diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d4d0e29..03a3a5d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,7 +37,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        run: uv sync
+        run: uv sync --all-packages
 
       - name: Generate proto stubs
         run: uv run make proto
@@ -80,7 +80,7 @@ jobs:
 
       - name: Install + generate proto
         run: |
-          uv sync
+          uv sync --all-packages
           uv run make proto
 
       - name: Integration tests
diff --git a/Makefile b/Makefile
index d789a65..edf4ece 100644
--- a/Makefile
+++ b/Makefile
@@ -54,7 +54,7 @@ lint:
 	ruff format --check coordinode/ langchain-coordinode/ llama-index-coordinode/ tests/
 
 clean:
-	rm -rf $(PROTO_OUT)/coordinode
+	rm -rf $(PROTO_OUT)
 	find . -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true
 	find . -type d -name "*.egg-info" -exec rm -rf {} + 2>/dev/null || true
 	find . -type d -name dist -exec rm -rf {} + 2>/dev/null || true
diff --git a/coordinode/_proto/__init__.py b/coordinode/_proto/__init__.py
deleted file mode 100644
index cabe24e..0000000
--- a/coordinode/_proto/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-# Generated gRPC stubs. Run `make proto` to regenerate.
-# This directory is .gitignore'd — stubs are not committed.
diff --git a/ruff.toml b/ruff.toml
index 1ecba6c..2a07ca7 100644
--- a/ruff.toml
+++ b/ruff.toml
@@ -3,7 +3,9 @@ target-version = "py311"
 
 exclude = [
     # Generated proto stubs — do not lint
-    "coordinode/_proto/",
+    "coordinode/coordinode/_proto/",
+    # Generated version files — do not lint
+    "**/_version.py",
 ]
 
 [lint]
@@ -11,3 +13,6 @@ select = ["E", "F", "I", "W", "UP"]
 ignore = [
     "E501",  # line length handled by formatter
 ]
+
+[lint.isort]
+known-first-party = ["coordinode", "langchain_coordinode", "llama_index_coordinode"]