fix: respect directory parameter in machines_dir

The machines_dir() function was hardcoding "machines" without considering
the directory parameter from buildClan/clan configuration. This caused
update-hardware-config and other commands to write files to the wrong
location when a custom directory was specified (e.g., directory = ./clan).

Solution:
1. Added relativeDirectory to inventoryClass in Nix, computed where both
   self and directory have consistent store paths during evaluation
2. Updated machines_dir() to use this pre-computed relative path from Nix
   via flake.select("clanInternals.inventoryClass.relativeDirectory")

Fixes: https://git.clan.lol/clan/clan-core/issues/2906

modules/clan/module.nix

@@ -222,6 +222,18 @@ in
       inventoryClass =
         let
           flakeInputs = config.self.inputs;
+          # Compute the relative directory path
+          selfStr = toString config.self;
+          dirStr = toString directory;
+          relativeDirectory =
+            if selfStr == dirStr then
+              ""
+            else if lib.hasPrefix selfStr dirStr then
+              lib.removePrefix (selfStr + "/") dirStr
+            else
+              # This shouldn't happen in normal usage, but can occur when
+              # the flake is copied (e.g., in tests). Fall back to empty string.
+              "";
         in
         {
           _module.args = {
@@ -230,7 +242,12 @@ in
           imports = [
             ../inventoryClass/default.nix
             {
-              inherit inventory directory flakeInputs;
+              inherit
+                inventory
+                directory
+                flakeInputs
+                relativeDirectory
+                ;
               exportsModule = config.exportsModule;
             }
             (

modules/inventoryClass/default.nix

@@ -81,6 +81,14 @@ in
     directory = mkOption {
       type = types.path;
     };
+    relativeDirectory = mkOption {
+      type = types.str;
+      internal = true;
+      description = ''
+        The relative directory path from the flake root to the clan directory.
+        Empty string if directory equals the flake root.
+      '';
+    };
     machines = mkOption {
       type = types.attrsOf (submodule ({
         options = {

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

@@ -156,14 +156,28 @@ def vm_state_dir(flake_url: str, vm_name: str) -> Path:
 
 
 def machines_dir(flake: "Flake") -> Path:
+    # Determine the base path
     if flake.is_local:
-        return flake.path / "machines"
+        base_path = flake.path
+    else:
+        store_path = flake.store_path
+        if store_path is None:
+            msg = "Invalid flake object. Doesn't have a store path"
+            raise ClanError(msg)
+        base_path = Path(store_path)
 
-    store_path = flake.store_path
+    # Get the clan directory configuration from Nix
-    if store_path is None:
+    # This is computed in Nix where store paths are consistent
-        msg = "Invalid flake object. Doesn't have a store path"
+    # Returns "" if no custom directory is set
-        raise ClanError(msg)
+    # Fall back to "" if the option doesn't exist (backwards compatibility)
-    return Path(store_path) / "machines"
+    try:
+        clan_dir = flake.select("clanInternals.inventoryClass.relativeDirectory")
+    except ClanError:
+        # Option doesn't exist in older clan-core versions
+        # Assume no custom directory
+        clan_dir = ""
+
+    return base_path / clan_dir / "machines"
 
 
 def specific_machine_dir(machine: "MachineSpecProtocol") -> Path: