diff --git a/.github/workflows/update-expected-output.yml b/.github/workflows/update-expected-output.yml
index b3b2672..71bef16 100644
--- a/.github/workflows/update-expected-output.yml
+++ b/.github/workflows/update-expected-output.yml
@@ -2,9 +2,10 @@ name: Update expected output
 
 on:
   pull_request:
-    # Don't update PRs on every push. PRs can be closed and
-    # reopened if the update action should be run again.
-    types: [opened, reopened]
+    # Don't update PRs on every push. PRs can be switched
+    # to draft status and back (or closed and reopened),
+    # if the update action should be run again.
+    types: [opened, reopened, ready_for_review]
     branches:
       - "**"
     paths:
diff --git a/changelog.d/20241108_162952_ncoghlan_fix_automatic_layer_versioning.rst b/changelog.d/20241108_162952_ncoghlan_fix_automatic_layer_versioning.rst
new file mode 100644
index 0000000..55d7fbf
--- /dev/null
+++ b/changelog.d/20241108_162952_ncoghlan_fix_automatic_layer_versioning.rst
@@ -0,0 +1,9 @@
+Added
+-----
+
+- Setting ``versioned = True`` in a layer definition will append a
+  lock version number to the layer name that automatically increments
+  each time the locked requirements change for that layer (``layer@1``,
+  ``layer@2``, etc). Layer dependency declarations and build environments,
+  use the unversioned name, but deployed environments and their metadata
+  will use the versioned name (implemented in :issue:`24`).
diff --git a/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst b/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst
index 8fa92f4..dca1c1e 100644
--- a/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst
+++ b/docs/api/stacks/venvstacks.stacks.ApplicationEnv.rst
@@ -15,7 +15,7 @@ venvstacks.stacks.ApplicationEnv
       ~ApplicationEnv.export_environment
       ~ApplicationEnv.get_constraint_paths
       ~ApplicationEnv.install_requirements
-      ~ApplicationEnv.link_base_runtime_paths
+      ~ApplicationEnv.link_base_runtime
       ~ApplicationEnv.link_layered_environments
       ~ApplicationEnv.lock_requirements
       ~ApplicationEnv.report_python_site_details
@@ -26,6 +26,7 @@ venvstacks.stacks.ApplicationEnv
 
    .. autosummary::
 
+      ~FrameworkEnv.base_runtime
       ~ApplicationEnv.category
       ~ApplicationEnv.env_name
       ~ApplicationEnv.env_spec
@@ -33,9 +34,7 @@ venvstacks.stacks.ApplicationEnv
       ~ApplicationEnv.kind
       ~ApplicationEnv.launch_module_name
       ~ApplicationEnv.linked_constraints_paths
-      ~ApplicationEnv.linked_dynlib_paths
       ~ApplicationEnv.linked_frameworks
-      ~ApplicationEnv.linked_pylib_paths
       ~ApplicationEnv.want_build
       ~ApplicationEnv.want_lock
       ~ApplicationEnv.want_publish
diff --git a/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst b/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst
index 14e21ee..d0aa889 100644
--- a/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst
+++ b/docs/api/stacks/venvstacks.stacks.FrameworkEnv.rst
@@ -16,7 +16,7 @@ venvstacks.stacks.FrameworkEnv
       ~FrameworkEnv.export_environment
       ~FrameworkEnv.get_constraint_paths
       ~FrameworkEnv.install_requirements
-      ~FrameworkEnv.link_base_runtime_paths
+      ~FrameworkEnv.link_base_runtime
       ~FrameworkEnv.lock_requirements
       ~FrameworkEnv.report_python_site_details
       ~FrameworkEnv.request_export
@@ -26,6 +26,7 @@ venvstacks.stacks.FrameworkEnv
 
    .. autosummary::
 
+      ~FrameworkEnv.base_runtime
       ~FrameworkEnv.category
       ~FrameworkEnv.env_name
       ~FrameworkEnv.env_spec
diff --git a/src/venvstacks/stacks.py b/src/venvstacks/stacks.py
index 8c02313..82a68fe 100755
--- a/src/venvstacks/stacks.py
+++ b/src/venvstacks/stacks.py
@@ -27,6 +27,7 @@
     Any,
     ClassVar,
     Iterable,
+    Iterator,
     Literal,
     Mapping,
     MutableMapping,
@@ -955,6 +956,9 @@ def get_build_platform() -> TargetPlatform:
 
 @dataclass
 class _PythonEnvironment(ABC):
+    # Python environment used to run tools like `uv` and `pip`
+    tools_python_path: ClassVar[Path] = Path(sys.executable)
+
     # Specified in concrete subclasses
     kind: ClassVar[LayerVariants]
     category: ClassVar[LayerCategories]
@@ -973,11 +977,12 @@ class _PythonEnvironment(ABC):
     python_path: Path = field(init=False, repr=False)
     env_lock: EnvironmentLock = field(init=False)
 
-    # Set in subclass or externally after creation
-    base_python_path: Path | None = field(init=False, repr=False)
-    tools_python_path: Path | None = field(init=False, repr=False)
+    # Derived from layer spec in subclass __post_init__
     py_version: str = field(init=False, repr=False)
 
+    # Set in subclass __post_init__, or when build environments are created
+    base_python_path: Path | None = field(init=False, repr=False)
+
     # Operation flags allow for requested commands to be applied only to selected layers
     # Notes:
     #   - the "build if needed" (want_build=None) option is fairly ineffective, since
@@ -1010,7 +1015,16 @@ def env_name(self) -> EnvNameBuild:
     def install_target(self) -> EnvNameDeploy:
         return self.env_lock.get_deployed_name(self.env_spec.env_name)
 
+    def get_deployed_path(self, build_path: Path) -> str:
+        """Get relative deployment location for a build env path"""
+        env_deployed_path = Path(self.install_target)
+        relative_path = build_path.relative_to(self.env_path)
+        return str(env_deployed_path / relative_path)
+
     def __post_init__(self) -> None:
+        # Concrete subclasses must set the version before finishing the base initialisation
+        # Assert its existence here to make failures to do so easier to diagnose
+        assert self.py_version is not None, "Subclass failed to set 'py_version'"
         self.env_path = self.build_path / self.env_name
         self.pylib_path = self._get_py_scheme_path("purelib")
         self.executables_path = self._get_py_scheme_path("scripts")
@@ -1041,8 +1055,8 @@ def get_deployed_config(self) -> postinstall.LayerConfig:
 
     def _get_deployed_config(
         self,
-        pylib_paths: Iterable[Path],
-        dynlib_paths: Iterable[Path],
+        pylib_dirs: Iterable[str],
+        dynlib_dirs: Iterable[str],
         link_external_base: bool = True,
     ) -> postinstall.LayerConfig:
         # Helper for subclass get_deployed_config implementations
@@ -1053,18 +1067,13 @@ def _get_deployed_config(
         build_env_name = build_env_path.name
         build_path = build_env_path.parent
 
-        def from_internal_path(target_build_path: Path) -> str:
-            # Input path is an absolute path inside the environment
-            # Output path is relative to the base of the environment
-            return str(target_build_path.relative_to(build_env_path))
-
-        def from_relative_path(relative_build_path: Path) -> str:
+        def relative_to_env(relative_build_path: Path) -> str:
             # Input path is relative to the base of the build directory
             # Output path is relative to the base of the environment
             # Note: we avoid `walk_up=True` here, firstly to maintain
             #       Python 3.11 compatibility, but also to limit the
             #       the relative paths to *peer* environments, rather
-            #       than all potentially value relative path calculations
+            #       than all potentially valid relative path calculations
             if relative_build_path.is_absolute():
                 self._fail_build(f"{relative_build_path} is not a relative path")
             if relative_build_path.parts[0] == build_env_name:
@@ -1073,19 +1082,23 @@ def from_relative_path(relative_build_path: Path) -> str:
             # Emit relative reference to peer environment
             return str(Path("..", *relative_build_path.parts))
 
+        def from_internal_path(target_build_path: Path) -> str:
+            # Input path is an absolute path inside the environment
+            # Output path is relative to the base of the environment
+            return str(target_build_path.relative_to(build_env_path))
+
         def from_external_path(target_build_path: Path) -> str:
             # Input path is an absolute path, potentially from a peer environment
             # Output path is relative to the base of the environment
             relative_build_path = target_build_path.relative_to(build_path)
-            return from_relative_path(relative_build_path)
+            return relative_to_env(relative_build_path)
 
         layer_python = from_internal_path(self.python_path)
         if link_external_base:
             base_python = from_external_path(base_python_path)
         else:
-            # "base_python" in the runtime layer refers solely to
-            # the external environment used to set up the base
-            # runtime layer, rather than being a linked environment
+            # "base_python" in a runtime layer refers to the layer itself
+            assert layer_python == from_internal_path(base_python_path)
             base_python = layer_python
 
         return postinstall.LayerConfig(
@@ -1093,8 +1106,8 @@ def from_external_path(target_build_path: Path) -> str:
             py_version=self.py_version,
             base_python=base_python,
             site_dir=from_internal_path(self.pylib_path),
-            pylib_dirs=[from_relative_path(p) for p in pylib_paths],
-            dynlib_dirs=[from_relative_path(p) for p in dynlib_paths],
+            pylib_dirs=[relative_to_env(Path(d)) for d in pylib_dirs],
+            dynlib_dirs=[relative_to_env(Path(d)) for d in dynlib_dirs],
         )
 
     def _write_deployed_config(self) -> None:
@@ -1401,7 +1414,10 @@ def export_environment(
 
         # Define the input metadata that gets published in the export manifest
         export_request = self.request_export(output_path, previous_metadata, force)
-        return export_request.export_environment(env_path, previous_metadata)
+        return export_request.export_environment(
+            env_path,
+            previous_metadata,
+        )
 
 
 class RuntimeEnv(_PythonEnvironment):
@@ -1417,20 +1433,11 @@ def _get_python_dir_path(self) -> Path:
         return super()._get_python_dir_path()
 
     def __post_init__(self) -> None:
-        self.py_version = py_version = self.env_spec.py_version
+        # Ensure Python version is set before finishing base class initialisation
+        self.py_version = self.env_spec.py_version
         super().__post_init__()
-        tools_env_path = self.build_path / "build-tools"
-        if tools_env_path.exists():
-            tools_bin_path = Path(
-                _get_py_scheme_path("scripts", tools_env_path, py_version)
-            )
-            tools_python_path = tools_bin_path / _binary_with_extension("python")
-        else:
-            # No build tools environment created by wrapper script, so use the running Python
-            tools_python_path = Path(sys.executable)
-        # Runtimes have no base Python other than the build tools Python
-        self.base_python_path = tools_python_path
-        self.tools_python_path = tools_python_path
+        # Runtimes are their own base Python
+        self.base_python_path = self.python_path
 
     @property
     def env_spec(self) -> RuntimeSpec:
@@ -1481,16 +1488,16 @@ def create_build_environment(self, *, clean: bool = False) -> None:
 
 
 class _VirtualEnvironment(_PythonEnvironment):
+    base_runtime: RuntimeEnv | None = field(init=False, repr=False)
     linked_constraints_paths: list[Path] = field(init=False, repr=False)
-    linked_pylib_paths: list[Path] = field(init=False, repr=False)
-    linked_dynlib_paths: list[Path] = field(init=False, repr=False)
 
     def __post_init__(self) -> None:
+        # Ensure Python version is set before finishing base class initialisation
         self.py_version = self.env_spec.runtime.py_version
         super().__post_init__()
+        # Base runtime env will be linked when creating the build environments
+        self.base_runtime = None
         self.linked_constraints_paths = []
-        self.linked_pylib_paths = []
-        self.linked_dynlib_paths = []
 
     @property
     def env_spec(self) -> _VirtualEnvironmentSpec:
@@ -1498,18 +1505,51 @@ def env_spec(self) -> _VirtualEnvironmentSpec:
         assert isinstance(self._env_spec, _VirtualEnvironmentSpec)
         return self._env_spec
 
-    def link_base_runtime_paths(self, runtime: RuntimeEnv) -> None:
+    def _linked_environments(self) -> Iterator[_PythonEnvironment]:
+        runtime_env = self.base_runtime
+        # This is only ever invoked *after* the environment has been linked
+        assert runtime_env is not None
+        yield runtime_env
+
+    def _iter_build_pylib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            yield str(env.pylib_path.relative_to(self.build_path))
+
+    def _iter_build_dynlib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            dynlib_path = env.dynlib_path
+            if dynlib_path is not None:
+                yield str(dynlib_path.relative_to(self.build_path))
+
+    def _iter_deployed_pylib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            yield env.get_deployed_path(env.pylib_path)
+
+    def _iter_deployed_dynlib_dirs(self) -> Iterator[str]:
+        for env in self._linked_environments():
+            dynlib_path = env.dynlib_path
+            if dynlib_path is not None:
+                yield env.get_deployed_path(dynlib_path)
+
+    def link_base_runtime(self, runtime: RuntimeEnv) -> None:
+        if self.base_runtime is not None:
+            raise BuildEnvError(
+                f"Layered environment base runtime already linked {self}"
+            )
+        # Link the runtime environment
+        self.base_runtime = runtime
         # Link executable paths
         self.base_python_path = runtime.python_path
-        self.tools_python_path = runtime.tools_python_path
+        # Link runtime layer dependency constraints
         if self.linked_constraints_paths:
             self._fail_build("Layered environment base runtime already linked")
         self.linked_constraints_paths[:] = [runtime.requirements_path]
+        print(f"Linked {self}")
 
     def get_deployed_config(self) -> postinstall.LayerConfig:
         """Layer config to be published in `venvstacks_layer.json`"""
         return self._get_deployed_config(
-            self.linked_pylib_paths, self.linked_dynlib_paths
+            self._iter_deployed_pylib_dirs(), self._iter_deployed_dynlib_dirs()
         )
 
     def get_constraint_paths(self) -> list[Path]:
@@ -1544,8 +1584,8 @@ def _ensure_virtual_environment(self) -> subprocess.CompletedProcess[str]:
     def _link_build_environment(self) -> None:
         # Create sitecustomize file for the build environment
         build_path = self.build_path
-        build_pylib_paths = [build_path / p for p in self.linked_pylib_paths]
-        build_dynlib_paths = [build_path / p for p in self.linked_dynlib_paths]
+        build_pylib_paths = [build_path / d for d in self._iter_build_pylib_dirs()]
+        build_dynlib_paths = [build_path / d for d in self._iter_build_dynlib_dirs()]
         sc_contents = postinstall.generate_sitecustomize(
             build_pylib_paths, build_dynlib_paths
         )
@@ -1591,21 +1631,6 @@ def env_spec(self) -> FrameworkSpec:
         assert isinstance(self._env_spec, FrameworkSpec)
         return self._env_spec
 
-    def link_base_runtime_paths(self, runtime: RuntimeEnv) -> None:
-        super().link_base_runtime_paths(runtime)
-        # TODO: Reduce code duplication with ApplicationEnv
-        runtime_target_path = Path(runtime.install_target)
-
-        def _runtime_path(build_path: Path) -> Path:
-            relative_path = build_path.relative_to(runtime.env_path)
-            return runtime_target_path / relative_path
-
-        pylib_paths = self.linked_pylib_paths
-        dynlib_paths = self.linked_dynlib_paths
-        pylib_paths.append(_runtime_path(runtime.pylib_path))
-        if runtime.dynlib_path is not None:
-            dynlib_paths.append(_runtime_path(runtime.dynlib_path))
-
 
 class ApplicationEnv(_VirtualEnvironment):
     """Application layer build environment"""
@@ -1627,42 +1652,28 @@ def __post_init__(self) -> None:
         self.launch_module_name = self.env_spec.launch_module_path.stem
         self.linked_frameworks = []
 
+    def _linked_environments(self) -> Iterator[_PythonEnvironment]:
+        # Linked frameworks are emitted before the base runtime layer
+        for fw_env in self.linked_frameworks:
+            yield fw_env
+        yield from super()._linked_environments()
+
     def link_layered_environments(
         self, runtime: RuntimeEnv, frameworks: Mapping[LayerBaseName, FrameworkEnv]
     ) -> None:
-        self.link_base_runtime_paths(runtime)
+        self.link_base_runtime(runtime)
         constraints_paths = self.linked_constraints_paths
         if not constraints_paths:
             self._fail_build("Failed to add base environment constraints path")
         # The runtime site-packages folder is added here rather than via pyvenv.cfg
         # to ensure it appears in sys.path after the framework site-packages folders
-        pylib_paths = self.linked_pylib_paths
-        dynlib_paths = self.linked_dynlib_paths
         fw_envs = self.linked_frameworks
-        if pylib_paths or dynlib_paths or fw_envs:
+        if fw_envs:
             self._fail_build("Layered application environment already linked")
         for env_spec in self.env_spec.frameworks:
             env = frameworks[env_spec.name]
             fw_envs.append(env)
             constraints_paths.append(env.requirements_path)
-            install_target_path = Path(env.install_target)
-
-            def _fw_env_path(build_path: Path) -> Path:
-                relative_path = build_path.relative_to(env.env_path)
-                return install_target_path / relative_path
-
-            pylib_paths.append(_fw_env_path(env.pylib_path))
-            if env.dynlib_path is not None:
-                dynlib_paths.append(_fw_env_path(env.pylib_path))
-        runtime_target_path = Path(runtime.install_target)
-
-        def _runtime_path(build_path: Path) -> Path:
-            relative_path = build_path.relative_to(runtime.env_path)
-            return runtime_target_path / relative_path
-
-        pylib_paths.append(_runtime_path(runtime.pylib_path))
-        if runtime.dynlib_path is not None:
-            dynlib_paths.append(_runtime_path(runtime.dynlib_path))
 
     def _update_existing_environment(self, *, lock_only: bool = False) -> None:
         super()._update_existing_environment(lock_only=lock_only)
@@ -1850,7 +1861,7 @@ def define_build_environment(
         )
         for fw_env in frameworks.values():
             runtime = runtimes[fw_env.env_spec.runtime.name]
-            fw_env.link_base_runtime_paths(runtime)
+            fw_env.link_base_runtime(runtime)
         print("Defining application environments:")
         applications = self._define_envs(
             build_path, index_config, ApplicationEnv, self.applications
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
index 8a70e77..351ad8f 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "bb594ea66705fe5a122e930e2c48f1aaf6f720d568e37e0b590db95fb7261dea"
+    "sha256": "d932e554c35c9ce2cd1d594cb20e8a37c0195a5b82ffcb50627a96fc122e79a2"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 3004,
+  "archive_size": 3008,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:43.205589+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
index 64b962f..91213b7 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "8d69cfe0f408ba396dde664cd58c18b4541e6937f470e6e4f06a03d6ec069e46"
+    "sha256": "ec5be5ebc608e24bf32642cf0e071ce975f4650dac69c233c36124e53f4c10f9"
   },
-  "archive_name": "app-scipy-import.tar.xz",
+  "archive_name": "app-scipy-import@1.tar.xz",
   "archive_size": 2912,
-  "install_target": "app-scipy-import",
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:43.173589+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
   "runtime_name": "cpython@3.11",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
index ae73caf..91978f2 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "e8ef68225cfa6a016539a4db3c5dc1b984f53de0df51181eefeb0e9449771ea9"
+    "sha256": "622e3056ccf54d8723bf983c92f35bf4138d2fee5da3cdd56d25391f18906aab"
   },
-  "archive_name": "framework-scipy.tar.xz",
-  "archive_size": 23957800,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.tar.xz",
+  "archive_size": 23961760,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:42.825586+00:00",
diff --git a/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json b/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
index c9818e3..973d2e5 100644
--- a/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/linux_x86_64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "8d69cfe0f408ba396dde664cd58c18b4541e6937f470e6e4f06a03d6ec069e46"
+          "sha256": "ec5be5ebc608e24bf32642cf0e071ce975f4650dac69c233c36124e53f4c10f9"
         },
-        "archive_name": "app-scipy-import.tar.xz",
+        "archive_name": "app-scipy-import@1.tar.xz",
         "archive_size": 2912,
-        "install_target": "app-scipy-import",
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:43.173589+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
         "runtime_name": "cpython@3.11",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "bb594ea66705fe5a122e930e2c48f1aaf6f720d568e37e0b590db95fb7261dea"
+          "sha256": "d932e554c35c9ce2cd1d594cb20e8a37c0195a5b82ffcb50627a96fc122e79a2"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 3004,
+        "archive_size": 3008,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:43.205589+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
@@ -67,11 +67,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "e8ef68225cfa6a016539a4db3c5dc1b984f53de0df51181eefeb0e9449771ea9"
+          "sha256": "622e3056ccf54d8723bf983c92f35bf4138d2fee5da3cdd56d25391f18906aab"
         },
-        "archive_name": "framework-scipy.tar.xz",
-        "archive_size": 23957800,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.tar.xz",
+        "archive_size": 23961760,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:42.825586+00:00",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
index 2282818..290b09b 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "bf065fe724e53e03886117ff0a7d61e29910da9c46b4a14799581cfc1238c77f"
+    "sha256": "f0338c45382c53320d30dc99e4370075de52593adb46a969f0692e772dcfb3ca"
   },
   "archive_name": "app-scipy-client.tar.xz",
-  "archive_size": 2980,
+  "archive_size": 2984,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:33.147967+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
index 40a1486..cd4588b 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "3ab7e8458a233e96790809ad0437209bcbf1823d7883220a44554b1c3fd51afa"
+    "sha256": "3ef2198496159dca41b2fa5cdea6ec0afb40b6060f95f23dc3da02e99e2d435f"
   },
-  "archive_name": "app-scipy-import.tar.xz",
+  "archive_name": "app-scipy-import@1.tar.xz",
   "archive_size": 2896,
-  "install_target": "app-scipy-import",
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:33.121208+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
   "runtime_name": "cpython@3.11",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
index 996c5bd..0735cfd 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "6872599275f0b5448926033968ba5f3467b07bf09ac19af8538975a39bf7b712"
+    "sha256": "32f6135ea3b938e47c8897b0da7a51c6992397edbefe2b27358665b1c83d29aa"
   },
-  "archive_name": "framework-scipy.tar.xz",
-  "archive_size": 15078848,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.tar.xz",
+  "archive_size": 15076180,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:23:32.960668+00:00",
diff --git a/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json b/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
index 1006d12..08d663a 100644
--- a/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/macosx_arm64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "3ab7e8458a233e96790809ad0437209bcbf1823d7883220a44554b1c3fd51afa"
+          "sha256": "3ef2198496159dca41b2fa5cdea6ec0afb40b6060f95f23dc3da02e99e2d435f"
         },
-        "archive_name": "app-scipy-import.tar.xz",
+        "archive_name": "app-scipy-import@1.tar.xz",
         "archive_size": 2896,
-        "install_target": "app-scipy-import",
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:33.121208+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:36b0dbfec94b7de6507f348f0823cd02fdca2ea79eeafe92d571c26ae347d150",
         "runtime_name": "cpython@3.11",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "bf065fe724e53e03886117ff0a7d61e29910da9c46b4a14799581cfc1238c77f"
+          "sha256": "f0338c45382c53320d30dc99e4370075de52593adb46a969f0692e772dcfb3ca"
         },
         "archive_name": "app-scipy-client.tar.xz",
-        "archive_size": 2980,
+        "archive_size": 2984,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:33.147967+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:fb8a843c694d03d7ee74b457cdac2bd82b6b439de0ed308d72fe698c6c9c6cf4",
@@ -47,11 +47,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "6872599275f0b5448926033968ba5f3467b07bf09ac19af8538975a39bf7b712"
+          "sha256": "32f6135ea3b938e47c8897b0da7a51c6992397edbefe2b27358665b1c83d29aa"
         },
-        "archive_name": "framework-scipy.tar.xz",
-        "archive_size": 15078848,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.tar.xz",
+        "archive_size": 15076180,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:23:32.960668+00:00",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
index 0c350fb..4bf772b 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-client.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "9f3de2bf483797a9a93629feca94756de57d82e62b157a4836b96fa14a289180"
+    "sha256": "ca15fb796933f031340de069d53f6d3a821e481b1372eb4ff001368ac92a214c"
   },
   "archive_name": "app-scipy-client.zip",
-  "archive_size": 257112,
+  "archive_size": 257117,
   "install_target": "app-scipy-client",
   "layer_name": "app-scipy-client",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:36.468633+00:00",
   "required_layers": [
-    "framework-scipy",
+    "framework-scipy@1",
     "framework-http-client"
   ],
   "requirements_hash": "sha256:3bff0428616a2f1724732e78e7788e753dd5f1aa10aa5d3b87707b8dbde121de",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
index f679796..b68d0a2 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/app-scipy-import.json
@@ -3,16 +3,16 @@
   "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "3f4e2a19a1611db1139f9e68a268a963dd30139690ee6d8325896265007bf823"
+    "sha256": "9eae1f6e63422d58ccef53ae199ac55884c50f19e1faf5ecd98c2dfc651ce723"
   },
-  "archive_name": "app-scipy-import.zip",
-  "archive_size": 256621,
-  "install_target": "app-scipy-import",
+  "archive_name": "app-scipy-import@1.zip",
+  "archive_size": 256677,
+  "install_target": "app-scipy-import@1",
   "layer_name": "app-scipy-import",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:36.386938+00:00",
   "required_layers": [
-    "framework-scipy"
+    "framework-scipy@1"
   ],
   "requirements_hash": "sha256:9aba38b5efe287f35d58825dce6b1c47ed556b930056e6edc00ca9e1a165796b",
   "runtime_name": "cpython@3.11.10",
diff --git a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
index 34fa1a6..827d795 100644
--- a/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
+++ b/tests/sample_project/expected_manifests/win_amd64/env_metadata/framework-scipy.json
@@ -1,11 +1,11 @@
 {
   "archive_build": 1,
   "archive_hashes": {
-    "sha256": "71146182f2bcf36ed9af674ac146ee32228e8d0a2890fb9c51ebd87e7fe58b45"
+    "sha256": "ac2c6a48192ac3657c5cbec001aeddf48ddd45881ac86a0cfa9eb5b839d2e3d4"
   },
-  "archive_name": "framework-scipy.zip",
-  "archive_size": 45080726,
-  "install_target": "framework-scipy",
+  "archive_name": "framework-scipy@1.zip",
+  "archive_size": 45087226,
+  "install_target": "framework-scipy@1",
   "layer_name": "framework-scipy",
   "lock_version": 1,
   "locked_at": "2024-10-15T10:24:35.999197+00:00",
diff --git a/tests/sample_project/expected_manifests/win_amd64/venvstacks.json b/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
index b21d903..73a7469 100644
--- a/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
+++ b/tests/sample_project/expected_manifests/win_amd64/venvstacks.json
@@ -6,16 +6,16 @@
         "app_launch_module_hash": "sha256:d806d778921ad216c1f950886d27b4b77e5561fe3467046fec258805980cc6d1",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "3f4e2a19a1611db1139f9e68a268a963dd30139690ee6d8325896265007bf823"
+          "sha256": "9eae1f6e63422d58ccef53ae199ac55884c50f19e1faf5ecd98c2dfc651ce723"
         },
-        "archive_name": "app-scipy-import.zip",
-        "archive_size": 256621,
-        "install_target": "app-scipy-import",
+        "archive_name": "app-scipy-import@1.zip",
+        "archive_size": 256677,
+        "install_target": "app-scipy-import@1",
         "layer_name": "app-scipy-import",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:36.386938+00:00",
         "required_layers": [
-          "framework-scipy"
+          "framework-scipy@1"
         ],
         "requirements_hash": "sha256:9aba38b5efe287f35d58825dce6b1c47ed556b930056e6edc00ca9e1a165796b",
         "runtime_name": "cpython@3.11.10",
@@ -26,16 +26,16 @@
         "app_launch_module_hash": "sha256/bbe4da6de13a8f13a05cdd2bb3b90884861a6636b1450248d03aea799a7fc828",
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "9f3de2bf483797a9a93629feca94756de57d82e62b157a4836b96fa14a289180"
+          "sha256": "ca15fb796933f031340de069d53f6d3a821e481b1372eb4ff001368ac92a214c"
         },
         "archive_name": "app-scipy-client.zip",
-        "archive_size": 257112,
+        "archive_size": 257117,
         "install_target": "app-scipy-client",
         "layer_name": "app-scipy-client",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:36.468633+00:00",
         "required_layers": [
-          "framework-scipy",
+          "framework-scipy@1",
           "framework-http-client"
         ],
         "requirements_hash": "sha256:3bff0428616a2f1724732e78e7788e753dd5f1aa10aa5d3b87707b8dbde121de",
@@ -47,11 +47,11 @@
       {
         "archive_build": 1,
         "archive_hashes": {
-          "sha256": "71146182f2bcf36ed9af674ac146ee32228e8d0a2890fb9c51ebd87e7fe58b45"
+          "sha256": "ac2c6a48192ac3657c5cbec001aeddf48ddd45881ac86a0cfa9eb5b839d2e3d4"
         },
-        "archive_name": "framework-scipy.zip",
-        "archive_size": 45080726,
-        "install_target": "framework-scipy",
+        "archive_name": "framework-scipy@1.zip",
+        "archive_size": 45087226,
+        "install_target": "framework-scipy@1",
         "layer_name": "framework-scipy",
         "lock_version": 1,
         "locked_at": "2024-10-15T10:24:35.999197+00:00",
diff --git a/tests/sample_project/venvstacks.toml b/tests/sample_project/venvstacks.toml
index 9ceb843..17cb920 100644
--- a/tests/sample_project/venvstacks.toml
+++ b/tests/sample_project/venvstacks.toml
@@ -65,9 +65,7 @@ requirements = [
 
 [[frameworks]]
 name = "scipy"
-# Automatic versioning currently breaks venv layering
-# https://github.com/lmstudio-ai/venvstacks/issues/24
-# versioned = true
+versioned = true
 runtime = "cpython@3.11"
 requirements = [
     "scipy",
@@ -96,9 +94,7 @@ requirements = [
 
 [[applications]]
 name = "scipy-import"
-# Automatic versioning currently breaks venv layering
-# https://github.com/lmstudio-ai/venvstacks/issues/24
-# versioned = true
+versioned = true
 launch_module = "launch_modules/scipy_import.py"
 frameworks = ["scipy"]
 requirements = [
diff --git a/tests/support.py b/tests/support.py
index 8b790f6..d26fc25 100644
--- a/tests/support.py
+++ b/tests/support.py
@@ -243,6 +243,12 @@ class DeploymentTestCase(unittest.TestCase):
     def assertPathExists(self, expected_path: Path) -> None:
         self.assertTrue(expected_path.exists(), f"No such path: {str(expected_path)}")
 
+    def assertPathContains(self, containing_path: Path, contained_path: Path) -> None:
+        self.assertTrue(
+            contained_path.is_relative_to(containing_path),
+            f"{str(containing_path)!r} is not a parent folder of {str(contained_path)!r}",
+        )
+
     def assertSysPathEntry(self, expected: str, env_sys_path: Sequence[str]) -> None:
         self.assertTrue(
             any(expected in path_entry for path_entry in env_sys_path),
@@ -364,13 +370,16 @@ def check_deployed_environments(
             # Nothing at all should be emitted on stderr
             self.assertEqual(launch_result.stderr, "")
 
-    def check_environment_exports(self, export_paths: ExportedEnvironmentPaths) -> None:
+    def check_environment_exports(
+        self, export_path: Path, export_paths: ExportedEnvironmentPaths
+    ) -> None:
         metadata_path, snippet_paths, env_paths = export_paths
         exported_manifests = ManifestData(metadata_path, snippet_paths)
         env_name_to_path: dict[str, Path] = {}
         for env_metadata, env_path in zip(exported_manifests.snippet_data, env_paths):
             # TODO: Check more details regarding expected metadata contents
-            self.assertTrue(env_path.exists())
+            self.assertPathExists(env_path)
+            self.assertPathContains(export_path, env_path)
             env_name = EnvNameDeploy(env_metadata["install_target"])
             self.assertEqual(env_path.name, env_name)
             env_name_to_path[env_name] = env_path
diff --git a/tests/test_minimal_project.py b/tests/test_minimal_project.py
index 98f1f70..7bd2160 100644
--- a/tests/test_minimal_project.py
+++ b/tests/test_minimal_project.py
@@ -489,7 +489,7 @@ def get_deployed_env_details(
 
     def test_create_environments(self) -> None:
         # Fast test to check the links between build envs are set up correctly
-        # (if this fails, there's no point even trying to full slow test case)
+        # (if this fails, there's no point even trying the full slow test case)
         build_env = self.build_env
         build_env.create_environments()
         self.check_build_environments(self.build_env.all_environments())
@@ -596,7 +596,7 @@ def test_locking_and_publishing(self) -> None:
         with self.subTest("Check environment export"):
             export_path = self.working_path / "_export🦎"
             export_result = build_env.export_environments(export_path)
-            self.check_environment_exports(export_result)
+            self.check_environment_exports(export_path, export_result)
             subtests_passed += 1
         # Test stage: ensure published archives and manifests have the expected name
         #             and that unpacking them allows launch module execution
diff --git a/tests/test_sample_project.py b/tests/test_sample_project.py
index 94a1b93..1e3b184 100644
--- a/tests/test_sample_project.py
+++ b/tests/test_sample_project.py
@@ -267,7 +267,7 @@ def setUp(self) -> None:
 
     def test_create_environments(self) -> None:
         # Fast test to check the links between build envs are set up correctly
-        # (if this fails, there's no point even trying to full slow test case)
+        # (if this fails, there's no point even trying the full slow test case)
         build_env = self.build_env
         build_env.create_environments()
         self.check_build_environments(self.build_env.all_environments())
@@ -381,7 +381,7 @@ def test_build_is_reproducible(self) -> None:
         with self.subTest("Check environment export"):
             export_path = self.working_path / "_export🦎"
             export_result = build_env.export_environments(export_path)
-            self.check_environment_exports(export_result)
+            self.check_environment_exports(export_path, export_result)
             subtests_passed += 1
 
         # Work aroung pytest-subtests not failing the test case when subtests fail