diff --git a/gitnexus/src/cli/i18n/en.ts b/gitnexus/src/cli/i18n/en.ts
index 7984c9be3..8d8fc5fc1 100644
--- a/gitnexus/src/cli/i18n/en.ts
+++ b/gitnexus/src/cli/i18n/en.ts
@@ -135,7 +135,7 @@ export const en = {
   'help.command.watch.description':
     'Control scheduled repository clone/pull and analysis from GITNEXUS_HOME/watch_config.yml',
   'help.watch.details':
-    '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: only git@github.com:owner/repo.git, git@gitlab.com:group/repo.git, and git@gitee.com:owner/repo.git are allowed.\nRuns once immediately, then repeats on sync_interval_minutes.',
+    '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: only SSH URLs on github.com, gitlab.com, and gitee.com are allowed.\nRuns once immediately, then repeats on sync_interval_minutes.',
   'help.command.analyze.description': 'Index a repository (full analysis)',
   'help.command.index.description':
     'Register an existing .gitnexus/ folder into the global registry (no re-analysis needed)',
diff --git a/gitnexus/src/cli/i18n/zh-CN.ts b/gitnexus/src/cli/i18n/zh-CN.ts
index 758a4c2f3..aa6e06498 100644
--- a/gitnexus/src/cli/i18n/zh-CN.ts
+++ b/gitnexus/src/cli/i18n/zh-CN.ts
@@ -136,7 +136,7 @@ export const zhCN = {
   'help.command.watch.description':
     '控制基于 GITNEXUS_HOME/watch_config.yml 的定时 clone/pull 和分析',
   'help.watch.details':
-    '\n操作：init、start（默认）、restart、stop、status、reset\n配置：GITNEXUS_HOME/watch_config.yml\n运行时文件：GITNEXUS_HOME/watch/watch.pid、watch.mutex、watch.owner.json、watch.status.json、auto-sync-state.json\n恢复：已验证 owner 退出的 mutex 会自动回收；无效或旧版 mutex 会安全拒绝，确认没有 watch 进程运行后再手动删除。\n写入：GITNEXUS_HOME/watch/project_commit_info.txt\n远程地址：仅允许 git@github.com:owner/repo.git、git@gitlab.com:group/repo.git 和 git@gitee.com:owner/repo.git。\n启动后立即运行一次，之后按 sync_interval_minutes 重复。',
+    '\n操作：init、start（默认）、restart、stop、status、reset\n配置：GITNEXUS_HOME/watch_config.yml\n运行时文件：GITNEXUS_HOME/watch/watch.pid、watch.mutex、watch.owner.json、watch.status.json、auto-sync-state.json\n恢复：已验证 owner 退出的 mutex 会自动回收；无效或旧版 mutex 会安全拒绝，确认没有 watch 进程运行后再手动删除。\n写入：GITNEXUS_HOME/watch/project_commit_info.txt\n远程地址：仅允许 github.com、gitlab.com 和 gitee.com 上的 SSH 地址。\n启动后立即运行一次，之后按 sync_interval_minutes 重复。',
   'help.command.analyze.description': '索引仓库（完整分析）',
   'help.command.index.description': '将现有 .gitnexus/ 文件夹注册到全局注册表（无需重新分析）',
   'help.command.serve.description': '启动供 Web UI 连接的本地 HTTP 服务器',
diff --git a/gitnexus/src/core/auto-sync/analysis-worker-launch.ts b/gitnexus/src/core/auto-sync/analysis-worker-launch.ts
index cda91902a..b92aaaa84 100644
--- a/gitnexus/src/core/auto-sync/analysis-worker-launch.ts
+++ b/gitnexus/src/core/auto-sync/analysis-worker-launch.ts
@@ -67,6 +67,7 @@ export function createAutoSyncAnalysisRunner(
 
       let terminalOutcome: WorkerMessage | undefined;
       let terminationGrace: ReturnType<typeof setTimeout> | undefined;
+      let terminationReason: 'timeout' | 'cancelled' | undefined;
       let settled = false;
       const cleanup = () => {
         deps.clearTimeoutFn(timeout);
@@ -80,28 +81,37 @@ export function createAutoSyncAnalysisRunner(
         if (error) reject(error);
         else resolve(result!);
       };
-      const timeout = deps.setTimeoutFn(() => {
+      const requestTermination = (reason: 'timeout' | 'cancelled') => {
+        if (settled || terminationReason) return;
+        terminationReason = reason;
+        deps.clearTimeoutFn(timeout);
         child.kill('SIGTERM');
         terminationGrace = deps.setTimeoutFn(() => {
           child.kill('SIGKILL');
-          settle(new Error(`Analysis timed out after ${timeoutMs}ms.`));
+          settle(
+            new Error(
+              reason === 'timeout' ? `Analysis timed out after ${timeoutMs}ms.` : 'Analysis cancelled.',
+            ),
+          );
         }, TERMINATION_GRACE_MS);
-      }, timeoutMs);
-      const onAbort = () => {
-        child.kill('SIGKILL');
-        settle(new Error('Analysis cancelled.'));
       };
+      const timeout = deps.setTimeoutFn(() => requestTermination('timeout'), timeoutMs);
+      const onAbort = () => requestTermination('cancelled');
       signal?.addEventListener('abort', onAbort, { once: true });
 
       child.on('message', (message: WorkerMessage) => {
-        if (message.type !== 'progress') terminalOutcome ??= message;
+        // Once timeout/cancellation requested shutdown, its reason owns the
+        // result. A terminal IPC can already be queued behind SIGTERM.
+        if (message.type === 'progress' || terminalOutcome || terminationReason) return;
+        terminalOutcome = message;
+        deps.clearTimeoutFn(timeout);
       });
       child.on('error', (error) => {
         settle(new Error(`Auto-sync analyze worker error: ${error.message}`));
       });
       child.on('exit', (code, childSignal) => {
         if (settled) return;
-        if (terminationGrace) {
+        if (terminationReason === 'timeout') {
           settle(
             new Error(
               `Analysis timed out after ${timeoutMs}ms and worker exited (${childSignal ?? code ?? 'unknown'}).`,
@@ -109,6 +119,10 @@ export function createAutoSyncAnalysisRunner(
           );
           return;
         }
+        if (terminationReason === 'cancelled') {
+          settle(new Error('Analysis cancelled.'));
+          return;
+        }
         if (terminalOutcome?.type === 'complete') {
           settle(undefined, { stats: terminalOutcome.result.stats });
           return;
diff --git a/gitnexus/src/core/auto-sync/config.ts b/gitnexus/src/core/auto-sync/config.ts
index f85c0b812..230df86c1 100644
--- a/gitnexus/src/core/auto-sync/config.ts
+++ b/gitnexus/src/core/auto-sync/config.ts
@@ -249,7 +249,7 @@ export function validateAutoSyncRemoteUrl(remoteUrl: string): void {
   const match = /^git@([^:\s/]+):([^\s]+)$/.exec(remoteUrl.trim());
   if (!match) {
     throw new Error(
-      'must use git@github.com:owner/repo.git, git@gitlab.com:group/repo.git, or git@gitee.com:owner/repo.git',
+      'must use an SSH URL on github.com, gitlab.com, or gitee.com',
     );
   }
   const host = match[1].toLowerCase();
@@ -270,6 +270,12 @@ export function validateAutoSyncBranchName(branch: string): void {
   if (branch.startsWith('-')) throw new Error('must not start with "-"');
   if (branch.includes('..')) throw new Error('must not contain ".."');
   if (branch.includes('`')) throw new Error('must not contain backticks');
+  if (branch.endsWith('/') || branch.endsWith('.'))
+    throw new Error('must not end with "/" or "."');
+  if (branch.includes('//')) throw new Error('must not contain consecutive slashes');
+  if (branch.includes('@{')) throw new Error('must not contain "@{"');
+  if (branch.split('/').some((component) => component.startsWith('.') || component.endsWith('.lock')))
+    throw new Error('must not contain hidden or .lock path components');
 }
 
 export function parseDurationMs(value: unknown): number {
diff --git a/gitnexus/src/core/auto-sync/path-security.ts b/gitnexus/src/core/auto-sync/path-security.ts
index 2b1d3e77b..a782c2028 100644
--- a/gitnexus/src/core/auto-sync/path-security.ts
+++ b/gitnexus/src/core/auto-sync/path-security.ts
@@ -1,4 +1,5 @@
 import fs from 'node:fs/promises';
+import { randomUUID } from 'node:crypto';
 import os from 'node:os';
 import path from 'node:path';
 import { getGlobalDir } from '../../storage/repo-manager.js';
@@ -115,7 +116,7 @@ export async function quarantineAutoSyncPartial(
   await fs.mkdir(quarantineRoot, { recursive: true, mode: 0o700 });
   const base = path.basename(targetDir);
   const stamp = new Date().toISOString().replace(/[:.]/g, '-');
-  const destination = path.join(quarantineRoot, `auto-sync-${stamp}-${process.pid}-${base}`);
+  const destination = path.join(quarantineRoot, `auto-sync-${stamp}-${process.pid}-${randomUUID()}-${base}`);
   try {
     await fs.rename(targetDir, destination);
   } catch (err: unknown) {
diff --git a/gitnexus/src/core/auto-sync/runner.ts b/gitnexus/src/core/auto-sync/runner.ts
index 70d159eba..f0b148a46 100644
--- a/gitnexus/src/core/auto-sync/runner.ts
+++ b/gitnexus/src/core/auto-sync/runner.ts
@@ -301,8 +301,9 @@ export async function runAutoSyncOnce(
 
     if (repoResult.project.groupName) {
       let groupMembershipOk = false;
+      let membershipAdded = false;
       try {
-        await deps.addRepoToGroup(
+        membershipAdded = await deps.addRepoToGroup(
           repoResult.project,
           getAutoSyncRepoIdentity(repoResult.remoteUrl),
           getAutoSyncRepoIdentity(repoResult.remoteUrl),
@@ -314,7 +315,10 @@ export async function runAutoSyncOnce(
           `[auto-sync] Group update failed for ${repoResult.project.groupName}: ${(err as Error).message}`,
         );
       }
-      if (groupMembershipOk && analyzeStatus === 'success') {
+      if (
+        groupMembershipOk &&
+        (analyzeStatus === 'success' || (membershipAdded && analyzeStatus === 'skipped'))
+      ) {
         groupsToSync.add(repoResult.project.groupName);
       }
     }
diff --git a/gitnexus/src/server/analyze-worker-core.ts b/gitnexus/src/server/analyze-worker-core.ts
index dcee256a4..916cce42c 100644
--- a/gitnexus/src/server/analyze-worker-core.ts
+++ b/gitnexus/src/server/analyze-worker-core.ts
@@ -27,7 +27,6 @@ import { IndexLockTimeoutError } from '../storage/index-lock.js';
 export interface WorkerAnalysisDeps {
   runFullAnalysis: typeof import('../core/run-analyze.js').runFullAnalysis;
   assertAnalysisFinalized: typeof import('../storage/repo-manager.js').assertAnalysisFinalized;
-  acquireAnalysisLock: (repoPath: string) => Promise<() => Promise<void>>;
   send: (msg: WorkerMessage) => void;
   /**
    * Claim the single terminal-outcome slot. Returns `true` for the first caller
@@ -52,38 +51,33 @@ export async function runWorkerAnalysis(
 ): Promise<void> {
   let terminal: WorkerMessage;
   try {
-    const releaseAnalysisLock = await deps.acquireAnalysisLock(repoPath);
-    try {
-      const bootstrapArgs: [] | [AnalyzerRunnerIdentity] = runnerIdentityAtBootstrap
-        ? [runnerIdentityAtBootstrap]
-        : [];
-      const result = await deps.runFullAnalysis(
-        repoPath,
-        // This worker force-exits right after reporting, so skip the native close
-        // (it can double-free in LadybugDB's ClientContext destructor after --pdg
-        // writes); flushWAL still persists the index, process.exit reclaims handles.
-        { ...options, skipNativeCloseOnExit: true },
-        {
-          onProgress: (phase, percent, message) =>
-            deps.send({ type: 'progress', phase, percent, message }),
-          onLog: (message) => deps.send({ type: 'progress', phase: 'log', percent: -1, message }),
-        },
-        ...bootstrapArgs,
-      );
-      // P2 (#2264): a half-finalized repo — meta.json written but the global
-      // registry entry missing (e.g. a prior collision-aborted run, or a wiped
-      // registry) — must NOT be reported as a successful analysis. Mirror the CLI's
-      // assertAnalysisFinalized guard so the worker surfaces it as an error instead
-      // of a false `complete` that leaves the repo invisible to list_repos.
-      await deps.assertAnalysisFinalized(repoPath);
+    const bootstrapArgs: [] | [AnalyzerRunnerIdentity] = runnerIdentityAtBootstrap
+      ? [runnerIdentityAtBootstrap]
+      : [];
+    const result = await deps.runFullAnalysis(
+      repoPath,
+      // This worker force-exits right after reporting, so skip the native close
+      // (it can double-free in LadybugDB's ClientContext destructor after --pdg
+      // writes); flushWAL still persists the index, process.exit reclaims handles.
+      { ...options, skipNativeCloseOnExit: true },
+      {
+        onProgress: (phase, percent, message) =>
+          deps.send({ type: 'progress', phase, percent, message }),
+        onLog: (message) => deps.send({ type: 'progress', phase: 'log', percent: -1, message }),
+      },
+      ...bootstrapArgs,
+    );
+    // P2 (#2264): a half-finalized repo — meta.json written but the global
+    // registry entry missing (e.g. a prior collision-aborted run, or a wiped
+    // registry) — must NOT be reported as a successful analysis. Mirror the CLI's
+    // assertAnalysisFinalized guard so the worker surfaces it as an error instead
+    // of a false `complete` that leaves the repo invisible to list_repos.
+    await deps.assertAnalysisFinalized(repoPath);
 
-      // Send a JSON-safe projection, NOT the raw result: the IPC channel is
-      // default-JSON serialization and `result.pipelineResult` carries the live
-      // KnowledgeGraph. See analyze-worker-ipc.ts.
-      terminal = { type: 'complete', result: projectAnalyzeResultForIpc(result) };
-    } finally {
-      await releaseAnalysisLock();
-    }
+    // Send a JSON-safe projection, NOT the raw result: the IPC channel is
+    // default-JSON serialization and `result.pipelineResult` carries the live
+    // KnowledgeGraph. See analyze-worker-ipc.ts.
+    terminal = { type: 'complete', result: projectAnalyzeResultForIpc(result) };
   } catch (err: unknown) {
     // Report the failure to the parent over IPC (the parent surfaces the message).
     const message = err instanceof Error ? err.message : 'Analysis failed';
diff --git a/gitnexus/src/server/analyze-worker.ts b/gitnexus/src/server/analyze-worker.ts
index b78699257..ad4632eb0 100644
--- a/gitnexus/src/server/analyze-worker.ts
+++ b/gitnexus/src/server/analyze-worker.ts
@@ -11,8 +11,6 @@
  *   Child -> Parent: { type: 'error', message: string }
  */
 
-import path from 'path';
-import { createHash } from 'crypto';
 import type { StartMessage, WorkerMessage } from './analyze-worker-protocol.js';
 import { runWorkerAnalysis, createTerminalClaim } from './analyze-worker-core.js';
 type BoundedCheckpointBeforeExit =
@@ -105,13 +103,12 @@ process.on('message', async (msg: StartMessage) => {
     const prepared = await identityModule.captureAnalyzerIdentityBeforeLoad(
       import.meta.url,
       async () => {
-        const [analysisModule, repoManager, shutdownHelpers, fileLock] = await Promise.all([
+        const [analysisModule, repoManager, shutdownHelpers] = await Promise.all([
           import('../core/run-analyze.js'),
           import('../storage/repo-manager.js'),
           import('../core/lbug/shutdown-helpers.js'),
-          import('../storage/file-lock.js'),
         ]);
-        return { analysisModule, repoManager, shutdownHelpers, fileLock };
+        return { analysisModule, repoManager, shutdownHelpers };
       },
     );
     boundedCheckpointBeforeExit = prepared.loaded.shutdownHelpers.boundedCheckpointBeforeExit;
@@ -125,18 +122,6 @@ process.on('message', async (msg: StartMessage) => {
       {
         runFullAnalysis: prepared.loaded.analysisModule.runFullAnalysis,
         assertAnalysisFinalized: prepared.loaded.repoManager.assertAnalysisFinalized,
-        acquireAnalysisLock: (repoPath) => {
-          const repoKey = createHash('sha256')
-            .update(prepared.loaded.repoManager.canonicalizePath(repoPath))
-            .digest('hex');
-          return prepared.loaded.fileLock.acquireFileLock(
-            path.join(
-              prepared.loaded.repoManager.getGlobalDir(),
-              'locks',
-              `analyze-${repoKey}.lock`,
-            ),
-          );
-        },
         send,
         claimTerminal,
       },
diff --git a/gitnexus/src/server/git-clone.ts b/gitnexus/src/server/git-clone.ts
index 71c6a98a7..7598068ad 100644
--- a/gitnexus/src/server/git-clone.ts
+++ b/gitnexus/src/server/git-clone.ts
@@ -523,6 +523,8 @@ export async function cloneOrPull(
     await assertDirectoryOwnerAndPermissions(cloneRoot);
   }
   await assertNoSymlinkPath(cloneRoot, safeTarget, Boolean(options?.allowedCloneRoot));
+  await fs.mkdir(path.dirname(safeTarget), { recursive: true });
+  await assertNoSymlinkPath(cloneRoot, safeTarget, Boolean(options?.allowedCloneRoot));
   await assertPreRealpathContainment(cloneRoot, safeTarget);
 
   const exists = await fs.access(path.join(safeTarget, '.git')).then(
@@ -600,9 +602,6 @@ export async function cloneOrPull(
     if (targetExists && (await fs.readdir(safeTarget)).length > 0) {
       throw new Error(`Clone target already exists but is not a git repository: ${safeTarget}`);
     }
-    await fs.mkdir(path.dirname(safeTarget), { recursive: true });
-    await assertNoSymlinkPath(cloneRoot, safeTarget, Boolean(options?.allowedCloneRoot));
-    await assertPreRealpathContainment(cloneRoot, safeTarget);
     onProgress?.({ phase: 'cloning', message: `Cloning ${url}...` });
     try {
       const runGitImpl = options?.runGitForTest ?? runGit;
diff --git a/gitnexus/src/storage/file-lock.ts b/gitnexus/src/storage/file-lock.ts
index 2ed6a66cc..b509172b7 100644
--- a/gitnexus/src/storage/file-lock.ts
+++ b/gitnexus/src/storage/file-lock.ts
@@ -61,6 +61,7 @@ export async function acquireFileLock(
         if (
           await reclaimStaleLock(
             resolvedPath,
+            owner,
             options.isProcessAlive ?? isProcessAlive,
             options.readProcessStartTime ?? readProcessStartTime,
           )
@@ -81,14 +82,21 @@ export async function acquireFileLock(
 
 async function reclaimStaleLock(
   lockPath: string,
+  guardOwner: FileLockOwner,
   ownerIsAlive: (pid: number) => boolean,
   getProcessStartTime: (pid: number) => string | undefined,
 ): Promise<boolean> {
   const reclaimGuardPath = `${lockPath}.reclaim`;
+  let releaseReclaimGuard: () => Promise<void>;
   try {
-    await fs.mkdir(reclaimGuardPath);
+    releaseReclaimGuard = await acquireFileLock(reclaimGuardPath, {
+      pid: guardOwner.pid,
+      processStartTime: guardOwner.processStartTime,
+      isProcessAlive: ownerIsAlive,
+      readProcessStartTime: getProcessStartTime,
+    });
   } catch (error) {
-    if ((error as NodeJS.ErrnoException).code === 'EEXIST') return false;
+    if (error instanceof FileLockBusyError) return false;
     throw error;
   }
 
@@ -103,7 +111,7 @@ async function reclaimStaleLock(
     await fs.rm(lockPath, { force: true });
     return true;
   } finally {
-    await fs.rmdir(reclaimGuardPath);
+    await releaseReclaimGuard();
   }
 }
 
diff --git a/gitnexus/src/storage/repo-manager.ts b/gitnexus/src/storage/repo-manager.ts
index e1630b388..9c302a013 100644
--- a/gitnexus/src/storage/repo-manager.ts
+++ b/gitnexus/src/storage/repo-manager.ts
@@ -18,7 +18,6 @@ import fs from 'fs/promises';
 import { realpathSync } from 'fs';
 import path from 'path';
 import os from 'os';
-import { randomBytes } from 'crypto';
 import { getInferredRepoName, resolveRepoIdentityRoot, stripUrlCredentials } from './git.js';
 import { stripWindowsLongPathPrefix } from '../lib/utils.js';
 import { writeFileAtomic } from './fs-atomic.js';
@@ -642,17 +641,10 @@ export const readRegistry = async (): Promise<RegistryEntry[]> => {
 const writeRegistry = async (entries: RegistryEntry[]): Promise<void> => {
   const dir = getGlobalDir();
   await fs.mkdir(dir, { recursive: true });
-  // Atomic tmp+rename (mirrors saveMeta): a crash mid-write can never leave a
-  // truncated/half-written registry.json that the next load would treat as
-  // empty and silently drop every registered repo (#2106 R9).
-  const target = getGlobalRegistryPath();
-  const tmp = `${target}.${process.pid}.${randomBytes(8).toString('hex')}.tmp`;
-  try {
-    await fs.writeFile(tmp, JSON.stringify(sanitizeEntries(entries), null, 2), 'utf-8');
-    await fs.rename(tmp, target);
-  } finally {
-    await fs.unlink(tmp).catch(() => {});
-  }
+  await writeFileAtomic(
+    getGlobalRegistryPath(),
+    JSON.stringify(sanitizeEntries(entries), null, 2),
+  );
 };
 
 /**
diff --git a/gitnexus/test/unit/analyze-worker-core.test.ts b/gitnexus/test/unit/analyze-worker-core.test.ts
index 2309d34ea..06e3acd35 100644
--- a/gitnexus/test/unit/analyze-worker-core.test.ts
+++ b/gitnexus/test/unit/analyze-worker-core.test.ts
@@ -32,7 +32,6 @@ const baseResult: AnalyzeResult = {
 
 const okRun: WorkerAnalysisDeps['runFullAnalysis'] = vi.fn(async () => baseResult);
 const okFinalize: WorkerAnalysisDeps['assertAnalysisFinalized'] = vi.fn(async () => undefined);
-const okLock: WorkerAnalysisDeps['acquireAnalysisLock'] = vi.fn(async () => async () => undefined);
 const alwaysClaim: WorkerAnalysisDeps['claimTerminal'] = () => true;
 
 describe('runWorkerAnalysis — finalize guard (#2264 P2)', () => {
@@ -50,7 +49,6 @@ describe('runWorkerAnalysis — finalize guard (#2264 P2)', () => {
       {
         runFullAnalysis: okRun,
         assertAnalysisFinalized,
-        acquireAnalysisLock: okLock,
         send,
         claimTerminal: alwaysClaim,
       },
@@ -72,7 +70,6 @@ describe('runWorkerAnalysis — finalize guard (#2264 P2)', () => {
       {
         runFullAnalysis: okRun,
         assertAnalysisFinalized: okFinalize,
-        acquireAnalysisLock: okLock,
         send,
         claimTerminal: alwaysClaim,
       },
@@ -93,7 +90,6 @@ describe('runWorkerAnalysis — finalize guard (#2264 P2)', () => {
       {
         runFullAnalysis: run,
         assertAnalysisFinalized: okFinalize,
-        acquireAnalysisLock: okLock,
         send,
         claimTerminal: alwaysClaim,
       },
@@ -103,31 +99,6 @@ describe('runWorkerAnalysis — finalize guard (#2264 P2)', () => {
     expect(run.mock.calls[0]?.[3]).toBe(receipt);
   });
 
-  it('does not enter analysis when another worker holds the repo lock', async () => {
-    const send = vi.fn<(msg: WorkerMessage) => void>();
-    const run = vi.fn<WorkerAnalysisDeps['runFullAnalysis']>(async () => baseResult);
-
-    await runWorkerAnalysis(
-      '/repo',
-      {},
-      {
-        runFullAnalysis: run,
-        assertAnalysisFinalized: okFinalize,
-        acquireAnalysisLock: vi.fn(async () => {
-          throw new Error('Lock is already held for /repo');
-        }),
-        send,
-        claimTerminal: alwaysClaim,
-      },
-    );
-
-    expect(run).not.toHaveBeenCalled();
-    expect(send).toHaveBeenCalledWith({
-      type: 'error',
-      message: 'Lock is already held for /repo',
-    });
-  });
-
   it('reports error when finalization passes but the analysis itself throws', async () => {
     const send = vi.fn<(msg: WorkerMessage) => void>();
     const failingRun: WorkerAnalysisDeps['runFullAnalysis'] = vi.fn(async () => {
@@ -143,7 +114,6 @@ describe('runWorkerAnalysis — finalize guard (#2264 P2)', () => {
       {
         runFullAnalysis: failingRun,
         assertAnalysisFinalized: finalize,
-        acquireAnalysisLock: okLock,
         send,
         claimTerminal: alwaysClaim,
       },
@@ -196,7 +166,6 @@ describe('runWorkerAnalysis — terminal-claim coordination (#2264 P3)', () => {
       {
         runFullAnalysis: okRun,
         assertAnalysisFinalized: okFinalize,
-        acquireAnalysisLock: okLock,
         send,
         claimTerminal: alreadyClaimed,
       },
diff --git a/gitnexus/test/unit/auto-sync-analysis-worker.test.ts b/gitnexus/test/unit/auto-sync-analysis-worker.test.ts
index 2908bfc32..63a78ade4 100644
--- a/gitnexus/test/unit/auto-sync-analysis-worker.test.ts
+++ b/gitnexus/test/unit/auto-sync-analysis-worker.test.ts
@@ -80,7 +80,67 @@ describe('auto-sync analysis worker', () => {
     await expect(result).rejects.toThrow('Analysis timed out after 50ms');
   });
 
-  it('kills an active worker immediately when watch is stopped', async () => {
+  it('keeps the timeout outcome when complete arrives after termination begins', async () => {
+    const child = Object.assign(new EventEmitter(), {
+      send: vi.fn(),
+      kill: vi.fn(),
+    });
+    const timers: Array<() => void> = [];
+    const run = createAutoSyncAnalysisRunner({
+      forkWorker: vi.fn(() => child as any),
+      setTimeoutFn: vi.fn((callback: () => void) => {
+        timers.push(callback);
+        return timers.length as any;
+      }) as any,
+      clearTimeoutFn: vi.fn() as any,
+    });
+
+    const result = run('/tmp/repo', { branch: 'main' }, 50);
+    timers[0]();
+    child.emit('message', { type: 'complete', result: { stats: { files: 3 } } });
+    child.emit('exit', 0, null);
+
+    await expect(result).rejects.toThrow('Analysis timed out after 50ms');
+  });
+
+  it('clears the analysis deadline after complete before the worker exits', async () => {
+    vi.useFakeTimers();
+    try {
+      const child = Object.assign(new EventEmitter(), {
+        send: vi.fn(),
+        kill: vi.fn(),
+      });
+      const run = createAutoSyncAnalysisRunner({ forkWorker: vi.fn(() => child as any) });
+
+      const result = run('/tmp/repo', { branch: 'main' }, 50);
+      child.emit('message', { type: 'complete', result: { stats: { files: 3 } } });
+      await vi.advanceTimersByTimeAsync(50);
+
+      expect(child.kill).not.toHaveBeenCalled();
+      child.emit('exit', 0, null);
+      await expect(result).resolves.toEqual({ stats: { files: 3 } });
+    } finally {
+      vi.useRealTimers();
+    }
+  });
+
+  it('keeps the cancellation outcome when complete arrives after abort', async () => {
+    const child = Object.assign(new EventEmitter(), {
+      send: vi.fn(),
+      kill: vi.fn(),
+    });
+    const run = createAutoSyncAnalysisRunner({ forkWorker: vi.fn(() => child as any) });
+    const controller = new AbortController();
+
+    const result = run('/tmp/repo', { branch: 'main' }, 50, controller.signal);
+    controller.abort();
+    child.emit('message', { type: 'complete', result: { stats: { files: 3 } } });
+    child.emit('exit', 0, null);
+
+    await expect(result).rejects.toThrow('Analysis cancelled');
+  });
+
+  it('asks an active worker to stop gracefully when watch is stopped', async () => {
     const child = Object.assign(new EventEmitter(), {
       send: vi.fn(),
       kill: vi.fn(),
@@ -93,8 +153,9 @@ describe('auto-sync analysis worker', () => {
     const result = run('/tmp/repo', { branch: 'main' }, 50, controller.signal);
     controller.abort();
 
-    expect(child.kill).toHaveBeenCalledWith('SIGKILL');
-    child.emit('exit', null, 'SIGKILL');
+    expect(child.kill).toHaveBeenCalledWith('SIGTERM');
+    expect(child.kill).not.toHaveBeenCalledWith('SIGKILL');
+    child.emit('exit', null, 'SIGTERM');
     await expect(result).rejects.toThrow('Analysis cancelled');
   });
 });
diff --git a/gitnexus/test/unit/auto-sync-runner.test.ts b/gitnexus/test/unit/auto-sync-runner.test.ts
index 8a924c877..2bffaed9b 100644
--- a/gitnexus/test/unit/auto-sync-runner.test.ts
+++ b/gitnexus/test/unit/auto-sync-runner.test.ts
@@ -295,7 +295,7 @@ describe('auto-sync runner', () => {
       })),
       saveState: vi.fn(async () => {}),
       writeCommitInfo: vi.fn(async () => {}),
-      addRepoToGroup: vi.fn(async () => false),
+      addRepoToGroup: vi.fn(async () => true),
       syncGroupByName: vi.fn(async () => {}),
       getAvailableMemoryGB: vi.fn(() => 8),
     });
@@ -308,7 +308,7 @@ describe('auto-sync runner', () => {
     expect(result.analyzed).toBe(0);
     expect(result.skippedAnalysis).toBe(1);
     expect(deps.runAnalysis).not.toHaveBeenCalled();
-    expect(deps.syncGroupByName).not.toHaveBeenCalled();
+    expect(deps.syncGroupByName).toHaveBeenCalledWith('back_end');
   });
 
   it('uses remote identity under local_path as the clone target', async () => {
@@ -1115,13 +1115,14 @@ describe('auto-sync starter', () => {
       return timer;
     }) as unknown as typeof setInterval;
     const stderr = { write: vi.fn() };
-    let releaseRun: (() => void) | undefined;
+    const releaseRuns: Array<() => void> = [];
     const runOnce = vi.fn(
       () =>
         new Promise<any>((resolve) => {
-          releaseRun = () => resolve({ synced: 0, analyzed: 0, skippedAnalysis: 0, failed: 0 });
+          releaseRuns.push(() => resolve({ synced: 0, analyzed: 0, skippedAnalysis: 0, failed: 0 }));
         }),
     );
+    let handle: Awaited<ReturnType<typeof startAutoSyncWatch>> | undefined;
 
     try {
       process.env.GITNEXUS_HOME = tempDir;
@@ -1137,7 +1138,7 @@ describe('auto-sync starter', () => {
         ].join('\n'),
       );
 
-      await startAutoSyncWatch({ setIntervalFn, runOnce, stderr });
+      handle = await startAutoSyncWatch({ setIntervalFn, runOnce, stderr });
       scheduled?.();
 
       expect(runOnce).toHaveBeenCalledTimes(1);
@@ -1145,12 +1146,17 @@ describe('auto-sync starter', () => {
         '[auto-sync] Previous run is still active; skipping overlapping run.\n',
       );
 
-      releaseRun?.();
+      releaseRuns.shift()?.();
       await new Promise((resolve) => setTimeout(resolve, 0));
       scheduled?.();
 
       expect(runOnce).toHaveBeenCalledTimes(2);
+      releaseRuns.shift()?.();
+      await handle?.stop();
+      handle = undefined;
     } finally {
+      releaseRuns.splice(0).forEach((release) => release());
+      await handle?.stop();
       if (previousHome === undefined) delete process.env.GITNEXUS_HOME;
       else process.env.GITNEXUS_HOME = previousHome;
       await fs.rm(tempDir, { recursive: true, force: true });
diff --git a/gitnexus/test/unit/auto-sync.test.ts b/gitnexus/test/unit/auto-sync.test.ts
index 940f23871..00ac48ded 100644
--- a/gitnexus/test/unit/auto-sync.test.ts
+++ b/gitnexus/test/unit/auto-sync.test.ts
@@ -351,6 +351,24 @@ describe('auto-sync', () => {
     await expect(fs.access(target)).rejects.toThrow();
   });
 
+  it('gives concurrent partial clone quarantines unique destinations', async () => {
+    const quarantineRoot = path.join(gitnexusHome, 'watch', 'quarantine');
+    const first = path.join(tempDir, 'one', 'partial-repo');
+    const second = path.join(tempDir, 'two', 'partial-repo');
+    await Promise.all([fs.mkdir(first, { recursive: true }), fs.mkdir(second, { recursive: true })]);
+
+    const [firstDestination, secondDestination] = await Promise.all([
+      quarantineAutoSyncPartial(first, quarantineRoot),
+      quarantineAutoSyncPartial(second, quarantineRoot),
+    ]);
+
+    expect(firstDestination).not.toBe(secondDestination);
+    await expect(fs.access(firstDestination)).resolves.toBeUndefined();
+    await expect(fs.access(secondDestination)).resolves.toBeUndefined();
+    await expect(fs.access(first)).rejects.toThrow();
+    await expect(fs.access(second)).rejects.toThrow();
+  });
+
   it('rejects group-writable configured clone roots', async () => {
     if (process.platform === 'win32') return;
     const root = path.join(tempDir, 'group-writable-repos');
@@ -388,10 +406,17 @@ describe('auto-sync', () => {
 
   it('rejects unsafe auto-sync branch names', () => {
     expect(() => validateAutoSyncBranchName('feature/good-branch')).not.toThrow();
+    expect(() => validateAutoSyncBranchName('foo./bar')).not.toThrow();
     expect(() => validateAutoSyncBranchName('-upload-pack=evil')).toThrow('must not start');
     expect(() => validateAutoSyncBranchName('feature bad')).toThrow('whitespace');
     expect(() => validateAutoSyncBranchName('feature..bad')).toThrow('must not contain ".."');
     expect(() => validateAutoSyncBranchName('bad:ref')).toThrow('not allowed');
+    expect(() => validateAutoSyncBranchName('feature.')).toThrow('must not end');
+    expect(() => validateAutoSyncBranchName('feature/')).toThrow('must not end');
+    expect(() => validateAutoSyncBranchName('feature//branch')).toThrow('consecutive');
+    expect(() => validateAutoSyncBranchName('feature@{x')).toThrow('must not contain "@{"');
+    expect(() => validateAutoSyncBranchName('.hidden')).toThrow('hidden');
+    expect(() => validateAutoSyncBranchName('foo/bar.lock')).toThrow('hidden or .lock');
   });
 
   it('extracts safe repository names from remote URLs', () => {
@@ -411,6 +436,7 @@ describe('auto-sync', () => {
   });
 
   it('allows only github, gitlab, and gitee SSH SCP remote URLs', () => {
+    expect(() => validateAutoSyncRemoteUrl('git@github.com:owner/repo')).not.toThrow();
     expect(() => validateAutoSyncRemoteUrl('git@github.com:im-fan/multica.git')).not.toThrow();
     expect(() => validateAutoSyncRemoteUrl('git@gitlab.com:group/subgroup/repo.git')).not.toThrow();
     expect(() =>
diff --git a/gitnexus/test/unit/file-lock.test.ts b/gitnexus/test/unit/file-lock.test.ts
index b02704b10..aba2a2ac5 100644
--- a/gitnexus/test/unit/file-lock.test.ts
+++ b/gitnexus/test/unit/file-lock.test.ts
@@ -65,6 +65,15 @@ describe('file lock', () => {
     const lockPath = await tempLockPath();
     await acquireFileLock(lockPath, { pid: 111, processStartTime: 'old-start' });
 
+    await expect(
+      acquireFileLock(lockPath, {
+        pid: 222,
+        processStartTime: 'next-start',
+        isProcessAlive: () => true,
+        readProcessStartTime: () => 'old-start',
+      }),
+    ).rejects.toBeInstanceOf(FileLockBusyError);
+
     const nextRelease = await acquireFileLock(lockPath, {
       pid: 222,
       processStartTime: 'next-start',
@@ -83,6 +92,23 @@ describe('file lock', () => {
     await expect(fs.access(lockPath)).resolves.toBeUndefined();
   });
 
+  it('recovers when a stale reclaim guard was left by a crashed contender', async () => {
+    const lockPath = await tempLockPath();
+    await acquireFileLock(lockPath, { pid: 999, processStartTime: 'abandoned' });
+    await acquireFileLock(`${lockPath}.reclaim`, {
+      pid: 998,
+      processStartTime: 'abandoned-reclaimer',
+    });
+
+    const release = await acquireFileLock(lockPath, {
+      pid: 1000,
+      processStartTime: 'next',
+      isProcessAlive: () => false,
+    });
+
+    await release();
+  });
+
   it('waits for the current holder when retries are configured', async () => {
     const lockPath = await tempLockPath();
     const release = await acquireFileLock(lockPath);
diff --git a/gitnexus/test/unit/git-clone.test.ts b/gitnexus/test/unit/git-clone.test.ts
index ac3d3b396..cb05792ae 100644
--- a/gitnexus/test/unit/git-clone.test.ts
+++ b/gitnexus/test/unit/git-clone.test.ts
@@ -637,6 +637,29 @@ describe('git-clone', () => {
       }
     });
 
+    it('creates missing nested parents before checking controlled clone containment', async () => {
+      const root = await mkControlledRoot('gitnexus-controlled-root-');
+      const target = path.join(root, 'github.com', 'owner', 'repo');
+      const runGitForTest = vi.fn(async () => {
+        await fs.mkdir(path.join(target, '.git'), { recursive: true });
+        return '';
+      });
+      try {
+        await expect(
+          cloneOrPull('git@github.com:owner/repo', target, undefined, {
+            allowedCloneRoot: root,
+            expectedRepoName: 'repo',
+            allowAutoSyncSsh: true,
+            runGitForTest,
+          }),
+        ).resolves.toBe(target);
+
+        expect(runGitForTest).toHaveBeenCalledOnce();
+      } finally {
+        await fs.rm(root, { recursive: true, force: true });
+      }
+    });
+
     it('allows auto-sync SSH SCP clone URLs with a per-repo timeout', async () => {
       const root = await mkControlledRoot('gitnexus-controlled-root-');
       const target = path.join(root, 'repo');