diff --git a/src/index.ts b/src/index.ts
index e3bb4e5..aa597fa 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -45,6 +45,20 @@ export function apply(ctx: Context, config: PluginConfig): () => void {
   // autoIndex. Errors are logged, never thrown (the plugin stays usable — the
   // lazy first-search path will rebuild if the boot failed).
   let booted = false
+  let bootComplete = false
+  let refreshPending = false
+  let disposed = false
+  const refresh = (): void => {
+    if (disposed) return
+    if (!bootComplete) {
+      refreshPending = true
+      return
+    }
+    refreshPending = false
+    void index.build('refresh').catch((error) => {
+      logger.warn(`semantic-search refresh failed: ${error instanceof Error ? error.message : String(error)}`)
+    })
+  }
   const boot = async (): Promise<void> => {
     if (booted) return
     booted = true
@@ -62,25 +76,28 @@ export function apply(ctx: Context, config: PluginConfig): () => void {
       }
     } catch (error) {
       logger.error(`semantic-search boot failed: ${error instanceof Error ? error.message : String(error)}`)
+    } finally {
+      bootComplete = true
+      if (!disposed && refreshPending) {
+        refreshPending = false
+        refresh()
+      }
     }
   }
   void boot()
 
   let watcher: ReturnType<typeof createDirWatcher> | undefined
   if (resolved.watch) {
-    watcher = createDirWatcher(resolved.root, () => {
-      if (!index.ready) return
-      void index.build('refresh').catch((error) => {
-        logger.warn(`semantic-search refresh failed: ${error instanceof Error ? error.message : String(error)}`)
-      })
-    }, {
+    const dataDirName = index.config.dataDir.replace(/[\\/]+$/, '').split(/[\\/]/).pop() || '.sema'
+    watcher = createDirWatcher(resolved.root, refresh, {
       debounceMs: resolved.watchDebounceMs,
       // never let our own index writes feed back into a rebuild
-      exclude: [index.config.dataDir.split(/[\\/]/).pop() ?? '.sema'],
+      exclude: [dataDirName],
     })
   }
 
   return () => {
+    disposed = true
     watcher?.close()
     for (const dispose of disposers) {
       try {
diff --git a/src/watcher.ts b/src/watcher.ts
index 036f9d2..22977da 100644
--- a/src/watcher.ts
+++ b/src/watcher.ts
@@ -9,6 +9,8 @@
  */
 
 import { watch, type FSWatcher } from 'node:fs'
+import { readdir, stat } from 'node:fs/promises'
+import { join, relative } from 'node:path'
 
 export interface WatchHandle {
   close(): void
@@ -35,6 +37,8 @@ export function createDirWatcher(
   let closed = false
   let debounce: NodeJS.Timeout | undefined
   let polling: NodeJS.Timeout | undefined
+  let pollingRun: Promise<void> | undefined
+  let pollingSnapshot: Map<string, string> | undefined
   let watcher: FSWatcher | undefined
 
   const isExcluded = (name: string | null): boolean => {
@@ -54,11 +58,60 @@ export function createDirWatcher(
     }, debounceMs)
   }
 
+  const takePollingSnapshot = async (): Promise<Map<string, string>> => {
+    const entries = await readdir(root, { recursive: true, withFileTypes: true })
+    const snapshot = new Map<string, string>()
+    for (const entry of entries) {
+      const filePath = join(entry.parentPath, entry.name)
+      const name = relative(root, filePath).replace(/\\/g, '/')
+      if (entry.isDirectory() || isExcluded(name)) continue
+      try {
+        const info = await stat(filePath)
+        if (!info.isFile()) continue
+        snapshot.set(name, `${info.size}:${info.mtimeMs}:${info.ctimeMs}`)
+      } catch {
+        // Ignore files that disappear while the snapshot is being collected.
+      }
+    }
+    return snapshot
+  }
+
+  const snapshotsEqual = (left: Map<string, string>, right: Map<string, string>): boolean => {
+    if (left.size !== right.size) return false
+    for (const [name, signature] of left) {
+      if (right.get(name) !== signature) return false
+    }
+    return true
+  }
+
+  const poll = async (): Promise<void> => {
+    if (closed || pollingRun) return
+    pollingRun = (async () => {
+      try {
+        const next = await takePollingSnapshot()
+        if (closed) return
+        const previous = pollingSnapshot
+        pollingSnapshot = next
+        if (!previous || !snapshotsEqual(previous, next)) {
+          fire(null)
+        }
+      } catch {
+        // A transient scan failure should not create a refresh loop.
+      } finally {
+        pollingRun = undefined
+      }
+    })()
+    await pollingRun
+  }
+
   const startPolling = (): void => {
     if (polling) return
-    polling = setInterval(() => fire(null), pollingMs)
+    polling = setInterval(() => {
+      void poll()
+    }, pollingMs)
     // keep the event loop alive only while an index is being watched
     polling.unref?.()
+    void poll()
   }
 
   try {
diff --git a/tests/index-startup-watcher.test.ts b/tests/index-startup-watcher.test.ts
new file mode 100644
index 0000000..a825144
--- /dev/null
+++ b/tests/index-startup-watcher.test.ts
@@ -0,0 +1,78 @@
+import assert from 'node:assert/strict'
+import { mock, test } from 'node:test'
+
+let watcherCallback: (() => void) | undefined
+let releaseInit!: () => void
+let markInitStarted!: () => void
+const initStarted = new Promise<void>((resolve) => {
+  markInitStarted = resolve
+})
+const initGate = new Promise<void>((resolve) => {
+  releaseInit = resolve
+})
+const buildModes: string[] = []
+
+class FakeSearchIndex {
+  readonly config: any
+  readonly providerId = 'test-provider'
+  private isReady = false
+
+  constructor(config: any) {
+    this.config = config
+  }
+
+  get ready(): boolean {
+    return this.isReady
+  }
+
+  async init(): Promise<{ status: 'empty'; meta: null }> {
+    markInitStarted()
+    await initGate
+    return { status: 'empty', meta: null }
+  }
+
+  build(mode: 'full' | 'refresh'): Promise<Record<string, unknown>> {
+    buildModes.push(mode)
+    return Promise.resolve({ mode, files: 0, chunks: 0, truncated: false })
+  }
+}
+
+mock.module('../src/engine/search.ts', {
+  namedExports: { SearchIndex: FakeSearchIndex },
+})
+mock.module('../src/watcher.ts', {
+  namedExports: {
+    createDirWatcher: (_root: string, onChange: () => void) => {
+      watcherCallback = onChange
+      return { close(): void {} }
+    },
+  },
+})
+
+const { apply } = await import('../src/index.ts')
+
+test('entry: drains queued reconciliation for an initially empty index', async () => {
+  const ctx: any = {
+    tools: { register: () => () => undefined },
+    logger: () => ({ info: () => undefined, warn: () => undefined, error: () => undefined, debug: () => undefined }),
+  }
+  const dispose = apply(ctx, { autoIndex: false, autosave: false, watch: true })
+
+  try {
+    await initStarted
+    const callback = watcherCallback
+    assert.ok(callback)
+    callback()
+    assert.deepEqual(buildModes, [])
+
+    releaseInit()
+    await new Promise<void>((resolve) => setImmediate(resolve))
+    assert.deepEqual(buildModes, ['refresh'])
+
+    callback()
+    assert.deepEqual(buildModes, ['refresh', 'refresh'])
+  } finally {
+    releaseInit()
+    dispose()
+  }
+})
diff --git a/tests/index-watcher.test.ts b/tests/index-watcher.test.ts
new file mode 100644
index 0000000..c66860b
--- /dev/null
+++ b/tests/index-watcher.test.ts
@@ -0,0 +1,51 @@
+import assert from 'node:assert/strict'
+import { mkdtemp, rm } from 'node:fs/promises'
+import { mock, test } from 'node:test'
+import { join } from 'node:path'
+import { tmpdir } from 'node:os'
+
+const watcherOptions: Array<{ exclude?: string[] }> = []
+
+mock.module('../src/watcher.ts', {
+  namedExports: {
+    createDirWatcher: (...args: unknown[]) => {
+      watcherOptions.push(args[2] as { exclude?: string[] })
+      return { close(): void {} }
+    },
+  },
+})
+
+const { apply } = await import('../src/index.ts')
+
+test('entry: trims trailing separators before deriving the watcher exclusion name', async () => {
+  const root = await mkdtemp(join(tmpdir(), 'sema-index-watcher-'))
+  const registered: unknown[] = []
+  const ctx: any = {
+    tools: {
+      register: (tool: unknown) => {
+        registered.push(tool)
+        return () => undefined
+      },
+    },
+    logger: () => ({ info: () => undefined, warn: () => undefined, error: () => undefined, debug: () => undefined }),
+  }
+
+  try {
+    const dispose = apply(ctx, {
+      root,
+      dataDir: `${join(root, '.sema')}/`,
+      provider: { kind: 'lexical', dimension: 64 },
+      autoIndex: false,
+      autosave: false,
+      watch: true,
+    })
+
+    try {
+      assert.deepEqual(watcherOptions.at(-1)?.exclude, ['.sema'])
+    } finally {
+      dispose()
+    }
+  } finally {
+    await rm(root, { recursive: true, force: true })
+  }
+})
diff --git a/tests/watcher.test.ts b/tests/watcher.test.ts
index ea0d5fd..f2b7be0 100644
--- a/tests/watcher.test.ts
+++ b/tests/watcher.test.ts
@@ -3,7 +3,10 @@
  */
 
 import assert from 'node:assert/strict'
+import { mkdir, mkdtemp, rm, writeFile } from 'node:fs/promises'
 import { mock, test } from 'node:test'
+import { join } from 'node:path'
+import { tmpdir } from 'node:os'
 
 type WatchCallback = (event: string, filename: string | Buffer | null) => void
 interface FakeWatcher {
@@ -12,6 +15,7 @@ interface FakeWatcher {
 }
 
 const callbacks: WatchCallback[] = []
+let forcePolling = false
 const fakeWatcher: FakeWatcher = {
   on(): typeof fakeWatcher {
     return fakeWatcher
@@ -22,6 +26,7 @@ const fakeWatcher: FakeWatcher = {
 mock.module('node:fs', {
   namedExports: {
     watch: (...args: unknown[]) => {
+      if (forcePolling) throw new Error('recursive watch unavailable')
       callbacks.push(args[2] as WatchCallback)
       return fakeWatcher
     },
@@ -50,3 +55,33 @@ test('watcher: excludes matching directory names at any depth', async () => {
     mock.reset()
   }
 })
+
+test('watcher: polling reconciles once, then detects included changes without reacting to excluded changes', async () => {
+  forcePolling = true
+  const root = await mkdtemp(join(tmpdir(), 'sema-watcher-'))
+  await mkdir(join(root, '.sema'))
+  await writeFile(join(root, 'source.ts'), 'initial source')
+  await writeFile(join(root, '.sema', 'index.json'), 'initial index')
+
+  let changes = 0
+  const handle = createDirWatcher(root, () => {
+    changes += 1
+  }, { debounceMs: 0, pollingMs: 250, exclude: ['.sema'] })
+
+  try {
+    await new Promise((resolve) => setTimeout(resolve, 350))
+    assert.equal(changes, 1)
+
+    await writeFile(join(root, '.sema', 'index.json'), 'updated index')
+    await new Promise((resolve) => setTimeout(resolve, 350))
+    assert.equal(changes, 1)
+
+    await writeFile(join(root, 'source.ts'), 'updated source')
+    await new Promise((resolve) => setTimeout(resolve, 350))
+    assert.equal(changes, 2)
+  } finally {
+    handle.close()
+    forcePolling = false
+    await rm(root, { recursive: true, force: true })
+  }
+})