diff --git a/pkgs/clan-cli/clan_cli/clan/create.py b/pkgs/clan-cli/clan_cli/clan/create.py
index 861206790..fc63a6574 100644
--- a/pkgs/clan-cli/clan_cli/clan/create.py
+++ b/pkgs/clan-cli/clan_cli/clan/create.py
@@ -107,7 +107,7 @@ def create_clan(opts: CreateOptions) -> CreateClanResponse:
         response.flake_update = flake_update
 
     if opts.initial:
-        init_inventory(str(opts.dest), init=opts.initial)
+        init_inventory(Flake(str(opts.dest)), init=opts.initial)
 
     return response
 
diff --git a/pkgs/clan-cli/clan_cli/clan/inspect.py b/pkgs/clan-cli/clan_cli/clan/inspect.py
index 32e36299d..92ef3e8ca 100644
--- a/pkgs/clan-cli/clan_cli/clan/inspect.py
+++ b/pkgs/clan-cli/clan_cli/clan/inspect.py
@@ -3,8 +3,8 @@ from dataclasses import dataclass
 from pathlib import Path
 from typing import Any
 
+from clan_cli.clan_dirs import machine_gcroot
 from clan_cli.cmd import run
-from clan_cli.dirs import machine_gcroot
 from clan_cli.errors import ClanError
 from clan_cli.flake import Flake
 from clan_cli.machines.list import list_nixos_machines
diff --git a/pkgs/clan-cli/clan_cli/clan/update.py b/pkgs/clan-cli/clan_cli/clan/update.py
index 4955ac0cc..b1d87cf01 100644
--- a/pkgs/clan-cli/clan_cli/clan/update.py
+++ b/pkgs/clan-cli/clan_cli/clan/update.py
@@ -2,20 +2,21 @@ from dataclasses import dataclass
 
 from clan_lib.api import API
 
+from clan_cli.flake import Flake
 from clan_cli.inventory import Inventory, Meta, load_inventory_json, set_inventory
 
 
 @dataclass
 class UpdateOptions:
-    directory: str
+    flake: Flake
     meta: Meta
 
 
 @API.register
 def update_clan_meta(options: UpdateOptions) -> Inventory:
-    inventory = load_inventory_json(options.directory)
+    inventory = load_inventory_json(options.flake)
     inventory["meta"] = options.meta
 
-    set_inventory(inventory, options.directory, "Update clan metadata")
+    set_inventory(inventory, options.flake, "Update clan metadata")
 
     return inventory
diff --git a/pkgs/clan-cli/clan_cli/clan_dirs.py b/pkgs/clan-cli/clan_cli/clan_dirs.py
new file mode 100644
index 000000000..c2b05deeb
--- /dev/null
+++ b/pkgs/clan-cli/clan_cli/clan_dirs.py
@@ -0,0 +1,43 @@
+import logging
+import urllib
+from pathlib import Path
+
+from clan_cli.flake import Flake
+
+from .dirs import user_data_dir, user_gcroot_dir
+
+log = logging.getLogger(__name__)
+
+
+def clan_key_safe(flake_url: str) -> str:
+    """
+    only embed the url in the path, not the clan name, as it would involve eval.
+    """
+    quoted_url = urllib.parse.quote_plus(flake_url)
+    return f"{quoted_url}"
+
+
+def machine_gcroot(flake_url: str) -> Path:
+    # Always build icon so that we can symlink it to the gcroot
+    gcroot_dir = user_gcroot_dir()
+    clan_gcroot = gcroot_dir / clan_key_safe(flake_url)
+    clan_gcroot.mkdir(parents=True, exist_ok=True)
+    return clan_gcroot
+
+
+def vm_state_dir(flake_url: str, vm_name: str) -> Path:
+    clan_key = clan_key_safe(str(flake_url))
+    return user_data_dir() / "clan" / "vmstate" / clan_key / vm_name
+
+
+def machines_dir(flake: Flake) -> Path:
+    if flake.is_local:
+        return flake.path / "machines"
+
+    store_path = flake.store_path
+    assert store_path is not None, "Invalid flake object"
+    return Path(store_path) / "machines"
+
+
+def specific_machine_dir(flake: Flake, machine: str) -> Path:
+    return machines_dir(flake) / machine
diff --git a/pkgs/clan-cli/clan_cli/dirs.py b/pkgs/clan-cli/clan_cli/dirs.py
index defe64fe5..8ff3e94e1 100644
--- a/pkgs/clan-cli/clan_cli/dirs.py
+++ b/pkgs/clan-cli/clan_cli/dirs.py
@@ -1,7 +1,6 @@
 import logging
 import os
 import sys
-import urllib
 from enum import Enum
 from pathlib import Path
 
@@ -24,14 +23,6 @@ def find_git_repo_root() -> Path | None:
     return find_toplevel([".git"])
 
 
-def clan_key_safe(flake_url: str) -> str:
-    """
-    only embed the url in the path, not the clan name, as it would involve eval.
-    """
-    quoted_url = urllib.parse.quote_plus(flake_url)
-    return f"{quoted_url}"
-
-
 def find_toplevel(top_level_files: list[str]) -> Path | None:
     """Returns the path to the toplevel of the clan flake"""
     for project_file in top_level_files:
@@ -114,31 +105,10 @@ def user_gcroot_dir() -> Path:
     return p
 
 
-def machine_gcroot(flake_url: str) -> Path:
-    # Always build icon so that we can symlink it to the gcroot
-    gcroot_dir = user_gcroot_dir()
-    clan_gcroot = gcroot_dir / clan_key_safe(flake_url)
-    clan_gcroot.mkdir(parents=True, exist_ok=True)
-    return clan_gcroot
-
-
 def user_history_file() -> Path:
     return user_config_dir() / "clan" / "history"
 
 
-def vm_state_dir(flake_url: str, vm_name: str) -> Path:
-    clan_key = clan_key_safe(str(flake_url))
-    return user_data_dir() / "clan" / "vmstate" / clan_key / vm_name
-
-
-def machines_dir(flake_dir: Path) -> Path:
-    return flake_dir / "machines"
-
-
-def specific_machine_dir(flake_dir: Path, machine: str) -> Path:
-    return machines_dir(flake_dir) / machine
-
-
 def module_root() -> Path:
     return Path(__file__).parent
 
diff --git a/pkgs/clan-cli/clan_cli/facts/public_modules/vm.py b/pkgs/clan-cli/clan_cli/facts/public_modules/vm.py
index 8788a199d..7bfe43184 100644
--- a/pkgs/clan-cli/clan_cli/facts/public_modules/vm.py
+++ b/pkgs/clan-cli/clan_cli/facts/public_modules/vm.py
@@ -1,7 +1,7 @@
 import logging
 from pathlib import Path
 
-from clan_cli.dirs import vm_state_dir
+from clan_cli.clan_dirs import vm_state_dir
 from clan_cli.errors import ClanError
 from clan_cli.machines.machines import Machine
 
diff --git a/pkgs/clan-cli/clan_cli/facts/secret_modules/vm.py b/pkgs/clan-cli/clan_cli/facts/secret_modules/vm.py
index 29209536e..f153e78a4 100644
--- a/pkgs/clan-cli/clan_cli/facts/secret_modules/vm.py
+++ b/pkgs/clan-cli/clan_cli/facts/secret_modules/vm.py
@@ -2,7 +2,7 @@ import shutil
 from pathlib import Path
 from typing import override
 
-from clan_cli.dirs import vm_state_dir
+from clan_cli.clan_dirs import vm_state_dir
 from clan_cli.machines.machines import Machine
 
 from . import SecretStoreBase
diff --git a/pkgs/clan-cli/clan_cli/inventory/__init__.py b/pkgs/clan-cli/clan_cli/inventory/__init__.py
index fe3d0715f..d5a1a6135 100644
--- a/pkgs/clan-cli/clan_cli/inventory/__init__.py
+++ b/pkgs/clan-cli/clan_cli/inventory/__init__.py
@@ -23,6 +23,7 @@ from clan_lib.api import API, dataclass_to_dict, from_dict
 
 from clan_cli.cmd import run_no_stdout
 from clan_cli.errors import ClanCmdError, ClanError
+from clan_cli.flake import Flake
 from clan_cli.git import commit_file
 from clan_cli.nix import nix_eval
 
@@ -49,11 +50,11 @@ __all__ = [
 ]
 
 
-def get_inventory_path(flake_dir: str | Path) -> Path:
+def get_inventory_path(flake: Flake) -> Path:
     """
     Get the path to the inventory file in the flake directory
     """
-    inventory_file = (Path(flake_dir) / "inventory.json").resolve()
+    inventory_file = (flake.path / "inventory.json").resolve()
     return inventory_file
 
 
@@ -61,7 +62,7 @@ def get_inventory_path(flake_dir: str | Path) -> Path:
 default_inventory: Inventory = {"meta": {"name": "New Clan"}}
 
 
-def load_inventory_eval(flake_dir: str | Path) -> Inventory:
+def load_inventory_eval(flake_dir: Flake) -> Inventory:
     """
     Loads the evaluated inventory.
     After all merge operations with eventual nix code in buildClan.
@@ -354,7 +355,7 @@ def determine_writeability(
     return results
 
 
-def get_inventory_current_priority(flake_dir: str | Path) -> dict:
+def get_inventory_current_priority(flake: Flake) -> dict:
     """
     Returns the current priority of the inventory values
 
@@ -374,7 +375,7 @@ def get_inventory_current_priority(flake_dir: str | Path) -> dict:
     """
     cmd = nix_eval(
         [
-            f"{flake_dir}#clanInternals.inventoryClass.introspection",
+            f"{flake}#clanInternals.inventoryClass.introspection",
             "--json",
         ]
     )
@@ -392,7 +393,7 @@ def get_inventory_current_priority(flake_dir: str | Path) -> dict:
 
 
 @API.register
-def load_inventory_json(flake_dir: str | Path) -> Inventory:
+def load_inventory_json(flake: Flake) -> Inventory:
     """
     Load the inventory FILE from the flake directory
     If no file is found, returns an empty dictionary
@@ -402,7 +403,7 @@ def load_inventory_json(flake_dir: str | Path) -> Inventory:
     Use load_inventory_eval instead
     """
 
-    inventory_file = get_inventory_path(flake_dir)
+    inventory_file = get_inventory_path(flake)
 
     if not inventory_file.exists():
         return {}
@@ -472,14 +473,14 @@ def patch(d: dict[str, Any], path: str, content: Any) -> None:
 
 
 @API.register
-def patch_inventory_with(base_dir: Path, section: str, content: dict[str, Any]) -> None:
+def patch_inventory_with(flake: Flake, section: str, content: dict[str, Any]) -> None:
     """
     Pass only the section to update and the content to update with.
     Make sure you pass only attributes that you would like to persist.
     ATTENTION: Don't pass nix eval values unintentionally.
     """
 
-    inventory_file = get_inventory_path(base_dir)
+    inventory_file = get_inventory_path(flake)
 
     curr_inventory = {}
     if inventory_file.exists():
@@ -491,7 +492,9 @@ def patch_inventory_with(base_dir: Path, section: str, content: dict[str, Any])
     with inventory_file.open("w") as f:
         json.dump(curr_inventory, f, indent=2)
 
-    commit_file(inventory_file, base_dir, commit_message=f"inventory.{section}: Update")
+    commit_file(
+        inventory_file, flake.path, commit_message=f"inventory.{section}: Update"
+    )
 
 
 @dataclass
@@ -503,16 +506,16 @@ class WriteInfo:
 
 @API.register
 def get_inventory_with_writeable_keys(
-    flake_dir: str | Path,
+    flake: Flake,
 ) -> WriteInfo:
     """
     Load the inventory and determine the writeable keys
     Performs 2 nix evaluations to get the current priority and the inventory
     """
-    current_priority = get_inventory_current_priority(flake_dir)
+    current_priority = get_inventory_current_priority(flake)
 
-    data_eval: Inventory = load_inventory_eval(flake_dir)
-    data_disk: Inventory = load_inventory_json(flake_dir)
+    data_eval: Inventory = load_inventory_eval(flake)
+    data_disk: Inventory = load_inventory_json(flake)
 
     writeables = determine_writeability(
         current_priority, dict(data_eval), dict(data_disk)
@@ -524,14 +527,14 @@ def get_inventory_with_writeable_keys(
 # TODO: remove this function in favor of a proper read/write API
 @API.register
 def set_inventory(
-    inventory: Inventory, flake_dir: str | Path, message: str, commit: bool = True
+    inventory: Inventory, flake: Flake, message: str, commit: bool = True
 ) -> None:
     """
     Write the inventory to the flake directory
     and commit it to git with the given message
     """
 
-    write_info = get_inventory_with_writeable_keys(flake_dir)
+    write_info = get_inventory_with_writeable_keys(flake)
 
     # Remove internals from the inventory
     inventory.pop("tags", None)  # type: ignore
@@ -552,43 +555,43 @@ def set_inventory(
     for delete_path in delete_set:
         delete_by_path(persisted, delete_path)
 
-    inventory_file = get_inventory_path(flake_dir)
+    inventory_file = get_inventory_path(flake)
     with inventory_file.open("w") as f:
         json.dump(persisted, f, indent=2)
 
     if commit:
-        commit_file(inventory_file, Path(flake_dir), commit_message=message)
+        commit_file(inventory_file, flake.path, commit_message=message)
 
 
 # TODO: wrap this in a proper persistence API
-def delete(directory: str | Path, delete_set: set[str]) -> None:
+def delete(flake: Flake, delete_set: set[str]) -> None:
     """
     Delete keys from the inventory
     """
-    write_info = get_inventory_with_writeable_keys(directory)
+    write_info = get_inventory_with_writeable_keys(flake)
 
     data_disk = dict(write_info.data_disk)
 
     for delete_path in delete_set:
         delete_by_path(data_disk, delete_path)
 
-    inventory_file = get_inventory_path(directory)
+    inventory_file = get_inventory_path(flake)
     with inventory_file.open("w") as f:
         json.dump(data_disk, f, indent=2)
 
     commit_file(
         inventory_file,
-        Path(directory),
+        flake.path,
         commit_message=f"Delete inventory keys {delete_set}",
     )
 
 
-def init_inventory(directory: str, init: Inventory | None = None) -> None:
+def init_inventory(flake: Flake, init: Inventory | None = None) -> None:
     inventory = None
     # Try reading the current flake
     if init is None:
         with contextlib.suppress(ClanCmdError):
-            inventory = load_inventory_eval(directory)
+            inventory = load_inventory_eval(flake)
 
     if init is not None:
         inventory = init
@@ -596,9 +599,9 @@ def init_inventory(directory: str, init: Inventory | None = None) -> None:
     # Write inventory.json file
     if inventory is not None:
         # Persist creates a commit message for each change
-        set_inventory(inventory, directory, "Init inventory")
+        set_inventory(inventory, flake, "Init inventory")
 
 
 @API.register
-def get_inventory(base_path: str | Path) -> Inventory:
-    return load_inventory_eval(base_path)
+def get_inventory(flake: Flake) -> Inventory:
+    return load_inventory_eval(flake)
diff --git a/pkgs/clan-cli/clan_cli/machines/create.py b/pkgs/clan-cli/clan_cli/machines/create.py
index 8ea74c9ad..3f9ef22fd 100644
--- a/pkgs/clan-cli/clan_cli/machines/create.py
+++ b/pkgs/clan-cli/clan_cli/machines/create.py
@@ -110,7 +110,7 @@ def create_machine(opts: CreateOptions, commit: bool = True) -> None:
         new_machine["deploy"] = {"targetHost": target_host}
 
     patch_inventory_with(
-        clan_dir, f"machines.{machine_name}", dataclass_to_dict(new_machine)
+        Flake(str(clan_dir)), f"machines.{machine_name}", dataclass_to_dict(new_machine)
     )
 
     # Commit at the end in that order to avoid committing halve-baked machines
diff --git a/pkgs/clan-cli/clan_cli/machines/delete.py b/pkgs/clan-cli/clan_cli/machines/delete.py
index 4f0698798..96b721b7e 100644
--- a/pkgs/clan-cli/clan_cli/machines/delete.py
+++ b/pkgs/clan-cli/clan_cli/machines/delete.py
@@ -6,8 +6,8 @@ from pathlib import Path
 from clan_lib.api import API
 
 from clan_cli import Flake, inventory
+from clan_cli.clan_dirs import specific_machine_dir
 from clan_cli.completions import add_dynamic_completer, complete_machines
-from clan_cli.dirs import specific_machine_dir
 from clan_cli.secrets.folders import sops_secrets_folder
 from clan_cli.secrets.machines import has_machine as secrets_has_machine
 from clan_cli.secrets.machines import remove_machine as secrets_machine_remove
@@ -23,7 +23,7 @@ log = logging.getLogger(__name__)
 @API.register
 def delete_machine(flake: Flake, name: str) -> None:
     try:
-        inventory.delete(str(flake.path), {f"machines.{name}"})
+        inventory.delete(flake, {f"machines.{name}"})
     except KeyError as exc:
         # louis@(2025-03-09): test infrastructure does not seem to set the
         # inventory properly, but more importantly only one machine in my
@@ -35,7 +35,7 @@ def delete_machine(flake: Flake, name: str) -> None:
 
     changed_paths: list[Path] = []
 
-    folder = specific_machine_dir(flake.path, name)
+    folder = specific_machine_dir(flake, name)
     if folder.exists():
         changed_paths.append(folder)
         shutil.rmtree(folder)
diff --git a/pkgs/clan-cli/clan_cli/machines/hardware.py b/pkgs/clan-cli/clan_cli/machines/hardware.py
index ac31f98d7..77b3b7d5a 100644
--- a/pkgs/clan-cli/clan_cli/machines/hardware.py
+++ b/pkgs/clan-cli/clan_cli/machines/hardware.py
@@ -7,9 +7,9 @@ from pathlib import Path
 
 from clan_lib.api import API
 
+from clan_cli.clan_dirs import specific_machine_dir
 from clan_cli.cmd import RunOpts, run_no_stdout
 from clan_cli.completions import add_dynamic_completer, complete_machines
-from clan_cli.dirs import specific_machine_dir
 from clan_cli.errors import ClanCmdError, ClanError
 from clan_cli.flake import Flake
 from clan_cli.git import commit_file
@@ -26,39 +26,39 @@ class HardwareConfig(Enum):
     NIXOS_GENERATE_CONFIG = "nixos-generate-config"
     NONE = "none"
 
-    def config_path(self, clan_dir: Path, machine_name: str) -> Path:
-        machine_dir = specific_machine_dir(clan_dir, machine_name)
+    def config_path(self, flake: Flake, machine_name: str) -> Path:
+        machine_dir = specific_machine_dir(flake, machine_name)
         if self == HardwareConfig.NIXOS_FACTER:
             return machine_dir / "facter.json"
         return machine_dir / "hardware-configuration.nix"
 
     @classmethod
     def detect_type(
-        cls: type["HardwareConfig"], clan_dir: Path, machine_name: str
+        cls: type["HardwareConfig"], flake: Flake, machine_name: str
     ) -> "HardwareConfig":
         hardware_config = HardwareConfig.NIXOS_GENERATE_CONFIG.config_path(
-            clan_dir, machine_name
+            flake, machine_name
         )
 
         if hardware_config.exists() and "throw" not in hardware_config.read_text():
             return HardwareConfig.NIXOS_GENERATE_CONFIG
 
-        if HardwareConfig.NIXOS_FACTER.config_path(clan_dir, machine_name).exists():
+        if HardwareConfig.NIXOS_FACTER.config_path(flake, machine_name).exists():
             return HardwareConfig.NIXOS_FACTER
 
         return HardwareConfig.NONE
 
 
 @API.register
-def show_machine_hardware_config(clan_dir: Path, machine_name: str) -> HardwareConfig:
+def show_machine_hardware_config(flake: Flake, machine_name: str) -> HardwareConfig:
     """
     Show hardware information for a machine returns None if none exist.
     """
-    return HardwareConfig.detect_type(clan_dir, machine_name)
+    return HardwareConfig.detect_type(flake, machine_name)
 
 
 @API.register
-def show_machine_hardware_platform(clan_dir: Path, machine_name: str) -> str | None:
+def show_machine_hardware_platform(flake: Flake, machine_name: str) -> str | None:
     """
     Show hardware information for a machine returns None if none exist.
     """
@@ -66,7 +66,7 @@ def show_machine_hardware_platform(clan_dir: Path, machine_name: str) -> str | N
     system = config["system"]
     cmd = nix_eval(
         [
-            f"{clan_dir}#clanInternals.machines.{system}.{machine_name}",
+            f"{flake}#clanInternals.machines.{system}.{machine_name}",
             "--apply",
             "machine: { inherit (machine.pkgs) system; }",
             "--json",
@@ -103,7 +103,7 @@ def generate_machine_hardware_info(opts: HardwareGenerateOptions) -> HardwareCon
         override_target_host=opts.target_host,
     )
 
-    hw_file = opts.backend.config_path(opts.flake.path, opts.machine)
+    hw_file = opts.backend.config_path(opts.flake, opts.machine)
     hw_file.parent.mkdir(parents=True, exist_ok=True)
 
     if opts.backend == HardwareConfig.NIXOS_FACTER:
@@ -152,7 +152,7 @@ def generate_machine_hardware_info(opts: HardwareGenerateOptions) -> HardwareCon
         f"machines/{opts.machine}/{hw_file.name}: update hardware configuration",
     )
     try:
-        show_machine_hardware_platform(opts.flake.path, opts.machine)
+        show_machine_hardware_platform(opts.flake, opts.machine)
         if backup_file:
             backup_file.unlink(missing_ok=True)
     except ClanCmdError as e:
diff --git a/pkgs/clan-cli/clan_cli/machines/install.py b/pkgs/clan-cli/clan_cli/machines/install.py
index 2c7b28ac1..707b8b06d 100644
--- a/pkgs/clan-cli/clan_cli/machines/install.py
+++ b/pkgs/clan-cli/clan_cli/machines/install.py
@@ -113,7 +113,7 @@ def install_machine(opts: InstallOptions) -> None:
                     str(opts.update_hardware_config.value),
                     str(
                         opts.update_hardware_config.config_path(
-                            machine.flake.path, machine.name
+                            machine.flake, machine.name
                         )
                     ),
                 ]
diff --git a/pkgs/clan-cli/clan_cli/machines/list.py b/pkgs/clan-cli/clan_cli/machines/list.py
index 263df33c1..81a30ce0e 100644
--- a/pkgs/clan-cli/clan_cli/machines/list.py
+++ b/pkgs/clan-cli/clan_cli/machines/list.py
@@ -12,16 +12,18 @@ from clan_lib.api.disk import MachineDiskMatter
 from clan_lib.api.modules import parse_frontmatter
 from clan_lib.api.serde import dataclass_to_dict
 
+from clan_cli.clan_dirs import specific_machine_dir
 from clan_cli.cmd import RunOpts, run
 from clan_cli.completions import add_dynamic_completer, complete_tags
-from clan_cli.dirs import specific_machine_dir
 from clan_cli.errors import ClanError
+from clan_cli.flake import Flake
 from clan_cli.inventory import (
     load_inventory_eval,
     patch_inventory_with,
 )
 from clan_cli.inventory.classes import Machine as InventoryMachine
 from clan_cli.machines.hardware import HardwareConfig
+from clan_cli.machines.machines import Machine
 from clan_cli.nix import nix_eval
 from clan_cli.tags import list_nixos_machines_by_tags
 
@@ -29,15 +31,13 @@ log = logging.getLogger(__name__)
 
 
 @API.register
-def set_machine(flake_url: Path, machine_name: str, machine: InventoryMachine) -> None:
-    patch_inventory_with(
-        flake_url, f"machines.{machine_name}", dataclass_to_dict(machine)
-    )
+def set_machine(flake: Flake, machine_name: str, machine: InventoryMachine) -> None:
+    patch_inventory_with(flake, f"machines.{machine_name}", dataclass_to_dict(machine))
 
 
 @API.register
-def list_machines(flake_url: str | Path) -> dict[str, InventoryMachine]:
-    inventory = load_inventory_eval(flake_url)
+def list_machines(flake: Flake) -> dict[str, InventoryMachine]:
+    inventory = load_inventory_eval(flake)
     return inventory.get("machines", {})
 
 
@@ -60,16 +60,16 @@ def extract_header(c: str) -> str:
 
 
 @API.register
-def get_machine_details(flake_url: Path, machine_name: str) -> MachineDetails:
-    inventory = load_inventory_eval(flake_url)
-    machine = inventory.get("machines", {}).get(machine_name)
-    if machine is None:
-        msg = f"Machine {machine_name} not found in inventory"
+def get_machine_details(machine: Machine) -> MachineDetails:
+    inventory = load_inventory_eval(machine.flake)
+    machine_inv = inventory.get("machines", {}).get(machine.name)
+    if machine_inv is None:
+        msg = f"Machine {machine.name} not found in inventory"
         raise ClanError(msg)
 
-    hw_config = HardwareConfig.detect_type(flake_url, machine_name)
+    hw_config = HardwareConfig.detect_type(machine.flake, machine.name)
 
-    machine_dir = specific_machine_dir(flake_url, machine_name)
+    machine_dir = specific_machine_dir(machine.flake, machine.name)
     disk_schema: MachineDiskMatter | None = None
     disk_path = machine_dir / "disko.nix"
     if disk_path.exists():
@@ -80,7 +80,9 @@ def get_machine_details(flake_url: Path, machine_name: str) -> MachineDetails:
             if data:
                 disk_schema = data  # type: ignore
 
-    return MachineDetails(machine=machine, hw_config=hw_config, disk_schema=disk_schema)
+    return MachineDetails(
+        machine=machine_inv, hw_config=hw_config, disk_schema=disk_schema
+    )
 
 
 def list_nixos_machines(flake_url: str | Path) -> list[str]:
diff --git a/pkgs/clan-cli/clan_cli/tests/test_dirs.py b/pkgs/clan-cli/clan_cli/tests/test_dirs.py
index ac2626834..e4528c59d 100644
--- a/pkgs/clan-cli/clan_cli/tests/test_dirs.py
+++ b/pkgs/clan-cli/clan_cli/tests/test_dirs.py
@@ -16,7 +16,7 @@
 #     (subdir / ".clan-flake").touch()
 #     assert _get_clan_flake_toplevel() == subdir
 
-from clan_cli.dirs import clan_key_safe, vm_state_dir
+from clan_cli.clan_dirs import clan_key_safe, vm_state_dir
 
 
 def test_clan_key_safe() -> None:
diff --git a/pkgs/clan-cli/clan_cli/tests/test_machines_cli.py b/pkgs/clan-cli/clan_cli/tests/test_machines_cli.py
index db708bce9..e8b2a0383 100644
--- a/pkgs/clan-cli/clan_cli/tests/test_machines_cli.py
+++ b/pkgs/clan-cli/clan_cli/tests/test_machines_cli.py
@@ -1,4 +1,5 @@
 import pytest
+from clan_cli.flake import Flake
 from clan_cli.inventory import load_inventory_json
 from clan_cli.secrets.folders import sops_machines_folder
 from clan_cli.tests import fixtures_flakes
@@ -24,7 +25,7 @@ def test_machine_subcommands(
         ]
     )
 
-    inventory: dict = dict(load_inventory_json(str(test_flake_with_core.path)))
+    inventory: dict = dict(load_inventory_json(Flake(str(test_flake_with_core.path))))
     assert "machine1" in inventory["machines"]
     assert "service" not in inventory
 
@@ -40,7 +41,7 @@ def test_machine_subcommands(
         ["machines", "delete", "--flake", str(test_flake_with_core.path), "machine1"]
     )
 
-    inventory_2: dict = dict(load_inventory_json(str(test_flake_with_core.path)))
+    inventory_2: dict = dict(load_inventory_json(Flake(str(test_flake_with_core.path))))
     assert "machine1" not in inventory_2["machines"]
     assert "service" not in inventory_2
 
diff --git a/pkgs/clan-cli/clan_cli/tests/test_modules.py b/pkgs/clan-cli/clan_cli/tests/test_modules.py
index bb1412f27..dff0751ab 100644
--- a/pkgs/clan-cli/clan_cli/tests/test_modules.py
+++ b/pkgs/clan-cli/clan_cli/tests/test_modules.py
@@ -88,7 +88,7 @@ def test_add_module_to_inventory(
             }
         }
 
-        set_inventory(inventory, base_path, "Add borgbackup service")
+        set_inventory(inventory, Flake(str(base_path)), "Add borgbackup service")
 
         # cmd = ["facts", "generate", "--flake", str(test_flake_with_core.path), "machine1"]
         cmd = [
diff --git a/pkgs/clan-cli/clan_cli/vars/public_modules/vm.py b/pkgs/clan-cli/clan_cli/vars/public_modules/vm.py
index 01eeecd73..0d1913338 100644
--- a/pkgs/clan-cli/clan_cli/vars/public_modules/vm.py
+++ b/pkgs/clan-cli/clan_cli/vars/public_modules/vm.py
@@ -3,7 +3,7 @@ import shutil
 from collections.abc import Iterable
 from pathlib import Path
 
-from clan_cli.dirs import vm_state_dir
+from clan_cli.clan_dirs import vm_state_dir
 from clan_cli.errors import ClanError
 from clan_cli.machines.machines import Machine
 from clan_cli.ssh.host import Host
diff --git a/pkgs/clan-cli/clan_cli/vars/secret_modules/vm.py b/pkgs/clan-cli/clan_cli/vars/secret_modules/vm.py
index 37818fcd5..138f2ab34 100644
--- a/pkgs/clan-cli/clan_cli/vars/secret_modules/vm.py
+++ b/pkgs/clan-cli/clan_cli/vars/secret_modules/vm.py
@@ -2,7 +2,7 @@ import shutil
 from collections.abc import Iterable
 from pathlib import Path
 
-from clan_cli.dirs import vm_state_dir
+from clan_cli.clan_dirs import vm_state_dir
 from clan_cli.machines.machines import Machine
 from clan_cli.ssh.host import Host
 from clan_cli.vars._types import StoreBase
diff --git a/pkgs/clan-cli/clan_cli/vms/run.py b/pkgs/clan-cli/clan_cli/vms/run.py
index a65886737..dc4ebf9de 100644
--- a/pkgs/clan-cli/clan_cli/vms/run.py
+++ b/pkgs/clan-cli/clan_cli/vms/run.py
@@ -12,9 +12,10 @@ from dataclasses import dataclass
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
+from clan_cli.clan_dirs import vm_state_dir
 from clan_cli.cmd import CmdOut, Log, RunOpts, handle_io, run
 from clan_cli.completions import add_dynamic_completer, complete_machines
-from clan_cli.dirs import module_root, user_cache_dir, vm_state_dir
+from clan_cli.dirs import module_root, user_cache_dir
 from clan_cli.errors import ClanCmdError, ClanError
 from clan_cli.facts.generate import generate_facts
 from clan_cli.machines.machines import Machine
diff --git a/pkgs/clan-cli/clan_lib/api/disk.py b/pkgs/clan-cli/clan_lib/api/disk.py
index a524a6b6b..2ff98ea9e 100644
--- a/pkgs/clan-cli/clan_lib/api/disk.py
+++ b/pkgs/clan-cli/clan_lib/api/disk.py
@@ -2,12 +2,12 @@ import json
 import logging
 from collections.abc import Callable
 from dataclasses import dataclass
-from pathlib import Path
 from typing import Any, TypedDict
 from uuid import uuid4
 
 from clan_cli.dirs import TemplateType, clan_templates
 from clan_cli.errors import ClanError
+from clan_cli.flake import Flake
 from clan_cli.git import commit_file
 from clan_cli.machines.hardware import HardwareConfig, show_machine_hardware_config
 
@@ -75,7 +75,7 @@ templates: dict[str, dict[str, Callable[[dict[str, Any]], Placeholder]]] = {
 
 @API.register
 def get_disk_schemas(
-    base_path: Path, machine_name: str | None = None
+    flake: Flake, machine_name: str | None = None
 ) -> dict[str, DiskSchema]:
     """
     Get the available disk schemas
@@ -85,9 +85,7 @@ def get_disk_schemas(
     hw_report = {}
 
     if machine_name is not None:
-        hw_report_path = HardwareConfig.NIXOS_FACTER.config_path(
-            base_path, machine_name
-        )
+        hw_report_path = HardwareConfig.NIXOS_FACTER.config_path(flake, machine_name)
         if not hw_report_path.exists():
             msg = "Hardware configuration missing"
             raise ClanError(msg)
@@ -132,7 +130,7 @@ class MachineDiskMatter(TypedDict):
 
 @API.register
 def set_machine_disk_schema(
-    base_path: Path,
+    flake: Flake,
     machine_name: str,
     schema_name: str,
     # Placeholders are used to fill in the disk schema
@@ -144,8 +142,8 @@ 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(base_path, machine_name)
-    hw_config_path = hw_config.config_path(base_path, machine_name)
+    hw_config = show_machine_hardware_config(flake, machine_name)
+    hw_config_path = hw_config.config_path(flake, machine_name)
 
     if not hw_config_path.exists():
         msg = "Hardware configuration must exist before applying disk schema"
@@ -162,7 +160,7 @@ def set_machine_disk_schema(
         raise ClanError(msg)
 
     # Check that the placeholders are valid
-    disk_schema = get_disk_schemas(base_path, machine_name)[schema_name]
+    disk_schema = get_disk_schemas(flake, machine_name)[schema_name]
     # check that all required placeholders are present
     for placeholder_name, schema_placeholder in disk_schema.placeholders.items():
         if schema_placeholder.required and placeholder_name not in placeholders:
@@ -223,6 +221,6 @@ def set_machine_disk_schema(
 
         commit_file(
             disko_file_path,
-            base_path,
+            flake.path,
             commit_message=f"Set disk schema of machine: {machine_name} to {schema_name}",
         )
diff --git a/pkgs/clan-cli/clan_lib/tests/test_create.py b/pkgs/clan-cli/clan_lib/tests/test_create.py
index 05f6522a7..dbee211bf 100644
--- a/pkgs/clan-cli/clan_lib/tests/test_create.py
+++ b/pkgs/clan-cli/clan_lib/tests/test_create.py
@@ -8,8 +8,8 @@ from typing import Any
 
 import clan_cli.clan.create
 import pytest
+from clan_cli.clan_dirs import specific_machine_dir
 from clan_cli.cmd import RunOpts, run
-from clan_cli.dirs import specific_machine_dir
 from clan_cli.errors import ClanError
 from clan_cli.flake import Flake
 from clan_cli.inventory import patch_inventory_with
@@ -209,7 +209,7 @@ def test_clan_create_api(
 
     # ===== CREATE BASE INVENTORY ======
     inventory = create_base_inventory(ssh_keys)
-    patch_inventory_with(dest_clan_dir, "services", inventory.services)
+    patch_inventory_with(Flake(str(dest_clan_dir)), "services", inventory.services)
 
     # Invalidate cache because of new inventory
     clan_dir_flake.invalidate_cache()
@@ -240,7 +240,7 @@ def test_clan_create_api(
     facter_json = test_lib_root / "assets" / "facter.json"
     assert facter_json.exists(), f"Source facter file not found: {facter_json}"
 
-    dest_dir = specific_machine_dir(clan_dir_flake.path, machine.name)
+    dest_dir = specific_machine_dir(Flake(str(clan_dir_flake.path)), machine.name)
     # specific_machine_dir should create the directory, but ensure it exists just in case
     dest_dir.mkdir(parents=True, exist_ok=True)
 
@@ -254,7 +254,8 @@ def test_clan_create_api(
 
     # ===== Create Disko Config ======
     facter_path = (
-        specific_machine_dir(clan_dir_flake.path, machine.name) / "facter.json"
+        specific_machine_dir(Flake(str(clan_dir_flake.path)), machine.name)
+        / "facter.json"
     )
     with facter_path.open("r") as f:
         facter_report = json.load(f)
@@ -264,9 +265,7 @@ def test_clan_create_api(
     assert disk_devs is not None
 
     placeholders = {"mainDisk": disk_devs[0]}
-    set_machine_disk_schema(
-        clan_dir_flake.path, machine.name, "single-disk", placeholders
-    )
+    set_machine_disk_schema(clan_dir_flake, machine.name, "single-disk", placeholders)
     clan_dir_flake.invalidate_cache()
 
     with pytest.raises(ClanError) as exc_info:
diff --git a/pkgs/clan-vm-manager/clan_vm_manager/components/vmobj.py b/pkgs/clan-vm-manager/clan_vm_manager/components/vmobj.py
index bceba2fed..3568fb74f 100644
--- a/pkgs/clan-vm-manager/clan_vm_manager/components/vmobj.py
+++ b/pkgs/clan-vm-manager/clan_vm_manager/components/vmobj.py
@@ -13,7 +13,7 @@ from typing import IO, ClassVar
 
 import gi
 from clan_cli import vms
-from clan_cli.dirs import vm_state_dir
+from clan_cli.clan_dirs import vm_state_dir
 from clan_cli.machines.machines import Machine
 from clan_cli.vms.inspect import inspect_vm
 from clan_cli.vms.qemu import QMPWrapper
diff --git a/pkgs/webview-ui/app/src/api/inventory.ts b/pkgs/webview-ui/app/src/api/inventory.ts
index ade59652d..b77f47c89 100644
--- a/pkgs/webview-ui/app/src/api/inventory.ts
+++ b/pkgs/webview-ui/app/src/api/inventory.ts
@@ -13,9 +13,9 @@ export async function get_inventory(client: QueryClient, base_path: string) {
     queryKey: [base_path, "inventory"],
     queryFn: () => {
       console.log("Refreshing inventory");
-      return callApi("get_inventory", { base_path }) as Promise<
-        ApiEnvelope<Inventory>
-      >;
+      return callApi("get_inventory", {
+        flake: { identifier: base_path },
+      }) as Promise<ApiEnvelope<Inventory>>;
     },
     revalidateIfStale: true,
     staleTime: 60 * 1000,
diff --git a/pkgs/webview-ui/app/src/api/wifi.ts b/pkgs/webview-ui/app/src/api/wifi.ts
index 6cb284554..0de237e8d 100644
--- a/pkgs/webview-ui/app/src/api/wifi.ts
+++ b/pkgs/webview-ui/app/src/api/wifi.ts
@@ -6,7 +6,7 @@ export const instance_name = (machine_name: string) =>
 
 export async function get_iwd_service(base_path: string, machine_name: string) {
   const r = await callApi("get_inventory", {
-    base_path,
+    flake: { identifier: base_path },
   });
   if (r.status == "error") {
     return null;
diff --git a/pkgs/webview-ui/app/src/queries/index.ts b/pkgs/webview-ui/app/src/queries/index.ts
index e7f0e8909..4baa550aa 100644
--- a/pkgs/webview-ui/app/src/queries/index.ts
+++ b/pkgs/webview-ui/app/src/queries/index.ts
@@ -43,7 +43,7 @@ export const tagsQuery = (uri: string | null) =>
       if (!uri) return [];
 
       const response = await callApi("get_inventory", {
-        base_path: uri,
+        flake: { identifier: uri },
       });
       if (response.status === "error") {
         toast.error("Failed to fetch data");
@@ -64,7 +64,7 @@ export const machinesQuery = (uri: string | null) =>
       if (!uri) return [];
 
       const response = await callApi("get_inventory", {
-        base_path: uri,
+        flake: { identifier: uri },
       });
       if (response.status === "error") {
         toast.error("Failed to fetch data");
diff --git a/pkgs/webview-ui/app/src/routes/clans/details.tsx b/pkgs/webview-ui/app/src/routes/clans/details.tsx
index 7696e4872..7f0b4945e 100644
--- a/pkgs/webview-ui/app/src/routes/clans/details.tsx
+++ b/pkgs/webview-ui/app/src/routes/clans/details.tsx
@@ -42,7 +42,7 @@ const EditClanForm = (props: EditClanFormProps) => {
       (async () => {
         await callApi("update_clan_meta", {
           options: {
-            directory: props.directory,
+            flake: { identifier: props.directory },
             meta: values,
           },
         });
diff --git a/pkgs/webview-ui/app/src/routes/disk/view.tsx b/pkgs/webview-ui/app/src/routes/disk/view.tsx
index 02eaf143b..5f90d0b9e 100644
--- a/pkgs/webview-ui/app/src/routes/disk/view.tsx
+++ b/pkgs/webview-ui/app/src/routes/disk/view.tsx
@@ -10,7 +10,9 @@ export function DiskView() {
       const currUri = activeURI();
       if (currUri) {
         // Example of calling an API
-        const result = await callApi("get_inventory", { base_path: currUri });
+        const result = await callApi("get_inventory", {
+          flake: { identifier: currUri },
+        });
         if (result.status === "error") throw new Error("Failed to fetch data");
         return result.data;
       }
diff --git a/pkgs/webview-ui/app/src/routes/machines/details.tsx b/pkgs/webview-ui/app/src/routes/machines/details.tsx
index c5742fd1e..b059a8c4f 100644
--- a/pkgs/webview-ui/app/src/routes/machines/details.tsx
+++ b/pkgs/webview-ui/app/src/routes/machines/details.tsx
@@ -115,7 +115,7 @@ const InstallMachine = (props: InstallMachineProps) => {
     if (shouldRunDisk) {
       setProgressText("Setting up disk ... (1/5)");
       const disk_response = await callApi("set_machine_disk_schema", {
-        base_path: curr_uri,
+        flake: { identifier: curr_uri },
         machine_name: props.name,
         placeholders: diskValues.placeholders,
         schema_name: diskValues.schema,
@@ -425,7 +425,9 @@ const MachineForm = (props: MachineDetailsProps) => {
     }
 
     const machine_response = await callApi("set_machine", {
-      flake_url: curr_uri,
+      flake: {
+        identifier: curr_uri,
+      },
       machine_name: props.initialData.machine.name || "My machine",
       machine: {
         ...values.machine,
@@ -646,8 +648,12 @@ export const MachineDetails = () => {
       const curr = activeURI();
       if (curr) {
         const result = await callApi("get_machine_details", {
-          flake_url: curr,
-          machine_name: params.id,
+          machine: {
+            flake: {
+              identifier: curr,
+            },
+            name: params.id,
+          },
         });
         if (result.status === "error") throw new Error("Failed to fetch data");
         return result.data;
diff --git a/pkgs/webview-ui/app/src/routes/machines/install/disk-step.tsx b/pkgs/webview-ui/app/src/routes/machines/install/disk-step.tsx
index 29b07c959..a12570506 100644
--- a/pkgs/webview-ui/app/src/routes/machines/install/disk-step.tsx
+++ b/pkgs/webview-ui/app/src/routes/machines/install/disk-step.tsx
@@ -37,7 +37,9 @@ export const DiskStep = (props: StepProps<DiskValues>) => {
     queryKey: [props.dir, props.machine_id, "disk_schemas"],
     queryFn: async () => {
       const result = await callApi("get_disk_schemas", {
-        base_path: props.dir,
+        flake: {
+          identifier: props.dir,
+        },
         machine_name: props.machine_id,
       });
       if (result.status === "error") throw new Error("Failed to fetch data");
diff --git a/pkgs/webview-ui/app/src/routes/machines/install/hardware-step.tsx b/pkgs/webview-ui/app/src/routes/machines/install/hardware-step.tsx
index c413ff899..daf6be0af 100644
--- a/pkgs/webview-ui/app/src/routes/machines/install/hardware-step.tsx
+++ b/pkgs/webview-ui/app/src/routes/machines/install/hardware-step.tsx
@@ -52,7 +52,9 @@ export const HWStep = (props: StepProps<HardwareValues>) => {
     queryKey: [props.dir, props.machine_id, "hw_report"],
     queryFn: async () => {
       const result = await callApi("show_machine_hardware_config", {
-        clan_dir: props.dir,
+        flake: {
+          identifier: props.dir,
+        },
         machine_name: props.machine_id,
       });
       if (result.status === "error") throw new Error("Failed to fetch data");
diff --git a/pkgs/webview-ui/app/src/routes/machines/list.tsx b/pkgs/webview-ui/app/src/routes/machines/list.tsx
index 35b90ac71..903954fd0 100644
--- a/pkgs/webview-ui/app/src/routes/machines/list.tsx
+++ b/pkgs/webview-ui/app/src/routes/machines/list.tsx
@@ -39,7 +39,9 @@ export const MachineListView: Component = () => {
       const uri = activeURI();
       if (uri) {
         const response = await callApi("list_machines", {
-          flake_url: uri,
+          flake: {
+            identifier: uri,
+          },
         });
         if (response.status === "error") {
           toast.error("Failed to fetch data");