diff --git a/setup.mjs b/setup.mjs
index f3b4e91..b25af6b 100644
--- a/setup.mjs
+++ b/setup.mjs
@@ -16,7 +16,7 @@
 import { spawnSync }                                    from 'node:child_process';
 import { existsSync, readFileSync, writeFileSync,
          unlinkSync, linkSync, copyFileSync,
-         readSync }                                     from 'node:fs';
+         readSync, readdirSync, rmSync }                 from 'node:fs';
 import { join, dirname }                               from 'node:path';
 import { fileURLToPath }                               from 'node:url';
 import { randomBytes }                                 from 'node:crypto';
@@ -59,6 +59,17 @@ function commandExists(cmd) {
   return capture(checker, [cmd]) !== null;
 }
 
+function removeIncompletePackageMetadata(sitePackages) {
+  if (!existsSync(sitePackages)) return;
+  for (const entry of readdirSync(sitePackages, { withFileTypes: true })) {
+    if (!entry.isDirectory() || !entry.name.endsWith('.dist-info')) continue;
+    const metadataDir = join(sitePackages, entry.name);
+    if (existsSync(join(metadataDir, 'RECORD'))) continue;
+    console.log(`  Removing incomplete package metadata: ${entry.name}`);
+    rmSync(metadataDir, { recursive: true, force: true });
+  }
+}
+
 function prompt(question) {
   process.stdout.write(question);
   const buf = Buffer.alloc(4096);
@@ -116,6 +127,14 @@ if (uninstall) {
 
 // -- Main setup ----------------------------------------------------------------
 
+// Stop the daemon before changing its Python environment. The stop command
+// waits for the process lock to be released, not just for the HTTP port to close.
+step(0, 'Stopping running daemon');
+if (existsSync(join(REPO, 'config.json')))
+  runOrDie('node', [join(REPO, 'ts.mjs'), 'stop'], 'ts stop');
+else
+  console.log('  No config.json yet; nothing to stop.');
+
 // [1] Register MCP
 step(1, 'Registering MCP server (Claude Code + GitHub Copilot)');
 run('claude', ['mcp', 'remove', '--scope', 'user', 'tscodesearch'], { stdio: 'pipe' });
@@ -181,9 +200,12 @@ step(2, 'Creating client venv (.client-venv)');
 
   runOrDie('uv', ['python', 'install', PYTHON_VER], `uv python install ${PYTHON_VER}`);
 
+  removeIncompletePackageMetadata(join(clientVenv, 'Lib', 'site-packages'));
+
   const needsCreate = !existsSync(pyExe);
   console.log(needsCreate ? '  Installing packages...' : '  Synchronizing packages...');
-  runOrDie('uv', ['sync', '--locked', '--no-dev', '--python', PYTHON_VER, '--project', REPO],
+  runOrDie('uv', ['sync', '--locked', '--no-dev', '--link-mode', 'copy',
+                  '--python', PYTHON_VER, '--project', REPO],
     'uv sync', {
       env: {
         ...process.env,
diff --git a/vscode-codesearch/.vscodeignore b/vscode-codesearch/.vscodeignore
index 716deb4..dc065c4 100644
--- a/vscode-codesearch/.vscodeignore
+++ b/vscode-codesearch/.vscodeignore
@@ -1,4 +1,5 @@
 .vscode/**
+.claude/**
 src/**
 out/test/**
 node_modules/**
@@ -8,3 +9,5 @@ node_modules/**
 tsconfig.json
 AGENTS.md
 setup-vscode-ext.cmd
+setup-out.txt
+test-virtual-scroll.js
diff --git a/vscode-codesearch/package.json b/vscode-codesearch/package.json
index bfb7bd3..d792b45 100644
--- a/vscode-codesearch/package.json
+++ b/vscode-codesearch/package.json
@@ -182,8 +182,9 @@
     }
   },
   "scripts": {
+    "clean": "node -e \"require('fs').rmSync('out',{recursive:true,force:true})\"",
     "prebuild": "node -e \"var d=new Date();require('fs').writeFileSync('src/buildInfo.ts','export const BUILD_DATE = \\\"'+d.toISOString().slice(0,16).replace('T',' ')+' UTC\\\";\\n')\"",
-    "precompile": "npm run prebuild",
+    "precompile": "npm run clean && npm run prebuild",
     "prewatch": "npm run prebuild",
     "compile": "tsc -p ./",
     "watch": "tsc -watch -p ./",