diff --git a/.gitignore b/.gitignore
index 8cd4fa79..10bf3048 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,5 +24,14 @@ tools/NNS/src/*.o
 # Stray R plotting artifact from headless regeneration
 Rplots.pdf
 
+# Workflow-local input file (sync/last_* reports stay tracked by design)
+/changed_files.json
+
+# Local working checkouts of upstream repos
+/upstream/
+
+# Local notes
+/NNS_LOCAL_REFERENCE.md
+
 # MkDocs build output
 /site/
diff --git a/changed_files.json b/changed_files.json
deleted file mode 100644
index 2baefa4e..00000000
--- a/changed_files.json
+++ /dev/null
@@ -1,3 +0,0 @@
-[
-  "R/ARMA.R"
-]
diff --git a/original_tests/testthat/Rplots.pdf b/original_tests/testthat/Rplots.pdf
deleted file mode 100644
index 46462869..00000000
Binary files a/original_tests/testthat/Rplots.pdf and /dev/null differ
diff --git a/pyproject.toml b/pyproject.toml
index 2f38388d..12e16e23 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,21 +59,23 @@ build-backend = "scikit_build_core.build"
 
 [tool.scikit-build]
 wheel.packages = ["src/nns"]
+# Everything git-tracked ships by default; include re-adds files under an
+# excluded directory (include patterns take priority over exclude).
 sdist.include = [
-    "/CMakeLists.txt",
-    "/LICENSE",
-    "/README.md",
-    "/docs",
-    "/sync",
-    "/extern/NNS-core",
+    "/sync/nns_source.json",
+]
+sdist.exclude = [
+    "/tests",
+    "/tools",
     "/original_tests",
     "/scripts",
-    "/tools/NNS",
-    "/tools/NNS_13.0.tar.gz",
-    "/tests/_r_cache.json",
-    "/tests/fixtures/original_tests_expected.json",
-    "/pyproject.toml",
-    "/src",
+    "/docs",
+    "/sync",
+    "/gists",
+    "/examples",
+    "/.github",
+    "/mkdocs.yml",
+    "/uv.lock",
 ]
 
 [tool.pytest.ini_options]
diff --git a/upstream/NNS b/upstream/NNS
deleted file mode 160000
index 7250bb62..00000000
--- a/upstream/NNS
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 7250bb627d12f6cdb1dbe60a8b8e50385e2a7c41