diff --git a/flux_local/git_repo.py b/flux_local/git_repo.py
index 4cf3de5c..5815552c 100644
--- a/flux_local/git_repo.py
+++ b/flux_local/git_repo.py
@@ -32,7 +32,6 @@
 import contextlib
 from dataclasses import dataclass, field
 import logging
-import networkx
 import os
 import tempfile
 from collections.abc import Callable, Awaitable, Iterable
@@ -47,7 +46,7 @@
 from .exceptions import FluxException
 from .manifest import (
     CRD_KIND,
-    CLUSTER_KUSTOMIZE_DOMAIN,
+    FLUXTOMIZE_DOMAIN,
     KUSTOMIZE_DOMAIN,
     Cluster,
     ClusterPolicy,
@@ -76,7 +75,10 @@
 GIT_REPO_KIND = "GitRepository"
 OCI_REPO_KIND = "OCIRepository"
 DEFAULT_NAMESPACE = "flux-system"
-ROOT_KUSTOMIZATION_NAME = "flux-system"
+DEFAULT_NAME = "flux-system"
+GREP_SOURCE_REF_KIND = f"spec.sourceRef.kind={GIT_REPO_KIND}|{OCI_REPO_KIND}"
+ERROR_DETAIL_BAD_PATH = "Try specifying another path within the git repo?"
+ERROR_DETAIL_BAD_KS = "Is a Kustomization pointing to a path that does not exist?"
 
 
 @dataclass
@@ -161,7 +163,7 @@ def func(doc: dict[str, Any]) -> bool:
     return func
 
 
-CLUSTER_KUSTOMIZE_DOMAIN_FILTER = domain_filter(CLUSTER_KUSTOMIZE_DOMAIN)
+FLUXTOMIZE_DOMAIN_FILTER = domain_filter(FLUXTOMIZE_DOMAIN)
 KUSTOMIZE_DOMAIN_FILTER = domain_filter(KUSTOMIZE_DOMAIN)
 
 
@@ -271,7 +273,7 @@ def predicate(
 
 def cluster_metadata_selector() -> MetadataSelector:
     """Create a new MetadataSelector for Kustomizations."""
-    return MetadataSelector(namespace=DEFAULT_NAMESPACE)
+    return MetadataSelector(name=DEFAULT_NAME, namespace=DEFAULT_NAMESPACE)
 
 
 def ks_metadata_selector() -> MetadataSelector:
@@ -314,8 +316,8 @@ class ResourceSelector:
     """ClusterPolicy objects to return."""
 
 
-async def get_flux_kustomizations(
-    root: Path, relative_path: Path
+async def get_fluxtomizations(
+    root: Path, relative_path: Path, build: bool
 ) -> list[Kustomization]:
     """Find all flux Kustomizations in the specified path.
 
@@ -323,13 +325,22 @@ async def get_flux_kustomizations(
     Kustomizations from the repo. Assumes that any flux Kustomization
     for a GitRepository is pointed at this cluster, following normal conventions.
     """
-    cmd = kustomize.grep(f"kind={CLUSTER_KUSTOMIZE_KIND}", root / relative_path).grep(
-        f"spec.sourceRef.kind={GIT_REPO_KIND}|{OCI_REPO_KIND}"
-    )
+    cmd: kustomize.Kustomize
+    if build:
+        _LOGGER.debug("kustomize.build")
+        cmd = (
+            kustomize.build(root / relative_path)
+            .grep(f"kind={CLUSTER_KUSTOMIZE_KIND}")
+            .grep(GREP_SOURCE_REF_KIND)
+        )
+    else:
+        _LOGGER.debug("kustomize.grep")
+        cmd = kustomize.grep(
+            f"kind={CLUSTER_KUSTOMIZE_KIND}", root / relative_path
+        ).grep(GREP_SOURCE_REF_KIND)
     docs = await cmd.objects()
     return [
-        Kustomization.parse_doc(doc)
-        for doc in filter(CLUSTER_KUSTOMIZE_DOMAIN_FILTER, docs)
+        Kustomization.parse_doc(doc) for doc in filter(FLUXTOMIZE_DOMAIN_FILTER, docs)
     ]
 
 
@@ -353,46 +364,27 @@ def find_path_parent(search: Path, prefixes: set[Path]) -> Path | None:
     return None
 
 
-async def kustomization_traversal(path_selector: PathSelector) -> list[Kustomization]:
+async def kustomization_traversal(
+    root_path_selector: PathSelector, path_selector: PathSelector, build: bool
+) -> list[Kustomization]:
     """Search for kustomizations in the specified path."""
 
     kustomizations: list[Kustomization] = []
     visited: set[Path] = set()  # Relative paths within the cluster
+    nodes: set[str] = set()
 
     path_queue: queue.Queue[Path] = queue.Queue()
     path_queue.put(path_selector.relative_path)
-    root = path_selector.root
     while not path_queue.empty():
         path = path_queue.get()
-        _LOGGER.debug("Visiting path (%s) %s", root, path)
+        _LOGGER.debug("Visiting path (%s) %s", root_path_selector.path, path)
         try:
-            docs = await get_flux_kustomizations(root, path)
+            docs = await get_fluxtomizations(root_path_selector.root, path, build=build)
         except FluxException as err:
-            if visited:
-                raise FluxException(
-                    f"Error building Fluxtomization in '{root}' path '{path}': {err}"
-                    f"Is a Kustomization pointing to a path that does not exist?"
-                )
+            detail = ERROR_DETAIL_BAD_KS if visited else ERROR_DETAIL_BAD_PATH
             raise FluxException(
-                f"Error building Fluxtomization in '{root}' path '{path}': {err}"
-                f"Try specifying another path within the git repo?"
-            )
-
-        # Source path is relative to the search path. Update to have the
-        # full prefix relative to the root.
-        for kustomization in docs:
-            if not kustomization.path:
-                _LOGGER.debug("Assigning implicit path %s", path_selector.relative_path)
-                kustomization.path = str(path_selector.relative_path)
-            if not kustomization.source_path:
-                continue
-            kustomization.source_path = str(
-                ((root / path) / kustomization.source_path).relative_to(root)
-            )
-            _LOGGER.debug(
-                "Updated relative path: %s => %s",
-                node_name(kustomization),
-                kustomization.source_path,
+                f"Error building Fluxtomization in '{root_path_selector.root}' "
+                f"path '{path}': {err} - {detail}"
             )
 
         visited |= set({path})
@@ -400,6 +392,20 @@ async def kustomization_traversal(path_selector: PathSelector) -> list[Kustomiza
         _LOGGER.debug("Found %s Kustomizations", len(docs))
         result_docs = []
         for doc in docs:
+            if doc.namespaced_name in nodes:
+                _LOGGER.debug(
+                    "Ignoring duplicate Kustomization %s", doc.namespaced_name
+                )
+                continue
+            nodes.add(doc.namespaced_name)
+            # Source path is relative to the search path. Update to have the
+            # full prefix relative to the root.
+            if not doc.path:
+                _LOGGER.debug(
+                    "Assigning implicit path %s", root_path_selector.relative_path
+                )
+                doc.path = str(root_path_selector.relative_path)
+
             found_path: Path | None = None
             _LOGGER.debug(
                 "Kustomization '%s' has sourceRef.kind '%s' of '%s'",
@@ -428,7 +434,7 @@ async def kustomization_traversal(path_selector: PathSelector) -> list[Kustomiza
                 _LOGGER.debug("Skipping kustomization %s; not known source", doc.name)
                 continue
 
-            if not find_path_parent(found_path, visited) and found_path not in visited:
+            if found_path not in visited:
                 path_queue.put(found_path)
             else:
                 _LOGGER.debug("Already visited %s", found_path)
@@ -446,125 +452,54 @@ def node_name(ks: Kustomization) -> str:
     return f"{ks.namespaced_name} @ {ks.id_name}"
 
 
-def make_clusters(
-    kustomizations: list[Kustomization], sources: list[Source] | None = None
-) -> list[Cluster]:
-    """Convert the flat list of Kustomizations into a Cluster.
-
-    This will reverse engineer which Kustomizations are root nodes for the cluster
-    based on the parent paths. Root Kustomizations are made the cluster and everything
-    else is made a child.
-    """
-    if not sources:
-        sources = []
-
-    # Build a directed graph from a kustomization path to the path
-    # of the kustomization that created it.
-    graph = networkx.DiGraph()
-    node_path_map = {Path(ks.path): ks for ks in kustomizations if ks.source_path}
-    for ks in kustomizations:
-        if not ks.source_path:
-            raise InputException(
-                "Kustomization did not have source path; Old kustomize?"
-            )
-
-        graph.add_node(node_name(ks), ks=ks)
-        if ks.name == ROOT_KUSTOMIZATION_NAME and ks.namespace == DEFAULT_NAMESPACE:
-            # Do not attempt parent search below
-            continue
-
-        # Find the parent Kustomization that produced this based on the
-        # matching the kustomize source parent paths with a Kustomization
-        # target path.
-        source = Path(ks.source_path)
-        _LOGGER.debug("--- Examining candidate Kustomization ---")
-        _LOGGER.debug("Ks         : %s", ks.namespaced_name)
-        _LOGGER.debug("Path       : %s", Path(ks.path))
-        _LOGGER.debug("Source path: %s", source)
-        source_kustomizations = find_source_kustomization(source, node_path_map)
-        _LOGGER.debug(
-            "Possible sources: %s", [f"{node_name(ks)}" for ks in source_kustomizations]
-        )
-        if source_kustomizations:
-            while source_kustomizations:
-                candidate = source_kustomizations.pop(0)
-                # These names can be compared since they are within the scope of
-                # the source path so within the same cluster.
-                if candidate.namespaced_name != ks.namespaced_name:
-                    _LOGGER.debug(
-                        "Found parent %s => %s",
-                        ks.namespaced_name,
-                        candidate.namespaced_name,
-                    )
-                    if graph.has_edge(node_name(ks), node_name(candidate)):
-                        _LOGGER.debug("Already has opposite edge; Skipping cycle")
-                    else:
-                        graph.add_edge(node_name(candidate), node_name(ks))
-                else:
-                    _LOGGER.debug(
-                        "Skipping candidate source %s", candidate.namespaced_name
-                    )
-        else:
-            _LOGGER.debug("No parent for %s (source=%s)", node_name(ks), source)
-
-    # Clusters are subgraphs within the graph that are connected, with the root
-    # node being the cluster itself. All children Kustomizations are flattended.
-    _LOGGER.debug("Creating clusters based on connectivity")
-    for node, degree in graph.in_degree():
-        _LOGGER.debug("Node: %s, degree: %s", node, degree)
-    roots = [node for node, degree in graph.in_degree() if degree == 0]
-    roots.sort()
-
-    clusters: list[Cluster] = []
-    _LOGGER.debug("roots=%s", roots)
-    for root in roots:
-        root_ks = graph.nodes[root]["ks"]
-        nodes = [root] + list(networkx.descendants(graph, root))
-        nodes.sort()
-        kustomizations = [graph.nodes[node]["ks"] for node in nodes]
-        clusters.append(
-            Cluster(
-                name=root_ks.name,
-                namespace=root_ks.namespace,
-                path=root_ks.path,
-                kustomizations=kustomizations,
-            )
-        )
-        _LOGGER.debug(
-            "Created cluster %s with %s kustomizations", root_ks.name, len(nodes)
-        )
-
-    return clusters
-
-
 async def get_clusters(
     path_selector: PathSelector,
     cluster_selector: MetadataSelector,
     kustomization_selector: MetadataSelector,
 ) -> list[Cluster]:
     """Load Cluster objects from the specified path."""
-
-    kustomizations = await kustomization_traversal(path_selector)
-    clusters = list(
-        filter(
-            cluster_selector.predicate,
-            make_clusters(kustomizations, path_selector.sources or []),
+    try:
+        roots = await get_fluxtomizations(
+            path_selector.root, path_selector.relative_path, build=False
         )
-    )
+    except FluxException as err:
+        raise FluxException(
+            f"Error building Fluxtomization in '{path_selector.root}' path "
+            f"'{path_selector.relative_path}': {err}"
+            f"Try specifying another path within the git repo?"
+        )
+    _LOGGER.debug("roots=%s", roots)
+    clusters = [
+        Cluster(name=ks.name, namespace=ks.namespace or "", path=ks.path)
+        for ks in roots
+        if cluster_selector.predicate(ks)
+    ]
+    build = True
+    if not clusters:
+        # There are no flux-system Kustomizations within this path. Fall back to
+        # assuming everything in the current directory is part of a cluster.
+        _LOGGER.debug(
+            "No clusters found; Processing as a Kustomization: %s",
+            path_selector.relative_path,
+        )
+        clusters = [
+            Cluster(name="cluster", namespace="", path=str(path_selector.relative_path))
+        ]
+        build = False
+
     for cluster in clusters:
-        cluster.kustomizations = list(
-            filter(kustomization_selector.predicate, cluster.kustomizations)
+        _LOGGER.debug("Building cluster %s %s", cluster.name, cluster.path)
+        results = await kustomization_traversal(
+            path_selector,
+            PathSelector(path=Path(cluster.path), sources=path_selector.sources),
+            build=build,
         )
+        results.sort(key=lambda x: (x.namespace, x.name))
+        cluster.kustomizations = results
+    clusters.sort(key=lambda x: (x.path, x.namespace, x.name))
     return clusters
 
 
-async def get_kustomizations(path: Path) -> list[dict[str, Any]]:
-    """Load Kustomization objects from the specified path."""
-    cmd = kustomize.grep(f"kind={KUSTOMIZE_KIND}", path)
-    docs = await cmd.objects()
-    return list(filter(KUSTOMIZE_DOMAIN_FILTER, docs))
-
-
 async def build_kustomization(
     kustomization: Kustomization,
     cluster_path: Path,
@@ -669,21 +604,6 @@ async def build_manifest(
     clusters = await get_clusters(
         selector.path, selector.cluster, selector.kustomization
     )
-    if not clusters and selector.path.path:
-        _LOGGER.debug("No clusters found; Processing as a Kustomization: %s", selector)
-        # The argument path may be a Kustomization inside a cluster. Create a synthetic
-        # cluster with any found Kustomizations
-        cluster = Cluster(
-            name="cluster", namespace="", path=str(selector.path.relative_path)
-        )
-        objects = await get_kustomizations(selector.path.path)
-        if objects:
-            cluster.kustomizations = [
-                Kustomization(
-                    name="kustomization", path=str(selector.path.relative_path)
-                )
-            ]
-            clusters.append(cluster)
 
     async def update_kustomization(cluster: Cluster) -> None:
         build_tasks = []
diff --git a/flux_local/manifest.py b/flux_local/manifest.py
index 00f282fb..68378db9 100644
--- a/flux_local/manifest.py
+++ b/flux_local/manifest.py
@@ -28,7 +28,7 @@
 
 # Match a prefix of apiVersion to ensure we have the right type of object.
 # We don't check specific versions for forward compatibility on upgrade.
-CLUSTER_KUSTOMIZE_DOMAIN = "kustomize.toolkit.fluxcd.io"
+FLUXTOMIZE_DOMAIN = "kustomize.toolkit.fluxcd.io"
 KUSTOMIZE_DOMAIN = "kustomize.config.k8s.io"
 HELM_REPO_DOMAIN = "source.toolkit.fluxcd.io"
 HELM_RELEASE_DOMAIN = "helm.toolkit.fluxcd.io"
@@ -283,7 +283,7 @@ class Kustomization(BaseManifest):
     @classmethod
     def parse_doc(cls, doc: dict[str, Any]) -> "Kustomization":
         """Parse a partial Kustomization from a kubernetes resource."""
-        _check_version(doc, CLUSTER_KUSTOMIZE_DOMAIN)
+        _check_version(doc, FLUXTOMIZE_DOMAIN)
         if not (metadata := doc.get("metadata")):
             raise InputException(f"Invalid {cls} missing metadata: {doc}")
         if not (name := metadata.get("name")):
@@ -349,7 +349,7 @@ class Cluster(BaseManifest):
     @classmethod
     def parse_doc(cls, doc: dict[str, Any]) -> "Cluster":
         """Parse a partial Kustomization from a kubernetes resource."""
-        _check_version(doc, CLUSTER_KUSTOMIZE_DOMAIN)
+        _check_version(doc, FLUXTOMIZE_DOMAIN)
         if not (metadata := doc.get("metadata")):
             raise InputException(f"Invalid {cls} missing metadata: {doc}")
         if not (name := metadata.get("name")):
@@ -362,6 +362,11 @@ def parse_doc(cls, doc: dict[str, Any]) -> "Cluster":
             raise InputException(f"Invalid {cls} missing spec.path: {doc}")
         return Cluster(name=name, namespace=namespace, path=path)
 
+    @property
+    def namespaced_name(self, sep: str = "/") -> str:
+        """Return the namespace and name concatenated as an id."""
+        return f"{self.namespace}{sep}{self.name}"
+
     @property
     def id_name(self) -> str:
         """Identifier for the Cluster in tests."""
diff --git a/tests/test_git_repo.py b/tests/test_git_repo.py
index 7b72c5d2..575231ad 100644
--- a/tests/test_git_repo.py
+++ b/tests/test_git_repo.py
@@ -13,7 +13,6 @@
     kustomization_traversal,
     Source,
     PathSelector,
-    make_clusters,
 )
 from flux_local.kustomize import Kustomize
 from flux_local.manifest import Kustomization
@@ -327,10 +326,12 @@ async def fetch(root: Path, p: Path) -> list[Kustomization]:
         return results.pop(0)
 
     with patch("flux_local.git_repo.PathSelector.root", Path("/home/example")), patch(
-        "flux_local.git_repo.get_flux_kustomizations", fetch
+        "flux_local.git_repo.get_fluxtomizations", fetch
     ):
         kustomizations = await kustomization_traversal(
-            path_selector=PathSelector(path=Path(path))
+            root_path_selector=PathSelector(path=Path(path)),
+            path_selector=PathSelector(path=Path(path)),
+            build=True,
         )
     assert len(kustomizations) == 4
     assert paths == [
@@ -338,18 +339,6 @@ async def fetch(root: Path, p: Path) -> list[Kustomization]:
         ("/home/example", "kubernetes/apps"),
     ]
 
-    clusters = make_clusters(kustomizations)
-    assert len(clusters) == 1
-    cluster = clusters[0]
-    assert cluster.name == "cluster"
-    assert cluster.namespace == "flux-system"
-    assert [ks.path for ks in cluster.kustomizations] == [
-        "./kubernetes/flux",
-        "./kubernetes/apps",
-        "./kubernetes/apps/rook-ceph/rook-ceph/app",
-        "./kubernetes/apps/volsync/volsync/app",
-    ]
-
 
 async def test_kustomization_traversal_multi_cluster() -> None:
     """Test discovery of multiple clusters in the repo."""
@@ -404,10 +393,12 @@ async def fetch(root: Path, p: Path) -> list[Kustomization]:
         return results.pop(0)
 
     with patch("flux_local.git_repo.PathSelector.root", Path("/home/example")), patch(
-        "flux_local.git_repo.get_flux_kustomizations", fetch
+        "flux_local.git_repo.get_fluxtomizations", fetch
     ):
         kustomizations = await kustomization_traversal(
-            path_selector=PathSelector(path=Path("."))
+            root_path_selector=PathSelector(path=Path(".")),
+            path_selector=PathSelector(path=Path(".")),
+            build=True,
         )
     assert len(kustomizations) == 6
     # We don't need to visit the clusters subdirectories because the original
@@ -416,27 +407,6 @@ async def fetch(root: Path, p: Path) -> list[Kustomization]:
         ("/home/example", "."),
     ]
 
-    clusters = make_clusters(kustomizations)
-    assert len(clusters) == 2
-    cluster = clusters[0]
-    assert cluster.name == "cluster"
-    assert cluster.namespace == "flux-system"
-    assert cluster.path == "./clusters/dev"
-    assert [ks.path for ks in cluster.kustomizations] == [
-        "./certmanager/dev",
-        "./clusters/dev",
-        "./crds",
-    ]
-    cluster = clusters[1]
-    assert cluster.name == "cluster"
-    assert cluster.namespace == "flux-system"
-    assert cluster.path == "./clusters/prod"
-    assert [ks.path for ks in cluster.kustomizations] == [
-        "./certmanager/prod",
-        "./clusters/prod",
-        "./crds",
-    ]
-
 
 def test_source() -> None:
     """Test parsing a source from a string."""
diff --git a/tests/testdata/cluster3/clusters/cluster3/flux-system/gotk-sync.yaml b/tests/testdata/cluster3/clusters/cluster3/flux-system/gotk-sync.yaml
index f2d413e3..df553784 100644
--- a/tests/testdata/cluster3/clusters/cluster3/flux-system/gotk-sync.yaml
+++ b/tests/testdata/cluster3/clusters/cluster3/flux-system/gotk-sync.yaml
@@ -20,7 +20,7 @@ metadata:
   namespace: flux-system
 spec:
   interval: 10m0s
-  path: ./tests/testdata/cluster3/
+  path: ./tests/testdata/cluster3/clusters/cluster3
   prune: true
   sourceRef:
     kind: GitRepository
diff --git a/tests/testdata/cluster5/kustomization.yaml b/tests/testdata/cluster5/kustomization.yaml
index 6bb7dc20..e8e9cef7 100644
--- a/tests/testdata/cluster5/kustomization.yaml
+++ b/tests/testdata/cluster5/kustomization.yaml
@@ -4,3 +4,4 @@ kind: Kustomization
 resources:
   - metallb-release.yaml
   - weave-gitops-release.yaml
+  - repositories.yaml
diff --git a/tests/testdata/cluster5/repositories.yaml b/tests/testdata/cluster5/repositories.yaml
new file mode 100644
index 00000000..820cfd60
--- /dev/null
+++ b/tests/testdata/cluster5/repositories.yaml
@@ -0,0 +1,19 @@
+---
+apiVersion: source.toolkit.fluxcd.io/v1beta2
+kind: HelmRepository
+metadata:
+  name: bitnami
+  namespace: flux-system
+spec:
+  type: oci
+  interval: 30m
+  url: oci://registry-1.docker.io/bitnamicharts
+---
+apiVersion: source.toolkit.fluxcd.io/v1beta2
+kind: HelmRepository
+metadata:
+  name: weave-charts
+  namespace: flux-system
+spec:
+  interval: 1h
+  url: https://helm.gitops.weave.works
diff --git a/tests/testdata/cluster6/renovate/kustomization.yaml b/tests/testdata/cluster6/apps/renovate/kustomization.yaml
similarity index 100%
rename from tests/testdata/cluster6/renovate/kustomization.yaml
rename to tests/testdata/cluster6/apps/renovate/kustomization.yaml
diff --git a/tests/testdata/cluster6/renovate/release.yaml b/tests/testdata/cluster6/apps/renovate/release.yaml
similarity index 100%
rename from tests/testdata/cluster6/renovate/release.yaml
rename to tests/testdata/cluster6/apps/renovate/release.yaml
diff --git a/tests/testdata/cluster6/renovate/repository.yaml b/tests/testdata/cluster6/apps/renovate/repository.yaml
similarity index 100%
rename from tests/testdata/cluster6/renovate/repository.yaml
rename to tests/testdata/cluster6/apps/renovate/repository.yaml
diff --git a/tests/testdata/cluster6/cluster/apps.yaml b/tests/testdata/cluster6/cluster/apps.yaml
new file mode 100644
index 00000000..c83e511e
--- /dev/null
+++ b/tests/testdata/cluster6/cluster/apps.yaml
@@ -0,0 +1,11 @@
+---
+apiVersion: kustomize.toolkit.fluxcd.io/v1
+kind: Kustomization
+metadata:
+  name: apps
+  namespace: flux-system
+spec:
+  path: ./tests/testdata/cluster6/apps/
+  sourceRef:
+    kind: GitRepository
+    name: flux-system
diff --git a/tests/testdata/cluster6/cluster/flux-system/gotk-sync.yaml b/tests/testdata/cluster6/cluster/flux-system/gotk-sync.yaml
new file mode 100644
index 00000000..9704d5e7
--- /dev/null
+++ b/tests/testdata/cluster6/cluster/flux-system/gotk-sync.yaml
@@ -0,0 +1,26 @@
+---
+apiVersion: source.toolkit.fluxcd.io/v1beta1
+kind: GitRepository
+metadata:
+  name: flux-system
+  namespace: flux-system
+spec:
+  interval: 1m0s
+  ref:
+    branch: main
+  secretRef:
+    name: flux-system
+  url: ssh://git@github.com/allenporter/flux-local
+---
+apiVersion: kustomize.toolkit.fluxcd.io/v1beta2
+kind: Kustomization
+metadata:
+  name: flux-system
+  namespace: flux-system
+spec:
+  interval: 10m0s
+  path: ./tests/testdata/cluster6/cluster
+  prune: true
+  sourceRef:
+    kind: GitRepository
+    name: flux-system
diff --git a/tests/testdata/cluster6/cluster/flux-system/kustomization.yaml b/tests/testdata/cluster6/cluster/flux-system/kustomization.yaml
new file mode 100644
index 00000000..197efd8a
--- /dev/null
+++ b/tests/testdata/cluster6/cluster/flux-system/kustomization.yaml
@@ -0,0 +1,5 @@
+---
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - gotk-sync.yaml
diff --git a/tests/tool/testdata/build6.yaml b/tests/tool/testdata/build6.yaml
index fc4adf8b..32164b3a 100644
--- a/tests/tool/testdata/build6.yaml
+++ b/tests/tool/testdata/build6.yaml
@@ -57,4 +57,51 @@ stdout: |+
     interval: 30m
     url: https://docs.renovatebot.com/helm-charts
 
+  ---
+  apiVersion: kustomize.toolkit.fluxcd.io/v1
+  kind: Kustomization
+  metadata:
+    name: apps
+    namespace: flux-system
+    annotations:
+      config.kubernetes.io/index: '0'
+      internal.config.kubernetes.io/index: '0'
+  spec:
+    path: ./tests/testdata/cluster6/apps/
+    sourceRef:
+      kind: GitRepository
+      name: flux-system
+  ---
+  apiVersion: kustomize.toolkit.fluxcd.io/v1beta2
+  kind: Kustomization
+  metadata:
+    name: flux-system
+    namespace: flux-system
+    annotations:
+      config.kubernetes.io/index: '1'
+      internal.config.kubernetes.io/index: '1'
+  spec:
+    interval: 10m0s
+    path: ./tests/testdata/cluster6/cluster
+    prune: true
+    sourceRef:
+      kind: GitRepository
+      name: flux-system
+  ---
+  apiVersion: source.toolkit.fluxcd.io/v1beta1
+  kind: GitRepository
+  metadata:
+    name: flux-system
+    namespace: flux-system
+    annotations:
+      config.kubernetes.io/index: '2'
+      internal.config.kubernetes.io/index: '2'
+  spec:
+    interval: 1m0s
+    ref:
+      branch: main
+    secretRef:
+      name: flux-system
+    url: ssh://git@github.com/allenporter/flux-local
+
 ...
diff --git a/tests/tool/testdata/get_cluster2.yaml b/tests/tool/testdata/get_cluster2.yaml
index 722ed74b..eb4c1e39 100644
--- a/tests/tool/testdata/get_cluster2.yaml
+++ b/tests/tool/testdata/get_cluster2.yaml
@@ -4,5 +4,5 @@ args:
 - --path
 - tests/testdata/cluster2/
 stdout: |
-  NAME       PATH                              KUSTOMIZATIONS    
-  cluster    ./tests/testdata/cluster2/flux    5                 
+  NAME       PATH                       KUSTOMIZATIONS    
+  cluster    tests/testdata/cluster2    5                 
diff --git a/tests/tool/testdata/get_cluster3.yaml b/tests/tool/testdata/get_cluster3.yaml
index eea06a25..25187b88 100644
--- a/tests/tool/testdata/get_cluster3.yaml
+++ b/tests/tool/testdata/get_cluster3.yaml
@@ -6,5 +6,5 @@ args:
 - --sources
 - cluster=tests/testdata/cluster3
 stdout: |
-  NAME           PATH                          KUSTOMIZATIONS    
-  flux-system    ./tests/testdata/cluster3/    3                 
+  NAME           PATH                                           KUSTOMIZATIONS    
+  flux-system    ./tests/testdata/cluster3/clusters/cluster3    2                 
diff --git a/tests/tool/testdata/get_cluster4.yaml b/tests/tool/testdata/get_cluster4.yaml
index fb292d13..43984827 100644
--- a/tests/tool/testdata/get_cluster4.yaml
+++ b/tests/tool/testdata/get_cluster4.yaml
@@ -4,5 +4,5 @@ args:
 - --path
 - tests/testdata/cluster4/
 stdout: |
-  NAME       PATH                              KUSTOMIZATIONS    
-  cluster    ./tests/testdata/cluster4/flux    3                 
+  NAME       PATH                       KUSTOMIZATIONS    
+  cluster    tests/testdata/cluster4    3                 
diff --git a/tests/tool/testdata/get_cluster6.yaml b/tests/tool/testdata/get_cluster6.yaml
index 1f848216..291742d8 100644
--- a/tests/tool/testdata/get_cluster6.yaml
+++ b/tests/tool/testdata/get_cluster6.yaml
@@ -4,5 +4,5 @@ args:
 - --path
 - tests/testdata/cluster6/
 stdout: |
-  NAME       PATH                       KUSTOMIZATIONS    
-  cluster    tests/testdata/cluster6    1                 
+  NAME           PATH                                 KUSTOMIZATIONS    
+  flux-system    ./tests/testdata/cluster6/cluster    2                 
diff --git a/tests/tool/testdata/get_hr2.yaml b/tests/tool/testdata/get_hr2.yaml
new file mode 100644
index 00000000..1ddbec24
--- /dev/null
+++ b/tests/tool/testdata/get_hr2.yaml
@@ -0,0 +1,10 @@
+args:
+- get
+- hr
+- -A
+- --path
+- tests/testdata/cluster2
+stdout: |
+  NAMESPACE     NAME                    REVISION    CHART                              SOURCE                  
+  networking    ingress-nginx           4.5.2       networking-ingress-nginx           ingress-nginx           
+  monitoring    kubernetes-dashboard    6.0.0       monitoring-kubernetes-dashboard    kubernetes-dashboard    
diff --git a/tests/tool/testdata/get_hr3.yaml b/tests/tool/testdata/get_hr3.yaml
new file mode 100644
index 00000000..d6c17b8f
--- /dev/null
+++ b/tests/tool/testdata/get_hr3.yaml
@@ -0,0 +1,8 @@
+args:
+- get
+- hr
+- -A
+- --path
+- tests/testdata/cluster3
+stdout: |
+  no HelmRelease objects found in cluster
diff --git a/tests/tool/testdata/get_hr4.yaml b/tests/tool/testdata/get_hr4.yaml
new file mode 100644
index 00000000..118d92c1
--- /dev/null
+++ b/tests/tool/testdata/get_hr4.yaml
@@ -0,0 +1,9 @@
+args:
+- get
+- hr
+- -A
+- --path
+- tests/testdata/cluster4
+stdout: |
+  NAMESPACE     NAME                    REVISION    CHART                              SOURCE                  
+  monitoring    kubernetes-dashboard    6.0.0       monitoring-kubernetes-dashboard    kubernetes-dashboard    
diff --git a/tests/tool/testdata/get_hr5.yaml b/tests/tool/testdata/get_hr5.yaml
new file mode 100644
index 00000000..0faed139
--- /dev/null
+++ b/tests/tool/testdata/get_hr5.yaml
@@ -0,0 +1,10 @@
+args:
+- get
+- hr
+- -A
+- --path
+- tests/testdata/cluster5
+stdout: |
+  NAMESPACE      NAME            REVISION    CHART                       SOURCE          
+  flux-system    weave-gitops    4.0.22      flux-system-weave-gitops    weave-charts    
+  metallb        metallb         4.1.14      metallb-metallb             bitnami         
diff --git a/tests/tool/testdata/get_ks3.yaml b/tests/tool/testdata/get_ks3.yaml
new file mode 100644
index 00000000..64ed465a
--- /dev/null
+++ b/tests/tool/testdata/get_ks3.yaml
@@ -0,0 +1,12 @@
+args:
+- get
+- ks
+- -A
+- --path
+- tests/testdata/cluster3
+- --sources
+- cluster=tests/testdata/cluster3
+stdout: |
+  NAMESPACE      NAME          PATH                                                    
+  flux-system    namespaces    tests/testdata/cluster3/namespaces/overlays/cluster3    
+  flux-system    tenants       tests/testdata/cluster3/tenants/overlays/cluster3       
diff --git a/tests/tool/testdata/get_ks4.yaml b/tests/tool/testdata/get_ks4.yaml
new file mode 100644
index 00000000..21aeeda2
--- /dev/null
+++ b/tests/tool/testdata/get_ks4.yaml
@@ -0,0 +1,10 @@
+args:
+- get
+- ks
+- --path
+- tests/testdata/cluster4
+stdout: |
+  NAME                                 PATH                                                              
+  cluster                              ./tests/testdata/cluster4/flux                                    
+  cluster-apps                         ./tests/testdata/cluster4/apps                                    
+  cluster-apps-kubernetes-dashboard    ./tests/testdata/cluster4/apps/monitoring/kubernetes-dashboard    
diff --git a/tests/tool/testdata/get_ks5.yaml b/tests/tool/testdata/get_ks5.yaml
index 60cf634a..6f0c00ac 100644
--- a/tests/tool/testdata/get_ks5.yaml
+++ b/tests/tool/testdata/get_ks5.yaml
@@ -4,5 +4,6 @@ args:
 - --path
 - tests/testdata/cluster5
 stdout: |
-  NAME           PATH                                       
-  flux-system    ./tests/testdata/cluster5/clusters/prod    
+  NAME                 PATH                                       
+  infra-controllers    tests/testdata/cluster5                    
+  flux-system          ./tests/testdata/cluster5/clusters/prod    
diff --git a/tests/tool/testdata/get_ks6.yaml b/tests/tool/testdata/get_ks6.yaml
index 79d4491b..1e07ca40 100644
--- a/tests/tool/testdata/get_ks6.yaml
+++ b/tests/tool/testdata/get_ks6.yaml
@@ -4,5 +4,6 @@ args:
 - --path
 - tests/testdata/cluster6
 stdout: |
-  NAME             PATH                       
-  kustomization    tests/testdata/cluster6    
+  NAME           PATH                                 
+  apps           ./tests/testdata/cluster6/apps/      
+  flux-system    ./tests/testdata/cluster6/cluster    
diff --git a/tests/tool/testdata/get_ks_path_ks.yaml b/tests/tool/testdata/get_ks_path_ks.yaml
index 051393a5..7b0eb956 100644
--- a/tests/tool/testdata/get_ks_path_ks.yaml
+++ b/tests/tool/testdata/get_ks_path_ks.yaml
@@ -5,5 +5,4 @@ args:
 - --path
 - ./tests/testdata/cluster/apps/prod
 stdout: |
-  NAMESPACE    NAME             PATH                                
-  None         kustomization    tests/testdata/cluster/apps/prod    
+  no Kustomization objects found in cluster