fix nix flake build and add helper script to maintain deps sha in flake

flake.nix

@@ -6,8 +6,14 @@
     flake-utils.url = "github:numtide/flake-utils";
   };
 
-  outputs = { self, nixpkgs, flake-utils }:
-    flake-utils.lib.eachDefaultSystem (system:
+  outputs =
+    {
+      self,
+      nixpkgs,
+      flake-utils,
+    }:
+    flake-utils.lib.eachDefaultSystem (
+      system:
       let
         pkgs = nixpkgs.legacyPackages.${system};
 
@@ -27,15 +33,25 @@
           nativeBuildInputs = [
             pkgs.bun
             pkgs.makeWrapper
-            pkgs.python3  # needed by node-gyp to compile better-sqlite3
-          ] ++ pkgs.lib.optionals pkgs.stdenv.hostPlatform.isDarwin [
-            pkgs.darwin.cctools  # provides libtool needed by node-gyp on macOS
+            pkgs.python3 # needed by node-gyp to compile better-sqlite3
+          ]
+          ++ pkgs.lib.optionals pkgs.stdenv.hostPlatform.isDarwin [
+            pkgs.darwin.cctools # provides libtool needed by node-gyp on macOS
           ];
 
           buildInputs = [ pkgs.sqlite ];
 
+          dontConfigure = true;
+
           buildPhase = ''
             export HOME=$(mktemp -d)
+            # Copy pre-downloaded deps, then fix shebangs and run install scripts
+            cp -r ${bunDeps}/node_modules node_modules
+            chmod -R u+w node_modules
+            patchShebangs node_modules
+
+            # Run lifecycle scripts (e.g. better-sqlite3 native compilation)
+            # without allowing bun to reach the network.
             bun install --frozen-lockfile
           '';
 
@@ -60,6 +76,36 @@
             platforms = platforms.unix;
           };
         };
+
+        # Fixed-output derivation: download deps only (no lifecycle scripts).
+        # FODs get network access because the output is content-addressed.
+        # --ignore-scripts avoids native compilation, which would introduce
+        # Nix store references that FODs are not allowed to contain.
+        bunDeps = pkgs.stdenv.mkDerivation {
+          pname = "qmd-deps";
+          version = "1.0.0";
+
+          src = ./.;
+
+          nativeBuildInputs = [ pkgs.bun ];
+
+          dontConfigure = true;
+          dontFixup = true;
+
+          buildPhase = ''
+            export HOME=$(mktemp -d)
+            bun install --frozen-lockfile --ignore-scripts
+          '';
+
+          installPhase = ''
+            mkdir -p $out
+            cp -r node_modules $out/node_modules
+          '';
+
+          outputHashMode = "recursive";
+          outputHashAlgo = "sha256";
+          outputHash = "sha256-gfQmBdLdapDsZrG3QjoBvCNmzuTx4ek7l7Vi26z1Vbc=";
+        };
       in
       {
         packages = {

package.json

@@ -22,7 +22,8 @@
     "vsearch": "tsx src/qmd.ts vsearch",
     "rerank": "tsx src/qmd.ts rerank",
     "inspector": "npx @modelcontextprotocol/inspector tsx src/qmd.ts mcp",
-    "release": "./scripts/release.sh"
+    "release": "./scripts/release.sh",
+    "update-flake-hash": "./scripts/update-flake-hash.sh"
   },
   "publishConfig": {
     "access": "public"

scripts/update-flake-hash.sh

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+# Recompute the Bun dependency hash in flake.nix after bun.lock changes.
+#
+# Usage: ./scripts/update-flake-hash.sh
+#
+# How it works:
+#   1. Temporarily sets the outputHash to a known-wrong value
+#   2. Runs `nix build`, which fails but prints the correct hash
+#   3. Patches the correct hash back into flake.nix
+#
+# Requires: nix with flakes enabled, sed, grep
+
+set -uo pipefail
+
+FLAKE="flake.nix"
+FAKE_HASH="sha256-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="
+
+# 1. Replace current hash with a known-wrong one
+sed -i 's|outputHash = "sha256-[^"]*";|outputHash = "'"$FAKE_HASH"'";|' "$FLAKE"
+
+echo "Computing dependency hash (this will download deps in a sandbox)..."
+
+# 2. Build and capture the expected hash from the error output.
+#    nix build will exit non-zero (hash mismatch), which is expected.
+BUILD_OUTPUT=$(nix build 2>&1 || true)
+HASH=$(echo "$BUILD_OUTPUT" | grep -oP 'got:\s+\Ksha256-[A-Za-z0-9+/]+=*' | head -1)
+
+if [ -z "$HASH" ]; then
+	echo "ERROR: could not extract hash from nix build output." >&2
+	echo "" >&2
+	echo "nix build output:" >&2
+	echo "$BUILD_OUTPUT" >&2
+	# Restore the fake hash so it's obvious something went wrong
+	exit 1
+fi
+
+# 3. Write the real hash back
+sed -i 's|outputHash = "'"$FAKE_HASH"'";|outputHash = "'"$HASH"'";|' "$FLAKE"
+
+echo "Updated flake.nix with hash: $HASH"