diff --git a/Makefile b/Makefile
index 1fbcd30fa1..434575d9cb 100644
--- a/Makefile
+++ b/Makefile
@@ -268,7 +268,7 @@ clean:
 	find frontend/catalyst -name "*.so" -not -path "*/third_party/*" -exec rm -v {} +
 	git restore frontend/catalyst/_configuration.py
 	rm -rf $(MK_DIR)/frontend/catalyst/_revision.py
-	rm -rf $(MK_DIR)/frontend/mlir_quantum $(MK_DIR)/frontend/catalyst/lib $(MK_DIR)/frontend/catalyst/bin
+	rm -rf $(MK_DIR)/frontend/mlir_quantum $(MK_DIR)/frontend/catalyst/include $(MK_DIR)/frontend/catalyst/lib $(MK_DIR)/frontend/bin
 	rm -rf dist __pycache__
 	rm -rf .coverage coverage_html_report
 	rm -rf .benchmarks
diff --git a/frontend/catalyst/utils/runtime_environment.py b/frontend/catalyst/utils/runtime_environment.py
index 86ec00fd4f..901a02403b 100644
--- a/frontend/catalyst/utils/runtime_environment.py
+++ b/frontend/catalyst/utils/runtime_environment.py
@@ -22,47 +22,41 @@
 
 from catalyst._configuration import INSTALLED
 
-package_root = os.path.dirname(__file__)
+package_root = os.path.join(os.path.dirname(__file__), "..")
 
 # Default paths to dep libraries
 DEFAULT_LIB_PATHS = {
-    "llvm": os.path.join(package_root, "../../../mlir/llvm-project/build/lib"),
-    "runtime": os.path.join(package_root, "../../../runtime/build/lib"),
-    "enzyme": os.path.join(package_root, "../../../mlir/Enzyme/build/Enzyme"),
-    "oqc_runtime": os.path.join(package_root, "../../catalyst/third_party/oqc/src/build"),
-    "oqd_runtime": os.path.join(package_root, "../../../runtime/build/lib"),
+    "llvm": os.path.join(package_root, "..", "..", "mlir", "llvm-project", "build", "lib"),
+    "dialects": os.path.join(package_root, "..", "..", "mlir", "build", "lib"),
+    "runtime": os.path.join(package_root, "..", "..", "runtime", "build", "lib"),
+    "enzyme": os.path.join(package_root, "..", "..", "mlir", "Enzyme", "build", "Enzyme"),
+    "oqc_runtime": os.path.join(package_root, "third_party", "oqc", "src", "build"),
+    "oqd_runtime": os.path.join(package_root, "..", "..", "runtime", "build", "lib"),
 }
 
 DEFAULT_INCLUDE_PATHS = {
-    "mlir": os.path.join(package_root, "../../../mlir/include"),
+    "mlir": os.path.join(package_root, "..", "..", "mlir", "include"),
 }
 
 DEFAULT_BIN_PATHS = {
-    "cli": os.path.join(package_root, "../../../mlir/build/bin"),
+    "cli": os.path.join(package_root, "..", "..", "mlir", "build", "bin"),
 }
 
 
 def get_lib_path(project, env_var):
-    """Get the library path."""
+    """Get the path to Catalyst's shared libraries."""
     if INSTALLED:
-        return os.path.join(package_root, "..", "lib")  # pragma: no cover
+        return os.path.join(package_root, "lib")  # pragma: no cover
     return os.getenv(env_var, DEFAULT_LIB_PATHS.get(project, ""))
 
 
 def get_include_path():
     """Return the path to Catalyst's include directory."""
     if INSTALLED:
-        return os.path.join(package_root, "..", "include")  # pragma: no cover
+        return os.path.join(package_root, "include")  # pragma: no cover
     return os.getenv("CATALYST_INCLUDE_DIRS", DEFAULT_INCLUDE_PATHS.get("mlir", ""))
 
 
-def get_bin_path(project, env_var):
-    """Get the library path."""
-    if INSTALLED:
-        return os.path.join(package_root, "..", "bin")  # pragma: no cover
-    return os.getenv(env_var, DEFAULT_BIN_PATHS.get(project, ""))
-
-
 def get_cli_path() -> str:  # pragma: nocover
     """Method to obtain the Catalyst CLI path packaged via the data_files mechanism."""
     catalyst_cli = "catalyst"
@@ -88,6 +82,12 @@ def get_cli_path() -> str:  # pragma: nocover
     if os.path.isfile(path):
         return path
 
+    # Check the old bin directory location, which in rare scenarios may still be used
+    # (e.g. the configuration after `make wheel` has been run).
+    path = os.path.join(package_root, "..", "bin", catalyst_cli)
+    if os.path.isfile(path):
+        return path
+
     raise RuntimeError(
         "Could not locate the Catalyst executable, please report this issue on GitHub."
     )
diff --git a/frontend/test/lit/test_mlir_plugin.py b/frontend/test/lit/test_mlir_plugin.py
index 3528c03188..a533a02248 100644
--- a/frontend/test/lit/test_mlir_plugin.py
+++ b/frontend/test/lit/test_mlir_plugin.py
@@ -69,7 +69,7 @@ def module():
 import catalyst
 from catalyst import qjit
 from catalyst.compiler import _quantum_opt
-from catalyst.utils.runtime_environment import get_bin_path
+from catalyst.utils.runtime_environment import get_lib_path
 
 mlir_module = """
 module @module {
@@ -90,7 +90,7 @@ def module():
 """
 
 ext = "so" if platform.system() == "Linux" else "dylib"
-plugin_path = get_bin_path("cli", "CATALYST_BIN_DIR") + f"/../lib/StandalonePlugin.{ext}"
+plugin_path = get_lib_path("dialects", "") + f"/StandalonePlugin.{ext}"
 plugin = Path(plugin_path)
 custom_pipeline = [("run_only_plugin", ["builtin.module(apply-transform-sequence)"])]
 mlir_string = _quantum_opt(