@@ -59,6 +59,40 @@ describe('incremental builder', () => {
     await logger?.close()
   })
 
+  it('ignores directory notifications and refreshes removed subtrees without deleting directories as files', async () => {
+    await withTempDir(async (base) => {
+      const contentDir = path.join(base, 'content')
+      const outDir = path.join(base, 'out')
+      const assetsDir = path.join(contentDir, 'assets')
+      const emptyDir = path.join(contentDir, 'empty')
+      await fs.mkdir(assetsDir, { recursive: true })
+      await fs.mkdir(emptyDir)
+      await fs.mkdir(path.join(outDir, 'empty'), { recursive: true })
+      await fs.writeFile(path.join(assetsDir, 'example.txt'), 'asset content')
+      await fs.writeFile(path.join(contentDir, 'index.mdx'), '# Home')
+      const builder = await createIncrementalBuilder({
+        siteConfig: { rootDir: base, contentDir, outDir },
+      })
+      await builder.prepareForRequests()
+      await builder.prepareAssetByUrlPath('/assets/example.txt')
+      expect((await builder.applyChange(assetsDir)).fullRebuild).toBe(false)
+      expect((await builder.applyChange(contentDir)).fullRebuild).toBe(false)
+      expect(
+        await fs.readFile(path.join(outDir, 'assets', 'example.txt'), 'utf8'),
+      ).toBe('asset content')
+      await fs.rmdir(emptyDir)
+      expect((await builder.applyChange(emptyDir)).fullRebuild).toBe(false)
+      expect((await fs.stat(path.join(outDir, 'empty'))).isDirectory()).toBe(
+        true,
+      )
+      await fs.rm(assetsDir, { recursive: true, force: true })
+      expect((await builder.applyChange(assetsDir)).fullRebuild).toBe(true)
+      expect(
+        await fs.readFile(path.join(outDir, 'assets', 'example.txt'), 'utf8'),
+      ).toBe('asset content')
+    })
+  })
+
   it('removes deleted content outputs and updates manifest', async () => {
     await withTempDir(async (base) => {
       const contentDir = path.join(base, 'content')
 
@@ -1,3 +1,4 @@
+import fsPromises from 'node:fs/promises'
 import path from 'node:path'
 import type { SiteConfig } from '@purestack/ts-common'
 import { themes } from '@purestack/ts-style'
@@ -475,13 +476,37 @@ class IncrementalRuntime {
     const result = this.changeApplier.createResult(
       `content change: ${filePath}`,
     )
-    if (isOutsideContentRoot(relPath)) return result
+    if (!relPath || isOutsideContentRoot(relPath)) return result
+    const sourceStats = await fsPromises
+      .stat(filePath)
+      .catch((error: NodeJS.ErrnoException) => {
+        if (error.code === 'ENOENT' || error.code === 'ENOTDIR')
+          return undefined
+        throw error
+      })
+    // Recursive watchers also emit directory events. They are not asset files.
+    if (sourceStats?.isDirectory()) return result
     if (isSiteConfigFile(relPath)) {
       result.fullRebuild = true
       return result
     }
 
     await this.ensureContentReady()
+    if (!sourceStats) {
+      const prefix = `${toPosixPath(relPath)}/`
+      const removedDirectory =
+        this.context.contentRoutes.pages.some((file) =>
+          toPosixPath(file.relPath).startsWith(prefix),
+        ) ||
+        [...this.staticAssets.values()].some((file) =>
+          toPosixPath(file.relPath).startsWith(prefix),
+        )
+      if (removedDirectory) {
+        // Refresh discovery for a removed subtree; never rm its output as a file.
+        result.fullRebuild = true
+        return result
+      }
+    }
     this.contentState.takeMarkedPageCount()
     const ext = path.extname(relPath).toLowerCase()
     if (
@@ -494,9 +519,18 @@ class IncrementalRuntime {
       path.basename(relPath).toUpperCase() !==
         DEFAULT_NAV_FILENAME.toUpperCase()
     ) {
-      await removeFile(
-        path.join(this.config.outDir, toOutputAssetRelPath(relPath)),
+      const cachedAsset = this.manifest.assets[relPath]
+      const knownAsset = this.staticAssets.get(
+        `/${toPosixPath(toOutputAssetRelPath(relPath))}`,
       )
+      // A missing, empty directory can also arrive as an event. Only invalidate
+      // output for paths previously discovered or copied as actual files.
+      if (cachedAsset || knownAsset) {
+        await removeFile(
+          cachedAsset?.outPath ??
+            path.join(this.config.outDir, toOutputAssetRelPath(relPath)),
+        )
+      }
       delete this.manifest.assets[relPath]
       await this.discoverRequestAssets()
       this.contentState.refreshAssets(
 
@@ -96,7 +96,21 @@ export async function startDevServer(
 
   const { host, port, watch, liveReload, fullRender } =
     resolveDevServerOptions(input)
-  let fullBuild: Promise<unknown> | undefined
+  let setupReady: Promise<void> = Promise.resolve()
+  const activeResponses = new Set<Promise<void>>()
+  const beginSiteRequest = async () => {
+    while (true) {
+      const ready = setupReady
+      await ready
+      if (ready !== setupReady) continue
+      const finished = Promise.withResolvers<void>()
+      activeResponses.add(finished.promise)
+      return () => {
+        activeResponses.delete(finished.promise)
+        finished.resolve()
+      }
+    }
+  }
 
   const clients: LiveReloadClients = new Map()
   let liveReloadVersion = 0
@@ -169,7 +183,13 @@ export async function startDevServer(
     reason: string,
     options?: { recreateBuilder?: boolean; reloadConfig?: boolean },
   ) => {
+    const previousSetup = setupReady
+    const prepared = Promise.withResolvers<void>()
+    setupReady = prepared.promise
     try {
+      await previousSetup
+      // Output cleanup must not race HTML reads or streamed asset responses.
+      await Promise.all([...activeResponses])
       if (options?.reloadConfig) {
         buildInput = await projectConfig.load(baseBuildInput)
         watchConfigDependencies()
@@ -181,8 +201,7 @@ export async function startDevServer(
         devMiddleware = composeDevMiddleware(buildInput.options?.plugins ?? [])
       }
       if (fullRender && !initialSetupDone) {
-        fullBuild = incremental.buildAll(reason)
-        await fullBuild
+        await incremental.buildAll(reason)
       }
       await incremental.prepareForRequests()
       if (!initialSetupDone) {
@@ -194,6 +213,8 @@ export async function startDevServer(
       notifyReload(reason)
     } catch (error) {
       logError(log, error, 'dev setup failed')
+    } finally {
+      prepared.resolve()
     }
   }
 
@@ -248,9 +269,7 @@ export async function startDevServer(
       basePath: config.basePath,
       i18n: config.i18n,
       liveReload,
-      waitForFullBuild: async () => {
-        if (fullRender) await fullBuild
-      },
+      beginSiteRequest,
       // Config changes replace the builder, so requests ask for the current one.
       getIncremental: () => incremental,
       handlePluginRequest: (req, res) => devMiddleware(req, res),
@@ -267,16 +286,6 @@ export async function startDevServer(
   })
   server.keepAliveTimeout = 1000
   server.headersTimeout = 5000
-  server.listen(port, host, () => {
-    log.info('dev server listening', {
-      host,
-      port,
-      outDir: config.outDir,
-      liveReload,
-      watch,
-      fullRender,
-    })
-  })
 
   if (watch) {
     watcher = await watchTree(config.contentDir, (filePath) => {
@@ -287,6 +296,16 @@ export async function startDevServer(
   watchConfigDependencies()
 
   void requestRebuild()
+  server.listen(port, host, () => {
+    log.info('dev server listening', {
+      host,
+      port,
+      outDir: config.outDir,
+      liveReload,
+      watch,
+      fullRender,
+    })
+  })
 
   const shutdown = async () => {
     if (shuttingDown) return
@@ -376,7 +395,7 @@ type DevServerRequestHandlerInput = {
   basePath: string
   i18n: I18nConfig
   liveReload: boolean
-  waitForFullBuild: () => Promise<void>
+  beginSiteRequest: () => Promise<() => void>
   getIncremental: () => IncrementalBuilder
   /** Resolves true when a plugin's dev middleware responded. */
   handlePluginRequest: (
@@ -396,7 +415,7 @@ function createDevServerRequestHandler(input: DevServerRequestHandlerInput) {
     basePath,
     i18n,
     liveReload,
-    waitForFullBuild,
+    beginSiteRequest,
     getIncremental,
     handlePluginRequest,
     clients,
@@ -441,7 +460,13 @@ function createDevServerRequestHandler(input: DevServerRequestHandlerInput) {
     let fileResult: Awaited<ReturnType<typeof resolveRequestFile>>
     let incremental: IncrementalBuilder
     try {
-      await waitForFullBuild()
+      const finishRequest = await beginSiteRequest()
+      if (res.destroyed) {
+        finishRequest()
+        return
+      }
+      res.once('finish', finishRequest)
+      res.once('close', finishRequest)
       incremental = getIncremental()
       res.setTimeout(REQUEST_TIMEOUT_MS, () => {
         res.destroy()