diff --git a/flake.nix b/flake.nix
index 368b0a7..83c6de2 100644
--- a/flake.nix
+++ b/flake.nix
@@ -26,7 +26,9 @@
           version = "1.0";
           src = ./.;
 
-          nativeBuildInputs = [ pkgs.makeWrapper ];
+          # python3 is needed by checkPhase: `make test-c` shells out to
+          # `python3 tools/run_tests.py` (see c/Makefile, PYTHON ?= python3).
+          nativeBuildInputs = [ pkgs.makeWrapper pkgs.python3 ];
 
           buildInputs = [
             pkgs.gcc
@@ -44,18 +46,29 @@
 
           installPhase = ''
             runHook preInstall
-            mkdir -p $out/bin
-            cp c/glm $out/bin/glm
 
-            # Wrap coli (the Python CLI) so it finds the right python and the engine
-            mkdir -p $out/share/colibri
-            cp c/coli $out/share/colibri/coli
-            chmod +x $out/share/colibri/coli
-            cp -r c/tools $out/share/colibri/tools
+            # Self-contained layout under $out/lib/colibri that mirrors the
+            # source tree `coli` runs in (see the path-resolution logic at the
+            # top of c/coli): the engine, the coli CLI script, the support
+            # modules it imports (openai_server.py, resource_plan.py,
+            # doctor.py), and tools/ all sit next to each other.
+            mkdir -p $out/lib/colibri/tools $out/bin
+            cp c/glm             $out/lib/colibri/glm
+            cp c/coli            $out/lib/colibri/coli
+            chmod +x $out/lib/colibri/coli
+            cp c/openai_server.py c/resource_plan.py c/doctor.py $out/lib/colibri/
+            cp -r c/tools/*      $out/lib/colibri/tools/
 
+            # $out/bin holds the user-facing entry points.
+            ln -s ../lib/colibri/glm $out/bin/glm
+
+            # Wrap coli: point it at the bundled engine (COLI_ENGINE) so it is
+            # found by default, and at the module dir (PYTHONPATH) so
+            # `import openai_server` / `resource_plan` / `doctor` resolve.
             makeWrapper ${pythonEnv}/bin/python $out/bin/coli \
-              --add-flags "$out/share/colibri/coli" \
-              --set PYTHONPATH "${pythonEnv}/${pkgs.python3.sitePackages}"
+              --add-flags "$out/lib/colibri/coli" \
+              --set COLI_ENGINE "$out/lib/colibri/glm" \
+              --set PYTHONPATH "$out/lib/colibri:${pythonEnv}/${pkgs.python3.sitePackages}"
             runHook postInstall
           '';