyCheck.NONE)
+    deploy_info = DeployInfo.from_json(json.loads(data), "none")
 
     host = deploy_info.addrs[0]
     assert host.password == "scabbed-defender-headlock"
@@ -70,9 +69,7 @@ def test_from_json() -> None:
 @pytest.mark.with_core
 def test_find_reachable_host(hosts: list[Remote]) -> None:
     host = hosts[0]
-    deploy_info = DeployInfo.from_hostnames(
-        ["172.19.1.2", host.ssh_url()], HostKeyCheck.NONE
-    )
+    deploy_info = DeployInfo.from_hostnames(["172.19.1.2", host.ssh_url()], "none")
 
     assert deploy_info.addrs[0].address == "172.19.1.2"
 

pkgs/clan-cli/clan_cli/templates/__init__.py

@@ -0,0 +1,15 @@
+# !/usr/bin/env python3
+import argparse
+from .list import register_list_parser
+
+
+# takes a (sub)parser and configures it
+def register_parser(parser: argparse.ArgumentParser) -> None:
+    subparser = parser.add_subparsers(
+        title="command",
+        description="the command to run",
+        help="the command to run",
+        required=True,
+    )
+    list_parser = subparser.add_parser("list", help="List avilable templates")
+    register_list_parser(list_parser)

pkgs/clan-cli/clan_cli/templates/list.py

@@ -0,0 +1,60 @@
+import argparse
+import logging
+
+from clan_lib.nix_models.clan import TemplateClanType
+from clan_lib.templates import list_templates
+
+log = logging.getLogger(__name__)
+
+
+def list_command(args: argparse.Namespace) -> None:
+    templates = list_templates(args.flake)
+
+    # Display all templates
+    for i, (template_type, _builtin_template_set) in enumerate(
+        templates.builtins.items()
+    ):
+        builtin_template_set: TemplateClanType | None = templates.builtins.get(
+            template_type, None
+        )  # type: ignore
+        if not builtin_template_set:
+            continue
+
+        print(f"Avilable '{template_type}' templates")
+        print("├── <builtin>")
+        for i, (name, template) in enumerate(builtin_template_set.items()):
+            description = template.get("description", "no description")
+            is_last_template = i == len(builtin_template_set.items()) - 1
+            if not is_last_template:
+                print(f"│   ├── {name}: {description}")
+            else:
+                print(f"│   └── {name}: {description}")
+
+        for i, (input_name, input_templates) in enumerate(templates.custom.items()):
+            custom_templates: TemplateClanType | None = input_templates.get(
+                template_type, None
+            )  # type: ignore
+            if not custom_templates:
+                continue
+
+            is_last_input = i == len(templates.custom.items()) - 1
+            prefix = "│" if not is_last_input else " "
+            if not is_last_input:
+                print(f"├── inputs.{input_name}:")
+            else:
+                print(f"└── inputs.{input_name}:")
+
+            for i, (name, template) in enumerate(custom_templates.items()):
+                is_last_template = i == len(custom_templates.items()) - 1
+                if not is_last_template:
+                    print(
+                        f"{prefix}   ├── {name}: {template.get('description', 'no description')}"
+                    )
+                else:
+                    print(
+                        f"{prefix}   └── {name}: {template.get('description', 'no description')}"
+                    )
+
+
+def register_list_parser(parser: argparse.ArgumentParser) -> None:
+    parser.set_defaults(func=list_command)

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

@@ -4,7 +4,6 @@ from pathlib import Path
 
 import pytest
 from clan_cli.tests.sshd import Sshd
-from clan_lib.ssh.host_key import HostKeyCheck
 from clan_lib.ssh.remote import Remote
 
 
@@ -17,7 +16,7 @@ def hosts(sshd: Sshd) -> list[Remote]:
             port=sshd.port,
             user=login,
             private_key=Path(sshd.key),
-            host_key_check=HostKeyCheck.NONE,
+            host_key_check="none",
             command_prefix="local_test",
         )
     ]

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

@@ -1,63 +1,15 @@
-# mypy: disable-error-code="var-annotated"
-
-import json
-from pathlib import Path
-from typing import Any
-
 import pytest
+from pathlib import Path
+
 from clan_cli.tests.fixtures_flakes import FlakeForTest
 from clan_lib.cmd import run
 from clan_lib.flake import Flake
-from clan_lib.git import commit_file
-from clan_lib.locked_open import locked_open
 from clan_lib.nix import nix_command
-from clan_lib.templates import (
-    ClanExports,
-    InputName,
-    TemplateName,
-    get_clan_nix_attrset,
-    get_template,
-    list_templates,
-)
+
+from clan_lib.templates import list_templates
 from clan_lib.templates.filesystem import copy_from_nixstore
 
 
-# Function to write clan attributes to a file
-def write_clan_attr(clan_attrset: dict[str, Any], flake: FlakeForTest) -> None:
-    file = flake.path / "clan_attrs.json"
-    with locked_open(file, "w") as cfile:
-        json.dump(clan_attrset, cfile, indent=2)
-
-    commit_file(file, flake.path, "Add clan attributes")
-
-
-# Common function to test clan nix attrset
-def nix_attr_tester(
-    test_flake_with_core: FlakeForTest,
-    injected: dict[str, Any],
-    expected_self: dict[str, Any],
-    test_number: int,
-) -> ClanExports:
-    write_clan_attr(injected, test_flake_with_core)
-    clan_dir = Flake(str(test_flake_with_core.path))
-    nix_attrset = get_clan_nix_attrset(clan_dir)
-
-    def recursive_sort(item: Any) -> Any:
-        if isinstance(item, dict):
-            return {k: recursive_sort(item[k]) for k in sorted(item)}
-        if isinstance(item, list):
-            return sorted(recursive_sort(elem) for elem in item)
-        return item
-
-    returned_sorted = recursive_sort(nix_attrset["self"])
-    expected_sorted = recursive_sort(expected_self["self"])
-
-    assert json.dumps(returned_sorted, indent=2) == json.dumps(
-        expected_sorted, indent=2
-    )
-    return nix_attrset
-
-
 @pytest.mark.impure
 def test_copy_from_nixstore_symlink(
     monkeypatch: pytest.MonkeyPatch, temporary_home: Path
@@ -86,170 +38,37 @@ def test_clan_core_templates(
     temporary_home: Path,
 ) -> None:
     clan_dir = Flake(str(test_flake_with_core.path))
-    nix_attrset = get_clan_nix_attrset(clan_dir)
 
-    clan_core_templates = nix_attrset["inputs"][InputName("clan-core")]["templates"][
-        "clan"
+    templates = list_templates(clan_dir)
+
+    assert list(templates.builtins.get("clan", {}).keys()) == [
+        "default",
+        "flake-parts",
+        "minimal",
+        "minimal-flake-parts",
     ]
-    clan_core_template_keys = list(clan_core_templates.keys())
 
-    expected_templates = ["default", "flake-parts", "minimal", "minimal-flake-parts"]
-    assert clan_core_template_keys == expected_templates
+    # clan.default
+    default_template = templates.builtins.get("clan", {}).get("default")
+    assert default_template is not None
 
-    vlist_temps = list_templates("clan", clan_dir)
-    list_template_keys = list(vlist_temps.inputs[InputName("clan-core")].keys())
-    assert list_template_keys == expected_templates
-
-    default_template = get_template(
-        TemplateName("default"),
-        "clan",
-        input_prio=None,
-        clan_dir=clan_dir,
-    )
+    template_path = default_template.get("path", None)
+    assert template_path is not None
 
     new_clan = temporary_home / "new_clan"
+
     copy_from_nixstore(
-        Path(default_template.src["path"]),
+        Path(template_path),
         new_clan,
     )
-    assert (new_clan / "flake.nix").exists()
-    assert (new_clan / "machines").is_dir()
-    assert (new_clan / "machines" / "jon").is_dir()
-    config_nix_p = new_clan / "machines" / "jon" / "configuration.nix"
-    assert (config_nix_p).is_file()
 
-    # Test if we can write to the configuration.nix file
-    with config_nix_p.open("r+") as f:
+    flake_nix = new_clan / "flake.nix"
+    assert (flake_nix).exists()
+    assert (flake_nix).is_file()
+
+    assert (new_clan / "machines").is_dir()
+
+    # Test if we can write to the flake.nix file
+    with flake_nix.open("r+") as f:
         data = f.read()
         f.write(data)
-
-
-# Test Case 1: Minimal input with empty templates
-@pytest.mark.with_core
-def test_clan_get_nix_attrset_case_1(
-    monkeypatch: pytest.MonkeyPatch,
-    temporary_home: Path,
-    test_flake_with_core: FlakeForTest,
-) -> None:
-    test_number = 1
-    injected = {"templates": {"disko": {}, "machine": {}}}
-    expected = {
-        "inputs": {},
-        "self": {"templates": {"disko": {}, "machine": {}, "clan": {}}},
-    }
-    nix_attr_tester(test_flake_with_core, injected, expected, test_number)
-
-
-# Test Case 2: Input with one template under 'clan'
-@pytest.mark.with_core
-def test_clan_get_nix_attrset_case_2(
-    monkeypatch: pytest.MonkeyPatch,
-    temporary_home: Path,
-    test_flake_with_core: FlakeForTest,
-) -> None:
-    test_number = 2
-    injected = {
-        "templates": {
-            "clan": {
-                "example_template": {
-                    "description": "An example clan template.",
-                    "path": "/example/path",
-                }
-            }
-        }
-    }
-    expected = {
-        "inputs": {},
-        "self": {
-            "templates": {
-                "clan": {
-                    "example_template": {
-                        "description": "An example clan template.",
-                        "path": "/example/path",
-                    }
-                },
-                "disko": {},
-                "machine": {},
-            },
-        },
-    }
-
-    nix_attrset = nix_attr_tester(test_flake_with_core, injected, expected, test_number)
-
-    assert "default" in list(
-        nix_attrset["inputs"][InputName("clan-core")]["templates"]["clan"].keys()
-    )
-
-
-# Test Case 3: Input with templates under multiple types
-@pytest.mark.with_core
-def test_clan_get_nix_attrset_case_3(
-    monkeypatch: pytest.MonkeyPatch,
-    temporary_home: Path,
-    test_flake_with_core: FlakeForTest,
-) -> None:
-    test_number = 3
-    injected = {
-        "templates": {
-            "clan": {
-                "clan_template": {
-                    "description": "A clan template.",
-                    "path": "/clan/path",
-                }
-            },
-            "disko": {
-                "disko_template": {
-                    "description": "A disko template.",
-                    "path": "/disko/path",
-                }
-            },
-            "machine": {
-                "machine_template": {
-                    "description": "A machine template.",
-                    "path": "/machine/path",
-                }
-            },
-        }
-    }
-    expected = {
-        "inputs": {},
-        "self": {
-            "templates": {
-                "clan": {
-                    "clan_template": {
-                        "description": "A clan template.",
-                        "path": "/clan/path",
-                    }
-                },
-                "disko": {
-                    "disko_template": {
-                        "description": "A disko template.",
-                        "path": "/disko/path",
-                    }
-                },
-                "machine": {
-                    "machine_template": {
-                        "description": "A machine template.",
-                        "path": "/machine/path",
-                    }
-                },
-            },
-        },
-    }
-    nix_attr_tester(test_flake_with_core, injected, expected, test_number)
-
-
-# Test Case 6: Input with missing 'templates' and 'modules' (empty clan attrset)
-@pytest.mark.with_core
-def test_clan_get_nix_attrset_case_6(
-    monkeypatch: pytest.MonkeyPatch,
-    temporary_home: Path,
-    test_flake_with_core: FlakeForTest,
-) -> None:
-    test_number = 6
-    injected = {}
-    expected = {
-        "inputs": {},
-        "self": {"templates": {"disko": {}, "machine": {}, "clan": {}}},
-    }
-    nix_attr_tester(test_flake_with_core, injected, expected, test_number)

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

@@ -10,11 +10,11 @@ from clan_cli.tests.helpers import cli
 from clan_cli.vars.check import check_vars
 from clan_cli.vars.generate import (
     Generator,
-    generate_vars_for_machine,
-    generate_vars_for_machine_interactive,
-    get_generators_closure,
+    run_generators,
+    create_machine_vars_interactive,
+    get_generators,
 )
-from clan_cli.vars.get import get_var
+from clan_cli.vars.get import get_machine_var
 from clan_cli.vars.graph import all_missing_closure, requested_closure
 from clan_cli.vars.list import stringify_all_vars
 from clan_cli.vars.public_modules import in_repo
@@ -172,25 +172,23 @@ def test_generate_public_and_secret_vars(
         in commit_message
     )
     assert (
-        get_var(
+        get_machine_var(
             str(machine.flake.path), machine.name, "my_generator/my_value"
         ).printable_value
         == "public"
     )
     assert (
-        get_var(
+        get_machine_var(
             str(machine.flake.path), machine.name, "my_shared_generator/my_shared_value"
         ).printable_value
         == "shared"
     )
     vars_text = stringify_all_vars(machine)
     in_repo_store = in_repo.FactStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
+        machine="my_machine", flake=Flake(str(flake.path))
     )
     assert not in_repo_store.exists(Generator("my_generator"), "my_secret")
-    sops_store = sops.SecretStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
-    )
+    sops_store = sops.SecretStore(machine="my_machine", flake=Flake(str(flake.path)))
     assert sops_store.exists(Generator("my_generator"), "my_secret")
     assert sops_store.get(Generator("my_generator"), "my_secret").decode() == "secret"
     assert sops_store.exists(Generator("dependent_generator"), "my_secret")
@@ -265,12 +263,10 @@ def test_generate_secret_var_sops_with_default_group(
     cli.run(["secrets", "groups", "add-user", "my_group", sops_setup.user])
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
     in_repo_store = in_repo.FactStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
+        machine="my_machine", flake=Flake(str(flake.path))
     )
     assert not in_repo_store.exists(Generator("first_generator"), "my_secret")
-    sops_store = sops.SecretStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
-    )
+    sops_store = sops.SecretStore(machine="my_machine", flake=Flake(str(flake.path)))
     assert sops_store.exists(Generator("first_generator"), "my_secret")
     assert (
         sops_store.get(Generator("first_generator"), "my_secret").decode() == "hello\n"
@@ -355,8 +351,8 @@ def test_generated_shared_secret_sops(
     cli.run(["vars", "generate", "--flake", str(flake.path), "machine2"])
     assert check_vars(machine2.name, machine2.flake)
     assert check_vars(machine2.name, machine2.flake)
-    m1_sops_store = sops.SecretStore(machine1)
-    m2_sops_store = sops.SecretStore(machine2)
+    m1_sops_store = sops.SecretStore(machine1.name, machine1.flake)
+    m2_sops_store = sops.SecretStore(machine2.name, machine2.flake)
     assert m1_sops_store.exists(
         Generator("my_shared_generator", share=True), "my_shared_secret"
     )
@@ -403,12 +399,25 @@ def test_generate_secret_var_password_store(
     shutil.copytree(test_root / "data" / "password-store", password_store_dir)
     monkeypatch.setenv("PASSWORD_STORE_DIR", str(password_store_dir))
 
+    # Initialize password store as a git repository
+    import subprocess
+
+    subprocess.run(["git", "init"], cwd=password_store_dir, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@example.com"],
+        cwd=password_store_dir,
+        check=True,
+    )
+    subprocess.run(
+        ["git", "config", "user.name", "Test User"], cwd=password_store_dir, check=True
+    )
+
     machine = Machine(name="my_machine", flake=Flake(str(flake.path)))
     assert not check_vars(machine.name, machine.flake)
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
     assert check_vars(machine.name, machine.flake)
     store = password_store.SecretStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
+        machine="my_machine", flake=Flake(str(flake.path))
     )
     assert store.exists(Generator("my_generator", share=False, files=[]), "my_secret")
     assert not store.exists(
@@ -483,12 +492,8 @@ def test_generate_secret_for_multiple_machines(
     monkeypatch.chdir(flake.path)
     cli.run(["vars", "generate", "--flake", str(flake.path)])
     # check if public vars have been created correctly
-    in_repo_store1 = in_repo.FactStore(
-        Machine(name="machine1", flake=Flake(str(flake.path)))
-    )
-    in_repo_store2 = in_repo.FactStore(
-        Machine(name="machine2", flake=Flake(str(flake.path)))
-    )
+    in_repo_store1 = in_repo.FactStore(machine="machine1", flake=Flake(str(flake.path)))
+    in_repo_store2 = in_repo.FactStore(machine="machine2", flake=Flake(str(flake.path)))
     assert in_repo_store1.exists(Generator("my_generator"), "my_value")
     assert in_repo_store2.exists(Generator("my_generator"), "my_value")
     assert (
@@ -500,12 +505,8 @@ def test_generate_secret_for_multiple_machines(
         == "machine2\n"
     )
     # check if secret vars have been created correctly
-    sops_store1 = sops.SecretStore(
-        Machine(name="machine1", flake=Flake(str(flake.path)))
-    )
-    sops_store2 = sops.SecretStore(
-        Machine(name="machine2", flake=Flake(str(flake.path)))
-    )
+    sops_store1 = sops.SecretStore(machine="machine1", flake=Flake(str(flake.path)))
+    sops_store2 = sops.SecretStore(machine="machine2", flake=Flake(str(flake.path)))
     assert sops_store1.exists(Generator("my_generator"), "my_secret")
     assert sops_store2.exists(Generator("my_generator"), "my_secret")
     assert (
@@ -550,7 +551,7 @@ def test_prompt(
     )
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
     in_repo_store = in_repo.FactStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
+        machine="my_machine", flake=Flake(str(flake.path))
     )
     assert in_repo_store.exists(Generator("my_generator"), "line_value")
     assert (
@@ -563,9 +564,7 @@ def test_prompt(
         in_repo_store.get(Generator("my_generator"), "multiline_value").decode()
         == "my\nmultiline\ninput\n"
     )
-    sops_store = sops.SecretStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
-    )
+    sops_store = sops.SecretStore(machine="my_machine", flake=Flake(str(flake.path)))
     assert sops_store.exists(
         Generator(name="my_generator", share=False, files=[]), "prompt_persist"
     )
@@ -607,10 +606,10 @@ def test_multi_machine_shared_vars(
     monkeypatch.chdir(flake.path)
     machine1 = Machine(name="machine1", flake=Flake(str(flake.path)))
     machine2 = Machine(name="machine2", flake=Flake(str(flake.path)))
-    sops_store_1 = sops.SecretStore(machine1)
-    sops_store_2 = sops.SecretStore(machine2)
-    in_repo_store_1 = in_repo.FactStore(machine1)
-    in_repo_store_2 = in_repo.FactStore(machine2)
+    sops_store_1 = sops.SecretStore(machine1.name, machine1.flake)
+    sops_store_2 = sops.SecretStore(machine2.name, machine2.flake)
+    in_repo_store_1 = in_repo.FactStore(machine1.name, machine1.flake)
+    in_repo_store_2 = in_repo.FactStore(machine2.name, machine2.flake)
     generator = Generator("shared_generator", share=True)
     # generate for machine 1
     cli.run(["vars", "generate", "--flake", str(flake.path), "machine1"])
@@ -655,7 +654,7 @@ def test_api_set_prompts(
 
     monkeypatch.chdir(flake.path)
 
-    generate_vars_for_machine(
+    run_generators(
         machine_name="my_machine",
         base_dir=flake.path,
         generators=["my_generator"],
@@ -666,10 +665,10 @@ def test_api_set_prompts(
         },
     )
     machine = Machine(name="my_machine", flake=Flake(str(flake.path)))
-    store = in_repo.FactStore(machine)
+    store = in_repo.FactStore(machine.name, machine.flake)
     assert store.exists(Generator("my_generator"), "prompt1")
     assert store.get(Generator("my_generator"), "prompt1").decode() == "input1"
-    generate_vars_for_machine(
+    run_generators(
         machine_name="my_machine",
         base_dir=flake.path,
         generators=["my_generator"],
@@ -681,7 +680,7 @@ def test_api_set_prompts(
     )
     assert store.get(Generator("my_generator"), "prompt1").decode() == "input2"
 
-    generators = get_generators_closure(
+    generators = get_generators(
         machine_name="my_machine",
         base_dir=flake.path,
         full_closure=True,
@@ -714,11 +713,11 @@ def test_stdout_of_generate(
     flake_.refresh()
     monkeypatch.chdir(flake_.path)
     flake = Flake(str(flake_.path))
-    from clan_cli.vars.generate import generate_vars_for_machine_interactive
+    from clan_cli.vars.generate import create_machine_vars_interactive
 
     # with capture_output as output:
     with caplog.at_level(logging.INFO):
-        generate_vars_for_machine_interactive(
+        create_machine_vars_interactive(
             Machine(name="my_machine", flake=flake),
             "my_generator",
             regenerate=False,
@@ -731,7 +730,7 @@ def test_stdout_of_generate(
 
     set_var("my_machine", "my_generator/my_value", b"world", flake)
     with caplog.at_level(logging.INFO):
-        generate_vars_for_machine_interactive(
+        create_machine_vars_interactive(
             Machine(name="my_machine", flake=flake),
             "my_generator",
             regenerate=True,
@@ -742,7 +741,7 @@ def test_stdout_of_generate(
     caplog.clear()
     # check the output when nothing gets regenerated
     with caplog.at_level(logging.INFO):
-        generate_vars_for_machine_interactive(
+        create_machine_vars_interactive(
             Machine(name="my_machine", flake=flake),
             "my_generator",
             regenerate=True,
@@ -751,7 +750,7 @@ def test_stdout_of_generate(
     assert "hello" in caplog.text
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        generate_vars_for_machine_interactive(
+        create_machine_vars_interactive(
             Machine(name="my_machine", flake=flake),
             "my_secret_generator",
             regenerate=False,
@@ -766,7 +765,7 @@ def test_stdout_of_generate(
         Flake(str(flake.path)),
     )
     with caplog.at_level(logging.INFO):
-        generate_vars_for_machine_interactive(
+        create_machine_vars_interactive(
             Machine(name="my_machine", flake=flake),
             "my_secret_generator",
             regenerate=True,
@@ -817,11 +816,9 @@ def test_migration(
     assert "Migrated var my_generator/my_value" in caplog.text
     assert "Migrated secret var my_generator/my_secret" in caplog.text
     in_repo_store = in_repo.FactStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
-    )
-    sops_store = sops.SecretStore(
-        Machine(name="my_machine", flake=Flake(str(flake.path)))
+        machine="my_machine", flake=Flake(str(flake.path))
     )
+    sops_store = sops.SecretStore(machine="my_machine", flake=Flake(str(flake.path)))
     assert in_repo_store.exists(Generator("my_generator"), "my_value")
     assert in_repo_store.get(Generator("my_generator"), "my_value").decode() == "hello"
     assert sops_store.exists(Generator("my_generator"), "my_secret")
@@ -856,7 +853,7 @@ def test_fails_when_files_are_left_from_other_backend(
     flake.refresh()
     monkeypatch.chdir(flake.path)
     for generator in ["my_secret_generator", "my_value_generator"]:
-        generate_vars_for_machine_interactive(
+        create_machine_vars_interactive(
             Machine(name="my_machine", flake=Flake(str(flake.path))),
             generator,
             regenerate=False,
@@ -873,13 +870,13 @@ def test_fails_when_files_are_left_from_other_backend(
         # This should raise an error
         if generator == "my_secret_generator":
             with pytest.raises(ClanError):
-                generate_vars_for_machine_interactive(
+                create_machine_vars_interactive(
                     Machine(name="my_machine", flake=Flake(str(flake.path))),
                     generator,
                     regenerate=False,
                 )
         else:
-            generate_vars_for_machine_interactive(
+            create_machine_vars_interactive(
                 Machine(name="my_machine", flake=Flake(str(flake.path))),
                 generator,
                 regenerate=False,
@@ -887,7 +884,9 @@ def test_fails_when_files_are_left_from_other_backend(
 
 
 @pytest.mark.with_core
-def test_keygen(monkeypatch: pytest.MonkeyPatch, flake: ClanFlake) -> None:
+def test_create_sops_age_secrets(
+    monkeypatch: pytest.MonkeyPatch, flake: ClanFlake
+) -> None:
     monkeypatch.chdir(flake.path)
     cli.run(["vars", "keygen", "--flake", str(flake.path), "--user", "user"])
     # check public key exists
@@ -917,12 +916,12 @@ def test_invalidation(
     monkeypatch.chdir(flake.path)
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
     machine = Machine(name="my_machine", flake=Flake(str(flake.path)))
-    value1 = get_var(
+    value1 = get_machine_var(
         str(machine.flake.path), machine.name, "my_generator/my_value"
     ).printable_value
     # generate again and make sure nothing changes without the invalidation data being set
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
-    value1_new = get_var(
+    value1_new = get_machine_var(
         str(machine.flake.path), machine.name, "my_generator/my_value"
     ).printable_value
     assert value1 == value1_new
@@ -931,13 +930,13 @@ def test_invalidation(
     flake.refresh()
     # generate again and make sure the value changes
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
-    value2 = get_var(
+    value2 = get_machine_var(
         str(machine.flake.path), machine.name, "my_generator/my_value"
     ).printable_value
     assert value1 != value2
     # generate again without changing invalidation data -> value should not change
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
-    value2_new = get_var(
+    value2_new = get_machine_var(
         str(machine.flake.path), machine.name, "my_generator/my_value"
     ).printable_value
     assert value2 == value2_new

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

@@ -6,7 +6,7 @@ from pathlib import Path
 from typing import TYPE_CHECKING
 
 from clan_lib.errors import ClanError
-from clan_lib.machines import machines
+from clan_lib.flake import Flake
 from clan_lib.ssh.remote import Remote
 
 if TYPE_CHECKING:
@@ -29,8 +29,9 @@ class GeneratorUpdate:
 
 
 class StoreBase(ABC):
-    def __init__(self, machine: "machines.Machine") -> None:
+    def __init__(self, machine: str, flake: Flake) -> None:
         self.machine = machine
+        self.flake = flake
 
     @property
     @abstractmethod
@@ -86,10 +87,10 @@ class StoreBase(ABC):
     def rel_dir(self, generator: "Generator", var_name: str) -> Path:
         if generator.share:
             return Path("shared") / generator.name / var_name
-        return Path("per-machine") / self.machine.name / generator.name / var_name
+        return Path("per-machine") / self.machine / generator.name / var_name
 
     def directory(self, generator: "Generator", var_name: str) -> Path:
-        return Path(self.machine.flake_dir) / "vars" / self.rel_dir(generator, var_name)
+        return self.flake.path / "vars" / self.rel_dir(generator, var_name)
 
     def set(
         self,

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

@@ -82,11 +82,6 @@ class Generator:
             files = []
             gen_files = files_data.get(gen_name, {})
             for file_name, file_data in gen_files.items():
-                # Handle mode conversion properly
-                mode = file_data["mode"]
-                if isinstance(mode, str):
-                    mode = int(mode, 8)
-
                 var = Var(
                     id=f"{gen_name}/{file_name}",
                     name=file_name,
@@ -94,7 +89,11 @@ class Generator:
                     deploy=file_data["deploy"],
                     owner=file_data["owner"],
                     group=file_data["group"],
-                    mode=mode,
+                    mode=(
+                        file_data["mode"]
+                        if isinstance(file_data["mode"], int)
+                        else int(file_data["mode"], 8)
+                    ),
                     needed_for=file_data["neededFor"],
                 )
                 files.append(var)
@@ -424,7 +423,7 @@ def get_closure(
 
 
 @API.register
-def get_generators_closure(
+def get_generators(
     machine_name: str,
     base_dir: Path,
     full_closure: bool = False,
@@ -462,7 +461,7 @@ def _generate_vars_for_machine(
 
 
 @API.register
-def generate_vars_for_machine(
+def run_generators(
     machine_name: str,
     generators: list[str],
     all_prompt_values: dict[str, dict[str, str]],
@@ -487,7 +486,7 @@ def generate_vars_for_machine(
     )
 
 
-def generate_vars_for_machine_interactive(
+def create_machine_vars_interactive(
     machine: "Machine",
     generator_name: str | None,
     regenerate: bool,
@@ -541,7 +540,7 @@ def generate_vars(
     for machine in machines:
         errors = []
         try:
-            was_regenerated |= generate_vars_for_machine_interactive(
+            was_regenerated |= create_machine_vars_interactive(
                 machine,
                 generator_name,
                 regenerate,

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

@@ -3,19 +3,17 @@ import logging
 import sys
 
 from clan_cli.completions import add_dynamic_completer, complete_machines
-from clan_lib.api import API
 from clan_lib.errors import ClanError
 from clan_lib.flake import Flake
 
 from .generate import Var
-from .list import get_vars
+from .list import get_machine_vars
 
 log = logging.getLogger(__name__)
 
 
-@API.register
-def get_var(base_dir: str, machine_name: str, var_id: str) -> Var:
-    vars_ = get_vars(base_dir=base_dir, machine_name=machine_name)
+def get_machine_var(base_dir: str, machine_name: str, var_id: str) -> Var:
+    vars_ = get_machine_vars(base_dir=base_dir, machine_name=machine_name)
     results = []
     for var in vars_:
         if var.id == var_id:
@@ -41,7 +39,7 @@ def get_var(base_dir: str, machine_name: str, var_id: str) -> Var:
 
 
 def get_command(machine_name: str, var_id: str, flake: Flake) -> None:
-    var = get_var(str(flake.path), machine_name, var_id)
+    var = get_machine_var(str(flake.path), machine_name, var_id)
     if not var.exists:
         msg = f"Var {var.id} has not been generated yet"
         raise ClanError(msg)

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

@@ -12,12 +12,18 @@ from clan_lib.errors import ClanError
 log = logging.getLogger(__name__)
 
 
+# TODO: Unify with "create clan" should be done automatically
 @API.register
-def keygen(flake_dir: Path, user: str | None = None, force: bool = False) -> None:
+def create_secrets_user(
+    flake_dir: Path, user: str | None = None, force: bool = False
+) -> None:
+    """
+    initialize sops keys for vars
+    """
     if user is None:
         user = os.getenv("USER", None)
         if not user:
-            msg = "No user provided and $USER is not set. Please provide a user via --user."
+            msg = "No user provided and environment variable: '$USER' is not set. Please provide an explizit username via argument"
             raise ClanError(msg)
     pub_keys = maybe_get_admin_public_keys()
     if not pub_keys:
@@ -34,7 +40,7 @@ def keygen(flake_dir: Path, user: str | None = None, force: bool = False) -> Non
 def _command(
     args: argparse.Namespace,
 ) -> None:
-    keygen(
+    create_secrets_user(
         flake_dir=args.flake.path,
         user=args.user,
         force=args.force,

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

@@ -2,19 +2,15 @@ import argparse
 import logging
 
 from clan_cli.completions import add_dynamic_completer, complete_machines
-from clan_lib.api import API
-from clan_lib.errors import ClanError
 from clan_lib.flake import Flake
 from clan_lib.machines.machines import Machine
 
-from ._types import GeneratorUpdate
-from .generate import Generator, Prompt, Var, execute_generator
+from .generate import Var
 
 log = logging.getLogger(__name__)
 
 
-@API.register
-def get_vars(base_dir: str, machine_name: str) -> list[Var]:
+def get_machine_vars(base_dir: str, machine_name: str) -> list[Var]:
     machine = Machine(name=machine_name, flake=Flake(base_dir))
     pub_store = machine.public_vars_store
     sec_store = machine.secret_vars_store
@@ -32,70 +28,12 @@ def get_vars(base_dir: str, machine_name: str) -> list[Var]:
     return all_vars
 
 
-def _get_previous_value(
-    machine: Machine,
-    generator: Generator,
-    prompt: Prompt,
-) -> str | None:
-    if not prompt.persist:
-        return None
-
-    pub_store = machine.public_vars_store
-    if pub_store.exists(generator, prompt.name):
-        return pub_store.get(generator, prompt.name).decode()
-    sec_store = machine.secret_vars_store
-    if sec_store.exists(generator, prompt.name):
-        return sec_store.get(generator, prompt.name).decode()
-    return None
-
-
-@API.register
-def get_generators(base_dir: str, machine_name: str) -> list[Generator]:
-    from clan_cli.vars.generate import Generator
-
-    machine = Machine(name=machine_name, flake=Flake(base_dir))
-    generators: list[Generator] = Generator.generators_from_flake(
-        machine_name, machine.flake
-    )
-    for generator in generators:
-        for prompt in generator.prompts:
-            prompt.previous_value = _get_previous_value(machine, generator, prompt)
-    return generators
-
-
-# TODO: Ensure generator dependencies are met (executed in correct order etc.)
-# TODO: for missing prompts, default to existing values
-# TODO: raise error if mandatory prompt not provided
-@API.register
-def set_prompts(
-    base_dir: str, machine_name: str, updates: list[GeneratorUpdate]
-) -> None:
-    from clan_cli.vars.generate import Generator
-
-    machine = Machine(name=machine_name, flake=Flake(base_dir))
-    for update in updates:
-        generators = Generator.generators_from_flake(machine_name, machine.flake)
-        for generator in generators:
-            if generator.name == update.generator:
-                break
-        else:
-            msg = f"Generator '{update.generator}' not found in machine {machine.name}"
-            raise ClanError(msg)
-        execute_generator(
-            machine,
-            generator,
-            secret_vars_store=machine.secret_vars_store,
-            public_vars_store=machine.public_vars_store,
-            prompt_values=update.prompt_values,
-        )
-
-
 def stringify_vars(_vars: list[Var]) -> str:
     return "\n".join([str(var) for var in _vars])
 
 
 def stringify_all_vars(machine: Machine) -> str:
-    return stringify_vars(get_vars(str(machine.flake), machine.name))
+    return stringify_vars(get_machine_vars(str(machine.flake), machine.name))
 
 
 def list_command(args: argparse.Namespace) -> None:

pkgs/clan-cli/clan_cli/vars/public_modules/in_repo.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from clan_cli.vars._types import StoreBase
 from clan_cli.vars.generate import Generator, Var
 from clan_lib.errors import ClanError
-from clan_lib.machines.machines import Machine
+from clan_lib.flake import Flake
 from clan_lib.ssh.remote import Remote
 
 
@@ -14,8 +14,8 @@ class FactStore(StoreBase):
     def is_secret_store(self) -> bool:
         return False
 
-    def __init__(self, machine: Machine) -> None:
-        self.machine = machine
+    def __init__(self, machine: str, flake: Flake) -> None:
+        super().__init__(machine, flake)
         self.works_remotely = False
 
     @property
@@ -28,8 +28,8 @@ class FactStore(StoreBase):
         var: Var,
         value: bytes,
     ) -> Path | None:
-        if not self.machine.flake.is_local:
-            msg = f"in_flake fact storage is only supported for local flakes: {self.machine.flake}"
+        if not self.flake.is_local:
+            msg = f"in_flake fact storage is only supported for local flakes: {self.flake}"
             raise ClanError(msg)
         folder = self.directory(generator, var.name)
         file_path = folder / "value"
@@ -62,8 +62,8 @@ class FactStore(StoreBase):
         return [fact_folder]
 
     def delete_store(self) -> Iterable[Path]:
-        flake_root = Path(self.machine.flake_dir)
-        store_folder = flake_root / "vars/per-machine" / self.machine.name
+        flake_root = self.flake.path
+        store_folder = flake_root / "vars/per-machine" / self.machine
         if not store_folder.exists():
             return []
         shutil.rmtree(store_folder)

pkgs/clan-cli/clan_cli/vars/public_modules/vm.py

@@ -7,7 +7,7 @@ from clan_cli.vars._types import StoreBase
 from clan_cli.vars.generate import Generator, Var
 from clan_lib.dirs import vm_state_dir
 from clan_lib.errors import ClanError
-from clan_lib.machines.machines import Machine
+from clan_lib.flake import Flake
 from clan_lib.ssh.remote import Remote
 
 log = logging.getLogger(__name__)
@@ -18,11 +18,14 @@ class FactStore(StoreBase):
     def is_secret_store(self) -> bool:
         return False
 
-    def __init__(self, machine: Machine) -> None:
-        self.machine = machine
+    def __init__(self, machine: str, flake: Flake) -> None:
+        super().__init__(machine, flake)
         self.works_remotely = False
-        self.dir = vm_state_dir(machine.flake.identifier, machine.name) / "facts"
-        machine.debug(f"FactStore initialized with dir {self.dir}")
+        self.dir = vm_state_dir(flake.identifier, machine) / "facts"
+        log.debug(
+            f"FactStore initialized with dir {self.dir}",
+            extra={"command_prefix": machine},
+        )
 
     @property
     def store_name(self) -> str:

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

@@ -4,7 +4,7 @@ from pathlib import Path
 
 from clan_cli.vars._types import StoreBase
 from clan_cli.vars.generate import Generator, Var
-from clan_lib.machines.machines import Machine
+from clan_lib.flake import Flake
 from clan_lib.ssh.remote import Remote
 
 
@@ -13,8 +13,8 @@ class SecretStore(StoreBase):
     def is_secret_store(self) -> bool:
         return True
 
-    def __init__(self, machine: Machine) -> None:
-        self.machine = machine
+    def __init__(self, machine: str, flake: Flake) -> None:
+        super().__init__(machine, flake)
         self.dir = Path(tempfile.gettempdir()) / "clan_secrets"
         self.dir.mkdir(parents=True, exist_ok=True)
 
@@ -46,6 +46,17 @@ class SecretStore(StoreBase):
         shutil.copytree(self.dir, output_dir)
         shutil.rmtree(self.dir)
 
+    def delete(self, generator: Generator, name: str) -> list[Path]:
+        secret_file = self.dir / generator.name / name
+        if secret_file.exists():
+            secret_file.unlink()
+        return []
+
+    def delete_store(self) -> list[Path]:
+        if self.dir.exists():
+            shutil.rmtree(self.dir)
+        return []
+
     def upload(self, host: Remote, phases: list[str]) -> None:
         msg = "Cannot upload secrets with FS backend"
         raise NotImplementedError(msg)

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

@@ -1,18 +1,15 @@
 import io
 import logging
-import os
 import tarfile
+import subprocess
 from collections.abc import Iterable
-from itertools import chain
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
 from clan_cli.ssh.upload import upload
 from clan_cli.vars._types import StoreBase
 from clan_cli.vars.generate import Generator, Var
-from clan_lib.cmd import CmdOut, Log, RunOpts, run
-from clan_lib.machines.machines import Machine
-from clan_lib.nix import nix_shell
+from clan_lib.flake import Flake
 from clan_lib.ssh.remote import Remote
 
 log = logging.getLogger(__name__)
@@ -23,35 +20,78 @@ class SecretStore(StoreBase):
     def is_secret_store(self) -> bool:
         return True
 
-    def __init__(self, machine: Machine) -> None:
-        self.machine = machine
+    def __init__(self, machine: str, flake: Flake) -> None:
+        super().__init__(machine, flake)
         self.entry_prefix = "clan-vars"
+        self._store_dir: Path | None = None
 
     @property
     def store_name(self) -> str:
         return "password_store"
 
     @property
-    def _store_backend(self) -> str:
-        backend = self.machine.select("config.clan.core.vars.settings.passBackend")
-        return backend
+    def store_dir(self) -> Path:
+        """Get the password store directory, cached after first access."""
+        if self._store_dir is None:
+            result = self._run_pass("git", "rev-parse", "--show-toplevel", check=False)
+            if result.returncode != 0:
+                msg = "Password store must be a git repository"
+                raise ValueError(msg)
+            self._store_dir = Path(result.stdout.strip().decode())
+        return self._store_dir
 
     @property
-    def _password_store_dir(self) -> Path:
-        if self._store_backend == "passage":
-            lookup = os.environ.get("PASSAGE_DIR")
-            default = Path.home() / ".passage/store"
-        else:
-            lookup = os.environ.get("PASSWORD_STORE_DIR")
-            default = Path.home() / ".password-store"
-        return Path(lookup) if lookup else default
+    def _pass_command(self) -> str:
+        out_path = self.flake.select_machine(
+            self.machine, "config.clan.core.vars.password-store.passPackage.outPath"
+        )
+        main_program = (
+            self.flake.select_machine(
+                self.machine,
+                "config.clan.core.vars.password-store.passPackage.?meta.?mainProgram",
+            )
+            .get("meta", {})
+            .get("mainProgram")
+        )
+
+        if main_program:
+            binary_path = Path(out_path) / "bin" / main_program
+            if binary_path.exists():
+                return str(binary_path)
+
+        # Look for common password store binaries
+        bin_dir = Path(out_path) / "bin"
+        if bin_dir.exists():
+            for binary in ["pass", "passage"]:
+                binary_path = bin_dir / binary
+                if binary_path.exists():
+                    return str(binary_path)
+
+            # If only one binary exists, use it
+            binaries = [f for f in bin_dir.iterdir() if f.is_file()]
+            if len(binaries) == 1:
+                return str(binaries[0])
+
+        msg = "Could not find password store binary in package"
+        raise ValueError(msg)
 
     def entry_dir(self, generator: Generator, name: str) -> Path:
         return Path(self.entry_prefix) / self.rel_dir(generator, name)
 
-    def _run_pass(self, *args: str, options: RunOpts | None = None) -> CmdOut:
-        cmd = nix_shell(packages=["pass"], cmd=[self._store_backend, *args])
-        return run(cmd, options)
+    def _run_pass(
+        self, *args: str, input: bytes | None = None, check: bool = True
+    ) -> subprocess.CompletedProcess[bytes]:
+        cmd = [self._pass_command, *args]
+        # We need bytes support here, so we can not use clan cmd.
+        # If you change this to run( add bytes support to it first!
+        # otherwise we mangle binary secrets (which is annoying to debug)
+        return subprocess.run(
+            cmd,
+            input=input,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            check=check,
+        )
 
     def _set(
         self,
@@ -60,121 +100,77 @@ class SecretStore(StoreBase):
         value: bytes,
     ) -> Path | None:
         pass_call = ["insert", "-m", str(self.entry_dir(generator, var.name))]
-        self._run_pass(*pass_call, options=RunOpts(input=value, check=True))
+        self._run_pass(*pass_call, input=value, check=True)
         return None  # we manage the files outside of the git repo
 
     def get(self, generator: Generator, name: str) -> bytes:
         pass_name = str(self.entry_dir(generator, name))
-        return self._run_pass("show", pass_name).stdout.encode()
+        return self._run_pass("show", pass_name).stdout
 
     def exists(self, generator: Generator, name: str) -> bool:
-        extension = "age" if self._store_backend == "passage" else "gpg"
-        filename = f"{self.entry_dir(generator, name)}.{extension}"
-        return (self._password_store_dir / filename).exists()
+        pass_name = str(self.entry_dir(generator, name))
+        # Check if the file exists with either .age or .gpg extension
+        age_file = self.store_dir / f"{pass_name}.age"
+        gpg_file = self.store_dir / f"{pass_name}.gpg"
+        return age_file.exists() or gpg_file.exists()
 
     def delete(self, generator: Generator, name: str) -> Iterable[Path]:
         pass_name = str(self.entry_dir(generator, name))
-        self._run_pass("rm", "--force", pass_name, options=RunOpts(check=True))
+        self._run_pass("rm", "--force", pass_name, check=True)
         return []
 
     def delete_store(self) -> Iterable[Path]:
-        machine_dir = Path(self.entry_prefix) / "per-machine" / self.machine.name
-        if not (self._password_store_dir / machine_dir).exists():
-            # The directory may not exist if the machine
-            # has no vars, or they have been deleted already.
-            return []
-        pass_call = ["rm", "--force", "--recursive", str(machine_dir)]
-        self._run_pass(*pass_call, options=RunOpts(check=True))
+        machine_dir = Path(self.entry_prefix) / "per-machine" / self.machine
+        # Check if the directory exists in the password store before trying to delete
+        result = self._run_pass("ls", str(machine_dir), check=False)
+        if result.returncode == 0:
+            self._run_pass("rm", "--force", "--recursive", str(machine_dir), check=True)
         return []
 
     def generate_hash(self) -> bytes:
-        hashes = []
-        hashes.append(
-            run(
-                nix_shell(
-                    ["git"],
-                    [
-                        "git",
-                        "-C",
-                        str(self._password_store_dir),
-                        "log",
-                        "-1",
-                        "--format=%H",
-                        self.entry_prefix,
-                    ],
-                ),
-                RunOpts(check=False),
-            )
-            .stdout.strip()
-            .encode()
+        result = self._run_pass(
+            "git", "log", "-1", "--format=%H", self.entry_prefix, check=False
         )
-        shared_dir = self._password_store_dir / self.entry_prefix / "shared"
-        machine_dir = (
-            self._password_store_dir
-            / self.entry_prefix
-            / "per-machine"
-            / self.machine.name
-        )
-        for symlink in chain(shared_dir.glob("**/*"), machine_dir.glob("**/*")):
-            if symlink.is_symlink():
-                hashes.append(
-                    run(
-                        nix_shell(
-                            ["git"],
-                            [
-                                "git",
-                                "-C",
-                                str(self._password_store_dir),
-                                "log",
-                                "-1",
-                                "--format=%H",
-                                str(symlink),
-                            ],
-                        ),
-                        RunOpts(check=False),
-                    )
-                    .stdout.strip()
-                    .encode()
-                )
+        git_hash = result.stdout.strip()
 
-        # we sort the hashes to make sure that the order is always the same
-        hashes.sort()
+        if not git_hash:
+            return b""
 
         from clan_cli.vars.generate import Generator
 
         manifest = []
-        generators = Generator.generators_from_flake(
-            self.machine.name, self.machine.flake
-        )
+        generators = Generator.generators_from_flake(self.machine, self.flake)
         for generator in generators:
             for file in generator.files:
                 manifest.append(f"{generator.name}/{file.name}".encode())
-        manifest += hashes
+
+        manifest.append(git_hash)
         return b"\n".join(manifest)
 
     def needs_upload(self, host: Remote) -> bool:
         local_hash = self.generate_hash()
+        if not local_hash:
+            return True
+
+        from clan_lib.cmd import RunOpts, Log
+
         remote_hash = host.run(
-            # TODO get the path to the secrets from the machine
             [
                 "cat",
-                f"{self.machine.select('config.clan.vars.password-store.secretLocation')}/.{self._store_backend}_info",
+                f"{self.flake.select_machine(self.machine, 'config.clan.core.vars.password-store.secretLocation')}/.pass_info",
             ],
             RunOpts(log=Log.STDERR, check=False),
         ).stdout.strip()
 
         if not remote_hash:
-            print("remote hash is empty")
             return True
 
-        return local_hash.decode() != remote_hash
+        return local_hash != remote_hash.encode()
 
     def populate_dir(self, output_dir: Path, phases: list[str]) -> None:
         from clan_cli.vars.generate import Generator
 
-        vars_generators = Generator.generators_from_flake(
-            self.machine.name, self.machine.flake
-        )
+        vars_generators = Generator.generators_from_flake(self.machine, self.flake)
         if "users" in phases:
             with tarfile.open(
                 output_dir / "secrets_for_users.tar.gz", "w:gz"
@@ -233,7 +229,9 @@ class SecretStore(StoreBase):
                         out_file.parent.mkdir(parents=True, exist_ok=True)
                         out_file.write_bytes(self.get(generator, file.name))
 
-        (output_dir / f".{self._store_backend}_info").write_bytes(self.generate_hash())
+        hash_data = self.generate_hash()
+        if hash_data:
+            (output_dir / ".pass_info").write_bytes(hash_data)
 
     def upload(self, host: Remote, phases: list[str]) -> None:
         if "partitioning" in phases:
@@ -246,6 +244,8 @@ class SecretStore(StoreBase):
             pass_dir = Path(_tempdir).resolve()
             self.populate_dir(pass_dir, phases)
             upload_dir = Path(
-                self.machine.select("config.clan.vars.password-store.secretLocation")
+                self.flake.select_machine(
+                    self.machine, "config.clan.core.vars.password-store.secretLocation"
+                )
             )
             upload(host, pass_dir, upload_dir)

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

@@ -27,7 +27,7 @@ from clan_cli.vars._types import StoreBase
 from clan_cli.vars.generate import Generator
 from clan_cli.vars.var import Var
 from clan_lib.errors import ClanError
-from clan_lib.machines.machines import Machine
+from clan_lib.flake import Flake
 from clan_lib.ssh.remote import Remote
 
 
@@ -48,15 +48,13 @@ class SecretStore(StoreBase):
     def is_secret_store(self) -> bool:
         return True
 
-    def __init__(self, machine: Machine) -> None:
-        self.machine = machine
+    def __init__(self, machine: str, flake: Flake) -> None:
+        super().__init__(machine, flake)
 
         # no need to generate keys if we don't manage secrets
         from clan_cli.vars.generate import Generator
 
-        vars_generators = Generator.generators_from_flake(
-            self.machine.name, self.machine.flake
-        )
+        vars_generators = Generator.generators_from_flake(self.machine, self.flake)
         if not vars_generators:
             return
         has_secrets = False
@@ -67,18 +65,19 @@ class SecretStore(StoreBase):
         if not has_secrets:
             return
 
-        if has_machine(self.machine.flake_dir, self.machine.name):
+        if has_machine(self.flake.path, self.machine):
             return
         priv_key, pub_key = sops.generate_private_key()
         encrypt_secret(
-            self.machine.flake_dir,
-            sops_secrets_folder(self.machine.flake_dir)
-            / f"{self.machine.name}-age.key",
+            self.flake.path,
+            sops_secrets_folder(self.flake.path) / f"{self.machine}-age.key",
             priv_key,
-            add_groups=self.machine.select("config.clan.core.sops.defaultGroups"),
-            age_plugins=load_age_plugins(self.machine.flake),
+            add_groups=self.flake.select_machine(
+                self.machine, "config.clan.core.sops.defaultGroups"
+            ),
+            age_plugins=load_age_plugins(self.flake),
         )
-        add_machine(self.machine.flake_dir, self.machine.name, pub_key, False)
+        add_machine(self.flake.path, self.machine, pub_key, False)
 
     @property
     def store_name(self) -> str:
@@ -87,11 +86,11 @@ class SecretStore(StoreBase):
     def user_has_access(
         self, user: str, generator: Generator, secret_name: str
     ) -> bool:
-        key_dir = sops_users_folder(self.machine.flake_dir) / user
+        key_dir = sops_users_folder(self.flake.path) / user
         return self.key_has_access(key_dir, generator, secret_name)
 
     def machine_has_access(self, generator: Generator, secret_name: str) -> bool:
-        key_dir = sops_machines_folder(self.machine.flake_dir) / self.machine.name
+        key_dir = sops_machines_folder(self.flake.path) / self.machine
         return self.key_has_access(key_dir, generator, secret_name)
 
     def key_has_access(
@@ -117,9 +116,7 @@ class SecretStore(StoreBase):
         if generator is None:
             from clan_cli.vars.generate import Generator
 
-            generators = Generator.generators_from_flake(
-                self.machine.name, self.machine.flake
-            )
+            generators = Generator.generators_from_flake(self.machine, self.flake)
         else:
             generators = [generator]
         file_found = False
@@ -144,7 +141,7 @@ class SecretStore(StoreBase):
         if outdated:
             msg = (
                 "The local state of some secret vars is inconsistent and needs to be updated.\n"
-                f"Run 'clan vars fix {self.machine.name}' to apply the necessary changes."
+                f"Run 'clan vars fix {self.machine}' to apply the necessary changes."
                 "Problems to fix:\n"
                 "\n".join(o[2] for o in outdated if o[2])
             )
@@ -162,20 +159,22 @@ class SecretStore(StoreBase):
         secret_folder.mkdir(parents=True, exist_ok=True)
         # initialize the secret
         encrypt_secret(
-            self.machine.flake_dir,
+            self.flake.path,
             secret_folder,
             value,
-            add_machines=[self.machine.name] if var.deploy else [],
-            add_groups=self.machine.select("config.clan.core.sops.defaultGroups"),
+            add_machines=[self.machine] if var.deploy else [],
+            add_groups=self.flake.select_machine(
+                self.machine, "config.clan.core.sops.defaultGroups"
+            ),
             git_commit=False,
-            age_plugins=load_age_plugins(self.machine.flake),
+            age_plugins=load_age_plugins(self.flake),
         )
         return secret_folder
 
     def get(self, generator: Generator, name: str) -> bytes:
         return decrypt_secret(
             self.secret_path(generator, name),
-            age_plugins=load_age_plugins(self.machine.flake),
+            age_plugins=load_age_plugins(self.flake),
         ).encode("utf-8")
 
     def delete(self, generator: "Generator", name: str) -> Iterable[Path]:
@@ -184,8 +183,8 @@ class SecretStore(StoreBase):
         return [secret_dir]
 
     def delete_store(self) -> Iterable[Path]:
-        flake_root = Path(self.machine.flake_dir)
-        store_folder = flake_root / "vars/per-machine" / self.machine.name
+        flake_root = self.flake.path
+        store_folder = flake_root / "vars/per-machine" / self.machine
         if not store_folder.exists():
             return []
         shutil.rmtree(store_folder)
@@ -194,17 +193,15 @@ class SecretStore(StoreBase):
     def populate_dir(self, output_dir: Path, phases: list[str]) -> None:
         from clan_cli.vars.generate import Generator
 
-        vars_generators = Generator.generators_from_flake(
-            self.machine.name, self.machine.flake
-        )
+        vars_generators = Generator.generators_from_flake(self.machine, self.flake)
         if "users" in phases or "services" in phases:
-            key_name = f"{self.machine.name}-age.key"
-            if not has_secret(sops_secrets_folder(self.machine.flake_dir) / key_name):
+            key_name = f"{self.machine}-age.key"
+            if not has_secret(sops_secrets_folder(self.flake.path) / key_name):
                 # skip uploading the secret, not managed by us
                 return
             key = decrypt_secret(
-                sops_secrets_folder(self.machine.flake_dir) / key_name,
-                age_plugins=load_age_plugins(self.machine.flake),
+                sops_secrets_folder(self.flake.path) / key_name,
+                age_plugins=load_age_plugins(self.flake),
             )
             (output_dir / "key.txt").touch(mode=0o600)
             (output_dir / "key.txt").write_text(key)
@@ -258,10 +255,10 @@ class SecretStore(StoreBase):
             return
         secret_folder = self.secret_path(generator, name)
         add_secret(
-            self.machine.flake_dir,
-            self.machine.name,
+            self.flake.path,
+            self.machine,
             secret_folder,
-            age_plugins=load_age_plugins(self.machine.flake),
+            age_plugins=load_age_plugins(self.flake),
         )
 
     def collect_keys_for_secret(self, path: Path) -> set[sops.SopsKey]:
@@ -271,15 +268,17 @@ class SecretStore(StoreBase):
         )
 
         keys = collect_keys_for_path(path)
-        for group in self.machine.select("config.clan.core.sops.defaultGroups"):
+        for group in self.flake.select_machine(
+            self.machine, "config.clan.core.sops.defaultGroups"
+        ):
             keys.update(
                 collect_keys_for_type(
-                    self.machine.flake_dir / "sops" / "groups" / group / "machines"
+                    self.flake.path / "sops" / "groups" / group / "machines"
                 )
             )
             keys.update(
                 collect_keys_for_type(
-                    self.machine.flake_dir / "sops" / "groups" / group / "users"
+                    self.flake.path / "sops" / "groups" / group / "users"
                 )
             )
 
@@ -296,7 +295,7 @@ class SecretStore(StoreBase):
             f"One or more recipient keys were added to secret{' shared' if generator.share else ''} var '{var_id}', but it was never re-encrypted.\n"
             f"This could have been a malicious actor trying to add their keys, please investigate.\n"
             f"Added keys: {', '.join(f'{r.key_type.name}:{r.pubkey}' for r in recipients_to_add)}\n"
-            f"If this is intended, run 'clan vars fix {self.machine.name}' to re-encrypt the secret."
+            f"If this is intended, run 'clan vars fix {self.machine}' to re-encrypt the secret."
         )
         return needs_update, msg
 
@@ -309,9 +308,7 @@ class SecretStore(StoreBase):
         if generator is None:
             from clan_cli.vars.generate import Generator
 
-            generators = Generator.generators_from_flake(
-                self.machine.name, self.machine.flake
-            )
+            generators = Generator.generators_from_flake(self.machine, self.flake)
         else:
             generators = [generator]
         file_found = False
@@ -328,12 +325,14 @@ class SecretStore(StoreBase):
 
                 secret_path = self.secret_path(generator, file.name)
 
-                age_plugins = load_age_plugins(self.machine.flake)
+                age_plugins = load_age_plugins(self.flake)
 
-                for group in self.machine.select("config.clan.core.sops.defaultGroups"):
+                for group in self.flake.select_machine(
+                    self.machine, "config.clan.core.sops.defaultGroups"
+                ):
                     allow_member(
                         groups_folder(secret_path),
-                        sops_groups_folder(self.machine.flake_dir),
+                        sops_groups_folder(self.flake.path),
                         group,
                         # we just want to create missing symlinks, we call update_keys below:
                         do_update_keys=False,

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

@@ -5,7 +5,7 @@ from pathlib import Path
 from clan_cli.vars._types import StoreBase
 from clan_cli.vars.generate import Generator, Var
 from clan_lib.dirs import vm_state_dir
-from clan_lib.machines.machines import Machine
+from clan_lib.flake import Flake
 from clan_lib.ssh.remote import Remote
 
 
@@ -14,9 +14,9 @@ class SecretStore(StoreBase):
     def is_secret_store(self) -> bool:
         return True
 
-    def __init__(self, machine: Machine) -> None:
-        self.machine = machine
-        self.dir = vm_state_dir(machine.flake.identifier, machine.name) / "secrets"
+    def __init__(self, machine: str, flake: Flake) -> None:
+        super().__init__(machine, flake)
+        self.dir = vm_state_dir(flake.identifier, machine) / "secrets"
         self.dir.mkdir(parents=True, exist_ok=True)
 
     @property

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

@@ -3,7 +3,7 @@ import logging
 import sys
 
 from clan_cli.completions import add_dynamic_completer, complete_machines
-from clan_cli.vars.get import get_var
+from clan_cli.vars.get import get_machine_var
 from clan_cli.vars.prompt import PromptType
 from clan_lib.flake import Flake
 from clan_lib.git import commit_files
@@ -21,7 +21,7 @@ def set_var(machine: str | Machine, var: str | Var, value: bytes, flake: Flake)
     else:
         _machine = machine
     if isinstance(var, str):
-        _var = get_var(str(flake.path), _machine.name, var)
+        _var = get_machine_var(str(flake.path), _machine.name, var)
     else:
         _var = var
     path = _var.set(value)
@@ -35,7 +35,7 @@ def set_var(machine: str | Machine, var: str | Var, value: bytes, flake: Flake)
 
 def set_via_stdin(machine_name: str, var_id: str, flake: Flake) -> None:
     machine = Machine(name=machine_name, flake=flake)
-    var = get_var(str(flake.path), machine_name, var_id)
+    var = get_machine_var(str(flake.path), machine_name, var_id)
     if sys.stdin.isatty():
         new_value = ask(
             var.id,

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

@@ -254,6 +254,7 @@ API.register(open_file)
                 "type": "object",
                 "required": ["arguments", "return"],
                 "additionalProperties": False,
+                "description": func.__doc__,
                 "properties": {
                     "return": return_type,
                     "arguments": {

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

@@ -122,11 +122,12 @@ def blk_from_dict(data: dict) -> BlkInfo:
 
 
 @API.register
-def show_block_devices() -> Blockdevices:
+def list_block_devices() -> Blockdevices:
     """
-    Api method to show local block devices.
+    List local block devices by running `lsblk`.
 
-    It must return a list of block devices.
+    Returns:
+        A list of detected block devices with metadata like size, path, type, etc.
     """
 
     cmd = nix_shell(

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

@@ -10,7 +10,7 @@ from clan_lib.api.modules import Frontmatter, extract_frontmatter
 from clan_lib.dirs import TemplateType, clan_templates
 from clan_lib.errors import ClanError
 from clan_lib.git import commit_file
-from clan_lib.machines.hardware import HardwareConfig, show_machine_hardware_config
+from clan_lib.machines.hardware import HardwareConfig, get_machine_hardware_config
 from clan_lib.machines.machines import Machine
 
 log = logging.getLogger(__name__)
@@ -137,7 +137,7 @@ def set_machine_disk_schema(
     Set the disk placeholders of the template
     """
     # Assert the hw-config must exist before setting the disk
-    hw_config = show_machine_hardware_config(machine)
+    hw_config = get_machine_hardware_config(machine)
     hw_config_path = hw_config.config_path(machine)
 
     if not hw_config_path.exists():

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

@@ -88,7 +88,7 @@ def parse_avahi_output(output: str) -> DNSInfo:
 
 
 @API.register
-def show_mdns() -> DNSInfo:
+def list_mdns_services() -> DNSInfo:
     cmd = nix_shell(
         ["avahi"],
         [
@@ -107,7 +107,7 @@ def show_mdns() -> DNSInfo:
 
 
 def mdns_command(args: argparse.Namespace) -> None:
-    dns_info = show_mdns()
+    dns_info = list_mdns_services()
     for name, info in dns_info.services.items():
         print(f"Hostname: {name} - ip: {info.ip}")
 

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

@@ -168,7 +168,6 @@ def list_modules(base_path: str) -> ModuleLists:
     modules = flake.select(
         "clanInternals.inventoryClass.{?modulesPerSource,?localModules}"
     )
-    print("Modules found:", modules)
 
     return modules
 

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

@@ -17,7 +17,7 @@ BAKEND_THREADS: dict[str, WebThread] | None = None
 
 
 @API.register_abstract
-def cancel_task(task_id: str) -> None:
+def delete_task(task_id: str) -> None:
     """Cancel a task by its op_key."""
     assert BAKEND_THREADS is not None, "Backend threads not initialized"
     future = BAKEND_THREADS.get(task_id)

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

@@ -4,16 +4,12 @@ from pathlib import Path
 
 from clan_lib.api import API
 from clan_lib.cmd import RunOpts, run
+from clan_lib.dirs import clan_templates
 from clan_lib.errors import ClanError
 from clan_lib.flake import Flake
 from clan_lib.nix import nix_command, nix_metadata, nix_shell
 from clan_lib.persist.inventory_store import InventorySnapshot, InventoryStore
-from clan_lib.templates import (
-    InputPrio,
-    TemplateName,
-    get_template,
-)
-from clan_lib.templates.filesystem import copy_from_nixstore
+from clan_lib.templates.handler import clan_template
 
 log = logging.getLogger(__name__)
 
@@ -21,9 +17,9 @@ log = logging.getLogger(__name__)
 @dataclass
 class CreateOptions:
     dest: Path
-    template_name: str
+    template: str
+
     src_flake: Flake | None = None
-    input_prio: InputPrio | None = None
     setup_git: bool = True
     initial: InventorySnapshot | None = None
     update_clan: bool = True
@@ -47,44 +43,31 @@ def create_clan(opts: CreateOptions) -> None:
             log.warning("Setting src_flake to None")
             opts.src_flake = None
 
-    template = get_template(
-        TemplateName(opts.template_name),
-        "clan",
-        input_prio=opts.input_prio,
-        clan_dir=opts.src_flake,
-    )
-    log.info(f"Found template '{template.name}' in '{template.input_variant}'")
+    if opts.src_flake is None:
+        opts.src_flake = Flake(str(clan_templates()))
 
-    if dest.exists():
-        dest /= template.name
+    with clan_template(
+        opts.src_flake, template_ident=opts.template, dst_dir=opts.dest
+    ) as _clan_dir:
+        if opts.setup_git:
+            run(git_command(dest, "init"))
+            run(git_command(dest, "add", "."))
 
-    if dest.exists():
-        msg = f"Destination directory {dest} already exists"
-        raise ClanError(msg)
+            # check if username is set
+            has_username = run(
+                git_command(dest, "config", "user.name"), RunOpts(check=False)
+            )
+            if has_username.returncode != 0:
+                run(git_command(dest, "config", "user.name", "clan-tool"))
 
-    src = Path(template.src["path"])
+            has_username = run(
+                git_command(dest, "config", "user.email"), RunOpts(check=False)
+            )
+            if has_username.returncode != 0:
+                run(git_command(dest, "config", "user.email", "clan@example.com"))
 
-    copy_from_nixstore(src, dest)
-
-    if opts.setup_git:
-        run(git_command(dest, "init"))
-        run(git_command(dest, "add", "."))
-
-        # check if username is set
-        has_username = run(
-            git_command(dest, "config", "user.name"), RunOpts(check=False)
-        )
-        if has_username.returncode != 0:
-            run(git_command(dest, "config", "user.name", "clan-tool"))
-
-        has_username = run(
-            git_command(dest, "config", "user.email"), RunOpts(check=False)
-        )
-        if has_username.returncode != 0:
-            run(git_command(dest, "config", "user.email", "clan@example.com"))
-
-    if opts.update_clan:
-        run(nix_command(["flake", "update"]), RunOpts(cwd=dest))
+        if opts.update_clan:
+            run(nix_command(["flake", "update"]), RunOpts(cwd=dest))
 
     if opts.initial:
         inventory_store = InventoryStore(flake=Flake(str(opts.dest)))

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

@@ -1,12 +1,12 @@
 from clan_lib.api import API
 from clan_lib.errors import ClanError
 from clan_lib.flake import Flake
-from clan_lib.nix_models.clan import InventoryMeta as Meta
+from clan_lib.nix_models.clan import InventoryMeta
 from clan_lib.persist.inventory_store import InventoryStore
 
 
 @API.register
-def show_clan_meta(flake: Flake) -> Meta:
+def get_clan_details(flake: Flake) -> InventoryMeta:
     if flake.is_local and not flake.path.exists():
         msg = f"Path {flake} does not exist"
         raise ClanError(msg, description="clan directory does not exist")

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

@@ -14,7 +14,7 @@ class UpdateOptions:
 
 
 @API.register
-def update_clan_meta(options: UpdateOptions) -> InventorySnapshot:
+def set_clan_details(options: UpdateOptions) -> InventorySnapshot:
     inventory_store = InventoryStore(options.flake)
     inventory = inventory_store.read()
     set_value_by_path(inventory, "meta", options.meta)

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

@@ -290,6 +290,7 @@ class RunOpts:
     # Ask for sudo password in a graphical way.
     # This is needed for GUI applications
     graphical_perm: bool = False
+    trace: bool = True
 
 
 def cmd_with_root(cmd: list[str], graphical: bool = False) -> list[str]:
@@ -344,7 +345,7 @@ def run(
         # Use our sudo ask proxy here as well
         options.needs_user_terminal = True
 
-    if cmdlog.isEnabledFor(logging.DEBUG):
+    if cmdlog.isEnabledFor(logging.DEBUG) and options.trace:
         if options.input and isinstance(options.input, bytes):
             if any(
                 not ch.isprintable() for ch in options.input.decode("ascii", "replace")

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

@@ -345,6 +345,23 @@ class FlakeCacheEntry:
                 msg = f"Cannot insert {value} into cache, already have {self.value}"
                 raise TypeError(msg)
 
+    def _check_path_exists(self, path_str: str) -> bool:
+        """Check if a path exists, handling potential line number suffixes."""
+        path = Path(path_str)
+        if path.exists():
+            return True
+
+        # Try stripping line numbers if the path doesn't exist
+        # Handle format: /path/to/file:123 or /path/to/file:123:456
+        if ":" in path_str:
+            parts = path_str.split(":")
+            if len(parts) >= 2:
+                # Check if all parts after the first colon are numbers
+                if all(part.isdigit() for part in parts[1:]):
+                    base_path = parts[0]
+                    return Path(base_path).exists()
+        return False
+
     def is_cached(self, selectors: list[Selector]) -> bool:
         selector: Selector
 
@@ -353,12 +370,12 @@ class FlakeCacheEntry:
             # Check if it's a regular nix store path
             nix_store_dir = os.environ.get("NIX_STORE_DIR", "/nix/store")
             if self.value.startswith(nix_store_dir):
-                return Path(self.value).exists()
+                return self._check_path_exists(self.value)
 
             # Check if it's a test store path
             test_store = os.environ.get("CLAN_TEST_STORE")
             if test_store and self.value.startswith(test_store):
-                return Path(self.value).exists()
+                return self._check_path_exists(self.value)
 
         # if self.value is not dict but we request more selectors, we assume we are cached and an error will be thrown in the select function
         if isinstance(self.value, str | float | int | None):
@@ -621,7 +638,9 @@ class Flake:
         return self._is_local
 
     def get_input_names(self) -> list[str]:
-        return self.select("inputs", apply="builtins.attrNames")
+        log.debug("flake.get_input_names is deprecated and will be removed")
+        flakes = self.select("inputs.*._type")
+        return list(flakes.keys())
 
     @property
     def path(self) -> Path:
@@ -710,7 +729,6 @@ class Flake:
     def get_from_nix(
         self,
         selectors: list[str],
-        apply: str = "v: v",
     ) -> None:
         """
         Retrieves specific attributes from a Nix flake using the provided selectors.
@@ -729,7 +747,7 @@ class Flake:
             ClanError: If the number of outputs does not match the number of selectors.
             AssertionError: If the cache or flake cache path is not properly initialized.
         """
-        from clan_lib.cmd import Log, RunOpts, run
+        from clan_lib.cmd import run, RunOpts, Log
         from clan_lib.dirs import select_source
         from clan_lib.nix import (
             nix_build,
@@ -772,7 +790,7 @@ class Flake:
                 result = builtins.toJSON [
                     {" ".join(
                         [
-                            f"(({apply}) (selectLib.applySelectors (builtins.fromJSON ''{attr}'') flake))"
+                            f"(selectLib.applySelectors (builtins.fromJSON ''{attr}'') flake)"
                             for attr in str_selectors
                         ]
                     )}
@@ -795,11 +813,41 @@ class Flake:
                 ];
               }}
         """
+        if len(selectors) > 1:
+            log.debug(f"""
+selecting: {selectors}
+to debug run:
+nix repl --expr 'rec {{
+  flake = builtins.getFlake "self.identifier";
+  selectLib = (builtins.getFlake "path:{select_source()}?narHash={select_hash}").lib;
+  query = [
+      {" ".join(
+         [
+             f"(selectLib.select ''{selector}'' flake)"
+             for selector in selectors
+         ]
+      )}
+  ];
+}}'
+            """)
         # fmt: on
+        elif len(selectors) == 1:
+            log.debug(
+                f"""
+selecting: {selectors[0]}
+to debug run:
+nix repl --expr 'rec {{
+  flake = builtins.getFlake "{self.identifier}";
+  selectLib = (builtins.getFlake "path:{select_source()}?narHash={select_hash}").lib;
+  query = selectLib.select '"''{selectors[0]}''"' flake;
+}}'
+            """
+            )
 
         build_output = Path(
             run(
-                nix_build(["--expr", nix_code, *nix_options]), RunOpts(log=Log.NONE)
+                nix_build(["--expr", nix_code, *nix_options]),
+                RunOpts(log=Log.NONE, trace=False),
             ).stdout.strip()
         )
 
@@ -840,7 +888,6 @@ class Flake:
     def select(
         self,
         selector: str,
-        apply: str = "v: v",
     ) -> Any:
         """
         Selects a value from the cache based on the provided selector string.
@@ -856,6 +903,23 @@ class Flake:
 
         if not self._cache.is_cached(selector):
             log.debug(f"Cache miss for {selector}")
-            self.get_from_nix([selector], apply=apply)
+            self.get_from_nix([selector])
         value = self._cache.select(selector)
         return value
+
+    def select_machine(self, machine_name: str, selector: str) -> Any:
+        """
+        Select a nix attribute for a specific machine.
+
+        Args:
+            machine_name: The name of the machine
+            selector: The attribute selector string relative to the machine config
+            apply: Optional function to apply to the result
+        """
+        from clan_lib.nix import nix_config
+
+        config = nix_config()
+        system = config["system"]
+
+        full_selector = f'clanInternals.machines."{system}"."{machine_name}".{selector}'
+        return self.select(full_selector)

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

@@ -296,3 +296,81 @@ def test_cache_gc(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
     assert my_flake._cache.is_cached("testfile")  # noqa: SLF001
     subprocess.run(["nix-collect-garbage"], check=True)
     assert not my_flake._cache.is_cached("testfile")  # noqa: SLF001
+
+
+def test_cache_path_with_line_numbers(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    """Test that is_cached correctly handles store paths with line numbers appended.
+
+    This is a regression test for the bug where cached store paths with line numbers
+    (e.g., /nix/store/path:123) are not properly checked for existence.
+    """
+    # Create a temporary store
+    test_store = tmp_path / "test-store"
+    test_store.mkdir()
+
+    # Set CLAN_TEST_STORE environment variable
+    monkeypatch.setenv("CLAN_TEST_STORE", str(test_store))
+
+    # Create a fake store path
+    fake_store_path = test_store / "abc123-source-file.nix"
+    fake_store_path.write_text("# nix source file\n{ foo = 123; }")
+
+    # Create cache entries for paths with line numbers
+    cache = FlakeCacheEntry()
+
+    # Test single line number format
+    path_with_line = f"{fake_store_path}:42"
+    selectors = parse_selector("testPath1")
+    cache.insert(path_with_line, selectors)
+
+    # Test line:column format
+    path_with_line_col = f"{fake_store_path}:42:10"
+    selectors2 = parse_selector("testPath2")
+    cache.insert(path_with_line_col, selectors2)
+
+    # Test path with colon but non-numeric suffix (should not be treated as line number)
+    path_with_colon = test_store / "file:with:colons"
+    path_with_colon.write_text("test")
+    selectors3 = parse_selector("testPath3")
+    cache.insert(str(path_with_colon), selectors3)
+
+    # Before the fix: These would return True even though the exact paths don't exist
+    # After the fix: They check the base file path exists
+    assert cache.is_cached(parse_selector("testPath1")), (
+        "Path with line number should be cached when base file exists"
+    )
+    assert cache.is_cached(parse_selector("testPath2")), (
+        "Path with line:column should be cached when base file exists"
+    )
+    assert cache.is_cached(parse_selector("testPath3")), (
+        "Path with colons in filename should be cached when file exists"
+    )
+
+    # Now delete the base file
+    fake_store_path.unlink()
+
+    # After deletion, paths with line numbers should not be cached
+    assert not cache.is_cached(parse_selector("testPath1")), (
+        "Path with line number should not be cached when base file doesn't exist"
+    )
+    assert not cache.is_cached(parse_selector("testPath2")), (
+        "Path with line:column should not be cached when base file doesn't exist"
+    )
+
+    # Path with colons in name still exists
+    assert cache.is_cached(parse_selector("testPath3")), (
+        "Path with colons in filename should still be cached"
+    )
+
+    # Test with regular /nix/store paths
+    monkeypatch.delenv("CLAN_TEST_STORE", raising=False)
+    cache2 = FlakeCacheEntry()
+    nix_path_with_line = "/nix/store/fake-source.nix:123"
+    cache2.insert(nix_path_with_line, parse_selector("nixPath"))
+
+    # Should return False because neither the exact path nor base path exists
+    assert not cache2.is_cached(parse_selector("nixPath")), (
+        "Nix store path with line number should not be cached when file doesn't exist"
+    )

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

@@ -10,14 +10,3 @@ Which is an abstraction over the inventory
 
 Interacting with 'clan_lib.inventory' is NOT recommended and will be removed
 """
-
-from clan_lib.api import API
-from clan_lib.flake import Flake
-from clan_lib.persist.inventory_store import InventorySnapshot, InventoryStore
-
-
-@API.register
-def get_inventory(flake: Flake) -> InventorySnapshot:
-    inventory_store = InventoryStore(flake)
-    inventory = inventory_store.read()
-    return inventory

pkgs/clan-cli/clan_lib/log_manager/example_usage.py

@@ -17,7 +17,7 @@ def example_function() -> None:
     """Example function for creating logs."""
 
 
-def deploy_machine() -> None:
+def run_machine_deploy() -> None:
     """Function for deploying machines."""
 
 
@@ -41,7 +41,7 @@ def main() -> None:
     for repo in repos:
         for machine in machines:
             log_manager.create_log_file(
-                deploy_machine,
+                run_machine_deploy,
                 f"deploy_{machine}",
                 ["clans", repo, "machines", machine],
             )

pkgs/clan-cli/clan_lib/log_manager/test_log_manager.py

@@ -17,7 +17,7 @@ from clan_lib.log_manager import (
 
 
 # Test functions for log creation
-def deploy_machine() -> None:
+def run_machine_deploy() -> None:
     """Test function for deploying machines."""
 
 
@@ -194,13 +194,13 @@ class TestLogFileCreation:
         for repo in repos:
             for machine in machines:
                 log_file = configured_log_manager.create_log_file(
-                    deploy_machine,
+                    run_machine_deploy,
                     f"deploy_{machine}",
                     ["clans", repo, "machines", machine],
                 )
 
                 assert log_file.op_key == f"deploy_{machine}"
-                assert log_file.func_name == "deploy_machine"
+                assert log_file.func_name == "run_machine_deploy"
                 assert log_file.get_file_path().exists()
 
                 # Check the group structure includes URL encoding for dynamic parts
@@ -241,7 +241,7 @@ class TestFilterFunction:
         """Test that empty filter returns top-level groups."""
         # Create some log files first
         configured_log_manager.create_log_file(
-            deploy_machine, "test_op", ["clans", "repo1", "machines", "machine1"]
+            run_machine_deploy, "test_op", ["clans", "repo1", "machines", "machine1"]
         )
 
         top_level = configured_log_manager.filter([])
@@ -258,7 +258,7 @@ class TestFilterFunction:
         for repo in repos:
             for machine in machines:
                 configured_log_manager.create_log_file(
-                    deploy_machine,
+                    run_machine_deploy,
                     f"deploy_{machine}",
                     ["clans", repo, "machines", machine],
                 )
@@ -281,7 +281,7 @@ class TestFilterFunction:
         """Test filtering with specific date."""
         # Create log file
         log_file = configured_log_manager.create_log_file(
-            deploy_machine, "test_op", ["clans", "repo1", "machines", "machine1"]
+            run_machine_deploy, "test_op", ["clans", "repo1", "machines", "machine1"]
         )
 
         # Filter with the specific date
@@ -308,14 +308,16 @@ class TestGetLogFile:
         """Test getting log file by operation key."""
         # Create log file
         configured_log_manager.create_log_file(
-            deploy_machine, "deploy_wintux", ["clans", "repo1", "machines", "wintux"]
+            run_machine_deploy,
+            "deploy_wintux",
+            ["clans", "repo1", "machines", "wintux"],
         )
 
         # Find it by op_key
         found_log_file = configured_log_manager.get_log_file("deploy_wintux")
         assert found_log_file is not None
         assert found_log_file.op_key == "deploy_wintux"
-        assert found_log_file.func_name == "deploy_machine"
+        assert found_log_file.func_name == "run_machine_deploy"
 
     def test_get_log_file_with_selector(
         self, configured_log_manager: LogManager
@@ -323,10 +325,14 @@ class TestGetLogFile:
         """Test getting log file with specific selector like example_usage.py."""
         # Create log files in different locations
         configured_log_manager.create_log_file(
-            deploy_machine, "deploy_wintux", ["clans", "repo1", "machines", "wintux"]
+            run_machine_deploy,
+            "deploy_wintux",
+            ["clans", "repo1", "machines", "wintux"],
         )
         configured_log_manager.create_log_file(
-            deploy_machine, "deploy_wintux", ["clans", "repo2", "machines", "wintux"]
+            run_machine_deploy,
+            "deploy_wintux",
+            ["clans", "repo2", "machines", "wintux"],
         )
 
         # Find specific one using selector
@@ -341,7 +347,7 @@ class TestGetLogFile:
         """Test getting log file with specific date."""
         # Create log file
         log_file = configured_log_manager.create_log_file(
-            deploy_machine, "deploy_demo", ["clans", "repo1", "machines", "demo"]
+            run_machine_deploy, "deploy_demo", ["clans", "repo1", "machines", "demo"]
         )
 
         # Find it by op_key and date
@@ -378,10 +384,10 @@ class TestListLogDays:
         """Test listing log days when logs exist."""
         # Create log files
         configured_log_manager.create_log_file(
-            deploy_machine, "op1", ["clans", "repo1", "machines", "machine1"]
+            run_machine_deploy, "op1", ["clans", "repo1", "machines", "machine1"]
         )
         configured_log_manager.create_log_file(
-            deploy_machine, "op2", ["clans", "repo2", "machines", "machine2"]
+            run_machine_deploy, "op2", ["clans", "repo2", "machines", "machine2"]
         )
 
         days = configured_log_manager.list_log_days()
@@ -406,7 +412,7 @@ class TestApiCompatibility:
         for repo in repos:
             for machine in machines:
                 configured_log_manager.create_log_file(
-                    deploy_machine,
+                    run_machine_deploy,
                     f"deploy_{machine}",
                     ["clans", repo, "machines", machine],
                 )
@@ -741,19 +747,19 @@ class TestLogFileSorting:
         # This simulates the realistic scenario where the same operation runs on different machines
 
         configured_log_manager.create_log_file(
-            deploy_machine,
+            run_machine_deploy,
             "deploy_operation",
             ["clans", "repo1", "machines", "machine1"],
         )
 
         configured_log_manager.create_log_file(
-            deploy_machine,
+            run_machine_deploy,
             "deploy_operation",
             ["clans", "repo1", "machines", "machine2"],
         )
 
         configured_log_manager.create_log_file(
-            deploy_machine,
+            run_machine_deploy,
             "deploy_operation",
             ["clans", "repo2", "machines", "machine1"],
         )
@@ -819,7 +825,7 @@ class TestURLEncoding:
 
         # Create log file with special characters
         log_file = configured_log_manager.create_log_file(
-            deploy_machine,
+            run_machine_deploy,
             "deploy_special",
             ["clans", special_repo, "machines", special_machine],
         )

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

@@ -1,9 +1,9 @@
-from dataclasses import dataclass
 from typing import TypedDict
 
 from clan_lib.api import API
 from clan_lib.errors import ClanError
 from clan_lib.flake.flake import Flake
+from clan_lib.machines.machines import Machine
 from clan_lib.nix_models.clan import (
     InventoryMachine,
 )
@@ -65,16 +65,8 @@ def get_machine(flake: Flake, name: str) -> InventoryMachine:
     return InventoryMachine(**machine_inv)
 
 
-# TODO: remove this machine, once the Machine class is refactored
-# We added this now, to allow for dispatching actions. To require only 'name' and 'flake' of a machine.
-@dataclass(frozen=True)
-class MachineID:
-    name: str
-    flake: Flake
-
-
 @API.register
-def set_machine(machine: MachineID, update: InventoryMachine) -> None:
+def set_machine(machine: Machine, update: InventoryMachine) -> None:
     """
     Update the machine information in the inventory.
     """

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

@@ -9,7 +9,7 @@ from clan_cli.secrets.secrets import (
     list_secrets,
 )
 
-from clan_lib import inventory
+from clan_lib.persist.inventory_store import InventoryStore
 from clan_lib.api import API
 from clan_lib.dirs import specific_machine_dir
 from clan_lib.machines.machines import Machine
@@ -19,7 +19,7 @@ log = logging.getLogger(__name__)
 
 @API.register
 def delete_machine(machine: Machine) -> None:
-    inventory_store = inventory.InventoryStore(machine.flake)
+    inventory_store = InventoryStore(machine.flake)
     try:
         inventory_store.delete(
             {f"machines.{machine.name}"},

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

@@ -3,6 +3,7 @@ import logging
 from dataclasses import dataclass
 from enum import Enum
 from pathlib import Path
+from typing import TypedDict
 
 from clan_lib.api import API
 from clan_lib.cmd import RunOpts, run
@@ -40,19 +41,7 @@ class HardwareConfig(Enum):
         return HardwareConfig.NONE
 
 
-@API.register
-def show_machine_hardware_config(machine: Machine) -> HardwareConfig:
-    """
-    Show hardware information for a machine returns None if none exist.
-    """
-    return HardwareConfig.detect_type(machine)
-
-
-@API.register
-def show_machine_hardware_platform(machine: Machine) -> str | None:
-    """
-    Show hardware information for a machine returns None if none exist.
-    """
+def get_machine_target_platform(machine: Machine) -> str | None:
     config = nix_config()
     system = config["system"]
     cmd = nix_eval(
@@ -78,7 +67,7 @@ class HardwareGenerateOptions:
 
 
 @API.register
-def generate_machine_hardware_info(
+def run_machine_hardware_info(
     opts: HardwareGenerateOptions, target_host: Remote
 ) -> HardwareConfig:
     """
@@ -132,7 +121,7 @@ def generate_machine_hardware_info(
         f"machines/{opts.machine}/{hw_file.name}: update hardware configuration",
     )
     try:
-        show_machine_hardware_platform(opts.machine)
+        get_machine_target_platform(opts.machine)
         if backup_file:
             backup_file.unlink(missing_ok=True)
     except ClanCmdError as e:
@@ -150,3 +139,29 @@ def generate_machine_hardware_info(
         ) from e
 
     return opts.backend
+
+
+def get_machine_hardware_config(machine: Machine) -> HardwareConfig:
+    """
+    Detect and return the full hardware configuration for the given machine.
+
+    Returns:
+        HardwareConfig: Structured hardware information, or None if unavailable.
+    """
+    return HardwareConfig.detect_type(machine)
+
+
+class MachineHardwareBrief(TypedDict):
+    hardware_config: HardwareConfig
+    platform: str | None
+
+
+@API.register
+def get_machine_hardware_summary(machine: Machine) -> MachineHardwareBrief:
+    """
+    Return a high-level summary of hardware config and platform type.
+    """
+    return {
+        "hardware_config": get_machine_hardware_config(machine),
+        "platform": get_machine_target_platform(machine),
+    }

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

@@ -39,7 +39,7 @@ class InstallOptions:
 
 
 @API.register
-def install_machine(opts: InstallOptions, target_host: Remote) -> None:
+def run_machine_install(opts: InstallOptions, target_host: Remote) -> None:
     machine = opts.machine
 
     machine.debug(f"installing {machine.name}")

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

@@ -16,12 +16,12 @@ from clan_lib.nix_models.clan import InventoryMachine
 log = logging.getLogger(__name__)
 
 
-def convert_inventory_to_machines(
+def instantiate_inventory_to_machines(
     flake: Flake, machines: dict[str, InventoryMachine]
 ) -> dict[str, Machine]:
     return {
-        name: Machine.from_inventory(name, flake, inventory_machine)
-        for name, inventory_machine in machines.items()
+        name: Machine.from_inventory(name, flake, _inventory_machine)
+        for name, _inventory_machine in machines.items()
     }
 
 
@@ -31,26 +31,7 @@ def list_full_machines(flake: Flake) -> dict[str, Machine]:
     """
     machines = list_machines(flake)
 
-    return convert_inventory_to_machines(flake, machines)
-
-
-def query_machines_by_tags(
-    flake: Flake, tags: list[str]
-) -> dict[str, InventoryMachine]:
-    """
-    Query machines by their respective tags, if multiple tags are specified
-    then only machines that have those respective tags specified will be listed.
-    It is an intersection of the tags and machines.
-    """
-    machines = list_machines(flake)
-
-    filtered_machines = {}
-    for machine_name, machine in machines.items():
-        machine_tags = machine.get("tags", [])
-        if all(tag in machine_tags for tag in tags):
-            filtered_machines[machine_name] = machine
-
-    return filtered_machines
+    return instantiate_inventory_to_machines(flake, machines)
 
 
 @dataclass

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

@@ -13,8 +13,6 @@ from clan_cli.vars._types import StoreBase
 from clan_lib.api import API
 from clan_lib.errors import ClanCmdError, ClanError
 from clan_lib.flake import Flake
-from clan_lib.machines.actions import get_machine
-from clan_lib.nix import nix_config
 from clan_lib.nix_models.clan import InventoryMachine
 from clan_lib.ssh.remote import Remote
 
@@ -39,6 +37,9 @@ class Machine:
         return cls(name=name, flake=flake)
 
     def get_inv_machine(self) -> "InventoryMachine":
+        # Import on demand to avoid circular imports
+        from clan_lib.machines.actions import get_machine
+
         return get_machine(self.flake, self.name)
 
     def get_id(self) -> str:
@@ -103,13 +104,13 @@ class Machine:
     def secret_vars_store(self) -> StoreBase:
         secret_module = self.select("config.clan.core.vars.settings.secretModule")
         module = importlib.import_module(secret_module)
-        return module.SecretStore(machine=self)
+        return module.SecretStore(machine=self.name, flake=self.flake)
 
     @cached_property
     def public_vars_store(self) -> StoreBase:
         public_module = self.select("config.clan.core.vars.settings.publicModule")
         module = importlib.import_module(public_module)
-        return module.FactStore(machine=self)
+        return module.FactStore(machine=self.name, flake=self.flake)
 
     @property
     def facts_data(self) -> dict[str, dict[str, Any]]:
@@ -127,7 +128,7 @@ class Machine:
         return self.flake.path
 
     def target_host(self) -> Remote:
-        remote = get_host(self.name, self.flake, field="targetHost")
+        remote = get_machine_host(self.name, self.flake, field="targetHost")
         if remote is None:
             msg = f"'targetHost' is not set for machine '{self.name}'"
             raise ClanError(
@@ -142,7 +143,7 @@ class Machine:
         The host where the machine is built and deployed from.
         Can be the same as the target host.
         """
-        remote = get_host(self.name, self.flake, field="buildHost")
+        remote = get_machine_host(self.name, self.flake, field="buildHost")
 
         if remote:
             data = remote.data
@@ -158,13 +159,7 @@ class Machine:
         Select a nix attribute of the machine
         @attr: the attribute to get
         """
-
-        config = nix_config()
-        system = config["system"]
-
-        return self.flake.select(
-            f'clanInternals.machines."{system}"."{self.name}".{attr}'
-        )
+        return self.flake.select_machine(self.name, attr)
 
 
 @dataclass(frozen=True)
@@ -174,7 +169,7 @@ class RemoteSource:
 
 
 @API.register
-def get_host(
+def get_machine_host(
     name: str, flake: Flake, field: Literal["targetHost", "buildHost"]
 ) -> RemoteSource | None:
     """
@@ -187,9 +182,10 @@ def get_host(
     host_str = inv_machine.get("deploy", {}).get(field)
 
     if host_str is None:
-        machine.warn(
-            f"'{field}' is not set in `inventory.machines.${name}.deploy.targetHost` - falling back to _slower_ nixos option: `clan.core.networking.targetHost`"
+        machine.info(
+            f"`inventory.machines.{machine.name}.deploy.{field}` is not set — falling back to `clan.core.networking.{field}`. See: https://docs.clan.lol/guides/target-host"
         )
+
         host_str = machine.select(f'config.clan.core.networking."{field}"')
         source = "machine"
 

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

@@ -48,9 +48,13 @@ def get_available_machines(flake: Flake) -> list[str]:
     return list(machines.keys())
 
 
-def validate_machine_names(machine_names: list[str], flake: Flake) -> None:
+def validate_machine_names(machine_names: list[str], flake: Flake) -> list[str]:
+    """
+    Returns a list of valid machine names
+    that are guaranteed to exist in the referenced clan
+    """
     if not machine_names:
-        return
+        return []
 
     available_machines = get_available_machines(flake)
     invalid_machines = [
@@ -70,3 +74,5 @@ def validate_machine_names(machine_names: list[str], flake: Flake) -> None:
             error_lines.append(f"Machine '{machine_name}' not found. {suggestion_text}")
 
         raise ClanError("\n".join(error_lines))
+
+    return machine_names

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

@@ -103,7 +103,7 @@ def upload_sources(machine: Machine, ssh: Remote) -> str:
 
 
 @API.register
-def deploy_machine(
+def run_machine_deploy(
     machine: Machine, target_host: Remote, build_host: Remote | None
 ) -> None:
     with ExitStack() as stack:
@@ -167,7 +167,11 @@ def deploy_machine(
         if become_root:
             host = sudo_host
 
-        remote_env = host.nix_ssh_env(control_master=False)
+        # Disable SSH_ASKPASS when using a build host (headless machines)
+        use_ssh_askpass = build_host is None
+        remote_env = host.nix_ssh_env(
+            control_master=False, use_ssh_askpass=use_ssh_askpass
+        )
         ret = host.run(
             switch_cmd,
             RunOpts(

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

@@ -1,15 +1,15 @@
 # Adapted from https://github.com/numtide/deploykit
 
-from enum import Enum
+from typing import Literal
 
 from clan_lib.errors import ClanError
 
-
-class HostKeyCheck(Enum):
-    STRICT = "strict"  # Strictly check ssh host keys, prompt for unknown ones
-    ASK = "ask"  # Ask for confirmation on first use
-    TOFU = "tofu"  # Trust on ssh keys on first use
-    NONE = "none"  # Do not check ssh host keys
+HostKeyCheck = Literal[
+    "strict",  # Strictly check ssh host keys, prompt for unknown ones
+    "ask",  # Ask for confirmation on first use
+    "tofu",  # Trust on ssh keys on first use
+    "none",  # Do not check ssh host keys
+]
 
 
 def hostkey_to_ssh_opts(host_key_check: HostKeyCheck) -> list[str]:
@@ -17,13 +17,13 @@ def hostkey_to_ssh_opts(host_key_check: HostKeyCheck) -> list[str]:
     Convert a HostKeyCheck value to SSH options.
     """
     match host_key_check:
-        case HostKeyCheck.STRICT:
+        case "strict":
             return ["-o", "StrictHostKeyChecking=yes"]
-        case HostKeyCheck.ASK:
+        case "ask":
             return []
-        case HostKeyCheck.TOFU:
+        case "tofu":
             return ["-o", "StrictHostKeyChecking=accept-new"]
-        case HostKeyCheck.NONE:
+        case "none":
             return [
                 "-o",
                 "StrictHostKeyChecking=no",

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

@@ -0,0 +1,51 @@
+"""
+Password prompt utilities for SSH and sudo operations.
+
+This module provides functions to create password prompts using either
+GUI (zenity) or terminal (dialog) interfaces based on the environment.
+"""
+
+import os
+import sys
+
+from clan_lib.nix import nix_shell
+
+
+def get_password_command(title: str = "SSH Password", message: str = "") -> list[str]:
+    """
+    Determine the appropriate password prompt command based on environment.
+
+    This function checks if a GUI environment is available and selects either zenity (for GUI)
+    or dialog (for terminal) to create a password prompt. It then returns a command that will
+    execute the selected tool within a Nix shell with the necessary dependencies.
+
+    Args:
+        title: Title for the password dialog
+        message: Optional message for the dialog (only used by dialog, not zenity)
+
+    Returns:
+        A list of strings representing the shell command to execute the password prompt
+    """
+    if (
+        os.environ.get("DISPLAY")
+        or os.environ.get("WAYLAND_DISPLAY")
+        or sys.platform == "darwin"
+    ):
+        # GUI environment - use zenity
+        cmd = ["zenity", "--password", "--title", title]
+        dependencies = ["zenity"]
+    else:
+        # Terminal environment - use dialog
+        cmd = [
+            "dialog",
+            "--stdout",
+            "--insecure",
+            "--title",
+            title,
+            "--passwordbox",
+            message or "Enter password:",
+            "10",
+            "50",
+        ]
+        dependencies = ["dialog"]
+    return nix_shell(dependencies, cmd)