diff --git a/docs/architecture.md b/docs/architecture.md
index 53863bd..148d420 100644
--- a/docs/architecture.md
+++ b/docs/architecture.md
@@ -106,9 +106,9 @@ Issue 检视结果明确要求代码变更、存在原文证据且无需补充
 
 控制面在自己的数据卷上为每个已启用仓库保留一份 bare mirror（`/data/git-cache/<仓库 ID>.git`，`BOT_GIT_CACHE_DIR` 可改位置），任务不必每次从 GitHub 重新下载整个仓库。任务准备时先把镜像更新到这次要检视或开发的提交，PR 任务还包括读取规则的默认分支提交：镜像里已有这些提交就不访问 GitHub；缺少时按 SHA `git fetch` 这些提交，GitHub 不按 SHA 提供时改取对应的 PR head 或分支 ref，而不是只更新默认分支。同一镜像的更新逐个进行；拉到的每个提交固定在 `refs/bot/commits/<sha>` 下，后续更新和维护不会删掉。安装令牌只作为一次性 HTTP 头经这次 fetch 的进程环境传给 git，只对 GitHub 返回的 clone 地址所在源生效，不写进 remote URL、镜像配置、FETCH_HEAD 或日志，也不进入项目容器；`github_read_token` 仍是只读，语义不变。规则文件和工作区文件随后都从镜像在固定提交上读取，镜像里已有的对象不再逐个调用 GitHub blob API；只有镜像不可用（fetch 失败、仓库没有 clone 地址、拉取后读不出等）或镜像缺某个 blob 时，才回到下面的 Git 数据 API 逐文件读取，任务不会因此失败，日志写明原因。工作副本按文件经 manager 以约 30 KB 分块写进该任务自己的工作目录，两个任务不共用工作目录；runner 校验 blob 与已接收文件的 tree，构建本地 Git 快照，`.git` 里没有 remote 和凭据。副本固定在任务的提交上，之后对镜像的 fetch 不改动已拷出的副本，任务也从不写镜像。副本不是完整上游历史克隆，模型上下文和评论覆盖说明明确标识这一点。文件数超过 2000、单文件超过 1 MiB、合计超过 32 MiB 都不再使准备失败；递归 tree 被截断时丢弃不完整列表，改为逐目录非递归列举。子模块不克隆，子模块和不支持的 Git mode 不下载，日志记录路径和 mode；回到 Git 数据 API 读取时，[GitHub blob API](https://docs.github.com/en/rest/git/blobs#get-a-blob) 支持约 100 MB 以内的 blob，接口明确因文件过大拒绝返回时记录路径、大小和 HTTP 状态并跳过，coverage 列出跳过数量。权限错误、限流和普通 HTTP 错误仍按原有故障处理。跳过条目保留在上游，发布时沿用源 tree 并校验合并后的完整 tree，避免误删。控制面一次仅处理一个文件的内容；快照 blob 下载不受普通 GitHub 响应的 48 MiB 限制，管理接口请求体上限保持不变。runner 的 Git 快照操作不再受 4 MiB 输出缓冲和 60 秒超时限制，读取候选 blob 时落盘后分块返回；模型命令的超时策略不变。初始上下文仍使用 `contextBytes < 100000` 和单文件 12000 字切片，大文件保留在工作区供工具读取。二进制和符号链接按 Git 对象处理，相对文件工具不跟随越界符号链接。哈希不一致、路径越界和工作区被替换仍然失败，说明包含路径、期望与实际 SHA 或具体原因。
 
-任务入队和准备、Agent 执行、策略测试、GitHub 发布阶段开始时即写入任务日志，包含仓库、固定提交 SHA、检视或开发模式、实际测试命令或发布目标；同一次尝试内的阶段开始去重，策略测试按实际命令操作记录，没有策略命令时不写测试开始日志。准备过程中每写完 100 个文件记录已写入数量、字节数和刚写完的路径，每个跳过条目立即记录路径及原因，构建本地 Git 树前再记一条，结束时保留 `snapshot` 汇总，其中记录文件来源（`git_cache` 或 `github_api`）和镜像状态（已有 `hit`、本次拉取 `fetched`、不可用 `unavailable`），跳过说明过长时标明省略条数。Pi 保留模型决策和工具结果事件，并在工具执行前写入 `tool_start`（文件路径、命令或动作名，不含写入内容），经现有 poll 复制到 `task_logs`；runner 在事件落盘前屏蔽已兑换的令牌，控制面继续经 Redactor 脱敏。运行中和成功后、失败或 `waiting_*`、`retry_wait` 的详情均保留完整时间线，故障步骤和侧栏直接展示 fault `detail`，无需打开原始数据；相同故障码、状态和说明在自动重试时只记录一次，自动重试用尽转为失败时另记一条。`src/agent/failures.ts` 把每个故障码归入一类原因并给出下一步，任务和日志接口在读取时附上 `error_cause`／`cause`，旧日志同样适用。GitHub 和模型请求失败写明方法与路径（或模型名与主机）、HTTP 状态、对方的简短说明，以及超时、DNS、连接重置、TLS 等网络原因；GitHub 5xx 附带 `X-GitHub-Request-Id`。日志截断保持合法 JSON，并保留故障说明。
+任务入队和准备、Agent 执行、策略测试、GitHub 发布阶段开始时即写入任务日志，包含仓库、固定提交 SHA、检视或开发模式、实际测试命令或发布目标；同一次尝试内的阶段开始去重，策略测试按实际命令操作记录，没有策略命令时不写测试开始日志。准备过程中每写完 100 个文件记录已写入数量、字节数和刚写完的路径，每个跳过条目立即记录路径及原因，构建本地 Git 树前再记一条，结束时保留 `snapshot` 汇总，其中记录文件来源（`git_cache` 或 `github_api`）和镜像状态（已有 `hit`、本次拉取 `fetched`、不可用 `unavailable`），跳过说明过长时标明省略条数。Pi 保留模型决策和工具结果事件，并在工具执行前写入 `tool_start`（文件路径、命令或动作名，不含写入内容），经现有 poll 复制到 `task_logs`；runner 在事件落盘前屏蔽已兑换的令牌，控制面继续经 Redactor 脱敏。运行中和成功后、失败或 `waiting_*`、`retry_wait` 的详情均保留完整时间线，故障步骤和侧栏直接展示 fault `detail`，无需打开原始数据；相同故障码、状态和说明在自动重试时只记录一次，自动重试用尽转为失败时另记一条。`retry_wait` 的自动重试依次等待 5、15、45、135 秒（限流按 `Retry-After`），第 5 次仍失败转为失败。`src/agent/failures.ts` 把每个故障码归入一类原因并给出下一步，任务和日志接口在读取时附上 `error_cause`／`cause`，旧日志同样适用。GitHub 和模型请求失败写明方法与路径（或模型名与主机）、HTTP 状态、对方的简短说明，以及超时、DNS、连接重置、TLS 等网络原因；GitHub 5xx 附带 `X-GitHub-Request-Id`。日志截断保持合法 JSON，并保留故障说明。
 
-开发候选由容器内 Git 生成，控制面保存候选 tree、文件清单、测试输出与本地提交映射，经 Git 数据 API 上传 blob/tree/commit。只有 GitHub 返回 tree 与已验证候选完全一致，才创建或更新登记的 bot 分支。更新固定 force:false；未知或变化的分支 head 会阻止发布。容器里没有 GitHub remote 认证、私钥或模型 Key；控制面只对仓库镜像运行 git fetch、ls-tree 和 cat-file，不检出代码，也不运行仓库里的脚本或钩子，命令仍不在 bot 宿主机上执行。真实仓库访问仍需为 App／账号提供相应 Contents、Issues 和 Pull requests 权限。
+开发候选由容器内 Git 生成，控制面保存候选 tree、文件清单、测试输出与本地提交映射，经 Git 数据 API 上传 blob/tree/commit。tree 只把改动、新增和删除的路径叠加在源快照的 tree 上（`base_tree`），不再每次列出整个仓库：大仓库的完整清单会让 GitHub 超过单个请求 10 秒的处理上限，每次重试都返回 502/504。路径在文件和目录之间转换，或 GitHub 算出的 tree 与候选不一致时，退回完整清单。只有 GitHub 返回 tree 与已验证候选完全一致，才创建或更新登记的 bot 分支。更新固定 force:false；未知或变化的分支 head 会阻止发布。容器里没有 GitHub remote 认证、私钥或模型 Key；控制面只对仓库镜像运行 git fetch、ls-tree 和 cat-file，不检出代码，也不运行仓库里的脚本或钩子，命令仍不在 bot 宿主机上执行。真实仓库访问仍需为 App／账号提供相应 Contents、Issues 和 Pull requests 权限。
 
 评论、Review、分支和 PR 都有持久 outbox。请求结果未知时按任务 marker、head 和远端对象先对账；未能确认就保持 waiting_publication，不盲目重复；人工重试视为确认，结果未知的写入先再对账一次，仍查不到才重新发送。分支已推送后，基础分支前进不再阻止创建对应 PR。控制面重启后恢复未完成阶段，已完成任务不重新入队；manager 中断的命令不当作通过，重新检查环境后在新 attempt 工作目录继续，旧目录保留。同代已完成工具通过原操作 ID 回放，generation 变化会阻止旧任务直接写入新环境。
 
diff --git a/src/agent/engine.ts b/src/agent/engine.ts
index 462d645..4bf152b 100644
--- a/src/agent/engine.ts
+++ b/src/agent/engine.ts
@@ -306,7 +306,10 @@ export class TaskEngine {
       const failure=error instanceof TaskError?error:new TaskError('task_runtime_failure',String((error as Error)?.message).includes('manager')?'waiting_environment':'failed',`任务在 ${task.phase} 阶段发生运行异常：${redactor.text(String((error as Error)?.message||'未知错误')).replace(/\s+/g,' ').slice(0,300)}`);
       const current=this.store.get('SELECT * FROM tasks WHERE id=?',id);
       const retries=Number(current?.retry_count||0)+(failure.state==='retry_wait'?1:0),state=failure.state==='retry_wait'&&retries>=5?'failed':failure.state;
-      const delay=failure.code==='github_rate_limited'?(failure.retryAfterMs??60000):state==='waiting_configuration'?30000:5000;
+      // Automatic retries back off (5 s, 15 s, 45 s, 135 s), so a GitHub or model outage of a few minutes is outlasted
+      // instead of using up all five attempts in half a minute.
+      const delay=failure.code==='github_rate_limited'?(failure.retryAfterMs??60000):state==='waiting_configuration'?30000
+        :state==='retry_wait'?Math.min(5000*3**(retries-1),300000):5000;
       if(current?.claim_token===token&&!['cancelled','superseded'].includes(current.status))update({status:state,error_code:failure.code,retry_count:retries,next_run_at:Date.now()+delay});
       if(failure.code==='execution_interrupted'&&task.phase!=='publish'&&task.attempt<3){
         log({type:'restart_attempt',preserved_workspace:task.workspace_id});
diff --git a/src/agent/failures.ts b/src/agent/failures.ts
index 85a62ab..58e8050 100644
--- a/src/agent/failures.ts
+++ b/src/agent/failures.ts
@@ -62,7 +62,7 @@ const codeActions: Record<string,string> = {
 };
 const causeActions: Record<FailureCause,(state:string)=>string> = {
   external: state => automatic.has(state) ? '不是配置问题，bot 会自动重试，一般无需处理。'
-    : '已自动重试多次仍失败。确认 GitHub、模型服务和网络恢复后点「重试」。',
+    : '已自动重试 5 次仍失败。先看 GitHub 状态页、模型服务和网络是否正常；都正常而同一个请求反复返回 502/504 时，多半是请求太大或太慢（GitHub 处理单个请求超过 10 秒会中止），请把任务链接反馈给 bot 维护者。恢复后点「重试」。',
   github_access: () => '按说明核对 GitHub App 是否安装到该仓库、授权的权限和仓库范围、账号凭据是否有效，' + retry,
   github_rejected: () => 'GitHub 收到了请求但不接受，通常是仓库当前状态与请求冲突（例如分支或 PR 已存在、分支保护规则）。按说明核对仓库后点「重试」；无法解释时请反馈给 bot 维护者。',
   model: () => '检查项目的模型地址、模型名和 API Key；模型输出不符合要求时可以点「重试」，或换用其他模型。',
diff --git a/src/github/publisher.ts b/src/github/publisher.ts
index 638f558..2b31934 100644
--- a/src/github/publisher.ts
+++ b/src/github/publisher.ts
@@ -73,16 +73,22 @@ export class Publisher {
       const blob=await this.github.request('POST',this.github.path('/git/blobs'),{content:file.base64,encoding:'base64'});
       if(blob.sha!==file.sha)stop('github_blob_mismatch',undefined,`GitHub 写入文件 ${file.path} 后返回的 SHA 不一致：预期 ${file.sha}，实际 ${blob.sha}。`);
     }
-    const entries=candidate.files.map((f:any)=>({path:f.path,mode:f.mode,type:'blob',sha:f.sha}));
-    let expected=candidate.tree_sha;
-    if(candidate.skipped_files?.length){
-      // Keep excluded upstream entries, including blobs GitHub will not let us download.
-      // Hashing the merged manifest also rejects a candidate that overwrites an excluded path.
-      expected=treeSha([...candidate.files,...candidate.skipped_files]);
-      const paths=new Set(candidate.files.map((f:any)=>f.path));
-      for(const file of candidate.snapshot_files)if(!paths.has(file.path))entries.push({path:file.path,mode:file.mode,type:'blob',sha:null});
-    }
-    const tree=await this.github.request('POST',this.github.path('/git/trees'),{...(candidate.skipped_files?.length?{base_tree:candidate.source_tree}:{}),tree:entries});
+    // Skipped upstream entries (submodules, blobs GitHub will not let us download) stay as they are in the source tree.
+    // Hashing the merged manifest also rejects a candidate that overwrites an excluded path.
+    const skipped=candidate.skipped_files||[],expected=skipped.length?treeSha([...candidate.files,...skipped]):candidate.tree_sha;
+    const entry=(f:any,sha=f.sha)=>({path:f.path,mode:f.mode,type:'blob',sha});
+    const snapshot=candidate.snapshot_files||[],upstream=new Map<string,any>(snapshot.map((f:any)=>[f.path,f])),paths=new Set(candidate.files.map((f:any)=>f.path));
+    const deletions=snapshot.filter((f:any)=>!paths.has(f.path)).map((f:any)=>entry(f,null));
+    const changes=candidate.files.filter((f:any)=>upstream.get(f.path)?.sha!==f.sha||upstream.get(f.path)?.mode!==f.mode).map((f:any)=>entry(f));
+    // Rebuilding a large repository's tree from every path can take GitHub longer than its 10-second request limit,
+    // which answers 502/504 on every retry, so only the changes go on top of the source tree. A path that turns from a
+    // file into a directory or back is not an update GitHub applies the same way; it, and any tree GitHub builds
+    // differently, falls back to the complete listing.
+    const before=[...upstream.keys(),...skipped.map((f:any)=>f.path)],files=new Set(before),directories=new Set(before.flatMap(parents));
+    const reshaped=changes.some((f:any)=>directories.has(f.path)||parents(f.path).some(path=>files.has(path)));
+    const create=(body:any)=>this.github.request('POST',this.github.path('/git/trees'),body);
+    let tree=candidate.source_tree&&changes.length+deletions.length&&!reshaped?await create({base_tree:candidate.source_tree,tree:[...changes,...deletions]}):null;
+    if(tree?.sha!==expected)tree=await create(skipped.length?{base_tree:candidate.source_tree,tree:[...candidate.files.map((f:any)=>entry(f)),...deletions]}:{tree:candidate.files.map((f:any)=>entry(f))});
     if(tree.sha!==expected)stop('github_tree_mismatch',undefined,`GitHub 创建的文件树不一致：预期 ${expected}，实际 ${tree.sha}。`);
     candidate.published_tree_sha=expected;
     const author={name:'Department Bot',email:this.github.authorEmail(),date:candidate.date};
@@ -136,6 +142,9 @@ export class Publisher {
   }
 }
 
+// a/b/c.txt -> ['a','a/b']
+function parents(path:string):string[]{const parts=path.split('/');return parts.slice(1).map((_,index)=>parts.slice(0,index+1).join('/'));}
+
 export function assertOwnedPR(owned:Row|undefined,pr:any,actorId:string,repositoryId:string): asserts owned is Row {
   if(!owned)throw new TaskError('bot_pr_identity_changed','waiting_permission',`PR #${pr.number} 没有对应的机器人归属记录。`);
   if(String(pr.id)!==owned.pr_id)stop('bot_pr_identity_changed','waiting_permission',`PR #${pr.number} 的标识与已登记的 PR ${owned.pr_id} 不一致。`);
diff --git a/test/agent-process.test.mjs b/test/agent-process.test.mjs
index f87aa9c..c97b2c0 100644
--- a/test/agent-process.test.mjs
+++ b/test/agent-process.test.mjs
@@ -337,6 +337,8 @@ test('create_pull_request with empty policy never reruns agent evidence and retu
   const state = await fetch(d.endpoint + '/fixture/state').then(r => r.json());
   assert.match(state.prs.at(-1).body, /Tests: agent-already-ran-tests/);
   assert.match(state.prs.at(-1).body, /not rerun by the control plane/); assert.doesNotMatch(state.prs.at(-1).body, /Exit code:/);
+  // Only the one edited file goes to GitHub, on top of the snapshot's source tree, and GitHub's tree is the verified one.
+  assert.deepEqual(state.trees.at(-1), { repository_id: 101, base_tree: d.candidate.source_tree, entries: 1 });
 });
 
 test('a later call for the same Issue appends to the same bot branch and PR', async t => {
diff --git a/test/failure-causes.test.mjs b/test/failure-causes.test.mjs
index 63cedd8..8edd4f9 100644
--- a/test/failure-causes.test.mjs
+++ b/test/failure-causes.test.mjs
@@ -98,13 +98,17 @@ test('a write that landed despite a 500 is found on retry and never sent twice',
   h.due();const task=await h.run();assert.deepEqual([task.status,h.comments.length],['succeeded',1]);
 });
 
-test('the retry that gives up is logged as its own 失败 entry with the next step',async t=>{
+test('automatic retries back off, and the retry that gives up is logged as its own 失败 entry with the next step',async t=>{
   const h=await emptyRepositoryFixture(t,{github(path,send){if(path!=='/user')return false;send({message:'Server Error'},502);return true;}});
-  for(let attempt=1;attempt<=5;attempt++){h.due();await h.run();}
+  for(let attempt=1;attempt<=5;attempt++){
+    h.due();const before=Date.now(),task=await h.run(),after=Date.now();if(attempt===5)break;
+    // Automatic retries back off: 5 s, 15 s, 45 s, 135 s.
+    const delay=5000*3**(attempt-1);assert.ok(task.next_run_at>=before+delay&&task.next_run_at<=after+delay,`attempt ${attempt}`);
+  }
   const task=h.store.get('SELECT * FROM tasks WHERE id=?',h.taskId);assert.deepEqual([task.status,task.error_code,task.retry_count],['failed','github_http_502',5]);
   assert.deepEqual(faults(h).map(log=>log.state),['retry_wait','failed']);
   assert.equal(faults(h)[1].detail,'GitHub 请求 GET /user 返回 HTTP 502：Server Error');
-  const detail=(await h.admin('/api/tasks/'+h.taskId)).value.task;assert.equal(detail.error_cause.cause,'external');assert.match(detail.error_cause.action,/已自动重试多次仍失败/);
+  const detail=(await h.admin('/api/tasks/'+h.taskId)).value.task;assert.equal(detail.error_cause.cause,'external');assert.match(detail.error_cause.action,/已自动重试 5 次仍失败/);
 });
 
 test('model failures name the model, its host and the provider explanation without the key',async t=>{
diff --git a/test/fixtures/agent-server.mjs b/test/fixtures/agent-server.mjs
index 37e4063..f012a56 100644
--- a/test/fixtures/agent-server.mjs
+++ b/test/fixtures/agent-server.mjs
@@ -24,7 +24,7 @@ function makeRepo(id){
 }
 for(const id of ['101','202','303'])repositories.set(id,makeRepo(id));
 let config={github_token:'',model_key:''},treeMismatch=false,staled=false,dropComment=true,pullFailures=0;
-const stats={requests:[],models,refWrites:[],reviews:[],comments:[],prs:[],labels:[]};
+const stats={requests:[],models,refWrites:[],reviews:[],comments:[],prs:[],labels:[],trees:[]};
 const call=(name,args,id)=>({id:'call-'+id,type:'function',function:{name,arguments:JSON.stringify(args)}});
 function model(input){
   const raw=input.messages.find(m=>m.role==='user').content,context=JSON.parse(Array.isArray(raw)?raw.map(c=>c.text||'').join(''):raw),repoId=context.repository.split('-').at(-1),repo=repositories.get(repoId),number=context.object.number;
@@ -132,7 +132,14 @@ export const server=createServer(async(req,res)=>{
     if((m=/^\/git\/trees\/(.+)$/.exec(suffix))){const files=trees.get(m[1]);return send({sha:m[1],tree:files.map(f=>({...f,size:blobs.get(f.sha).length})),truncated:false});}
     if((m=/^\/git\/blobs\/(.+)$/.exec(suffix))){const data=blobs.get(m[1]);return send({sha:m[1],size:data.length,encoding:'base64',content:data.toString('base64')});}
     if(suffix==='/git/blobs')return send({sha:blob(Buffer.from(body.content,'base64'))},201);
-    if(suffix==='/git/trees'){const hash=treeHash(body.tree);trees.set(hash,body.tree);return send({sha:treeMismatch?'f'.repeat(40):hash},201);}
+    if(suffix==='/git/trees'){
+      // Like GitHub: entries update the base tree, a null sha removes a path, and empty directories disappear.
+      if(body.base_tree&&!trees.has(body.base_tree))return send({message:'base_tree not found'},422);
+      let files=body.base_tree?[...trees.get(body.base_tree)]:[];
+      for(const entry of body.tree){files=files.filter(f=>f.path!==entry.path);if(entry.sha)files.push(entry);}
+      const hash=treeHash(files);trees.set(hash,files);stats.trees.push({repository_id:repo.id,base_tree:body.base_tree||null,entries:body.tree.length});
+      return send({sha:treeMismatch?'f'.repeat(40):hash},201);
+    }
     if(suffix==='/git/commits'){const sha=objectHash('commit',Buffer.from(JSON.stringify(body))),value={sha,tree:{sha:body.tree},parents:body.parents.map(sha=>({sha}))};commits.set(sha,value);return send(value,201);}
     if(suffix.startsWith('/compare/'))return send({status:'ahead'});
     return send({},404);
diff --git a/test/workspace-snapshot.test.mjs b/test/workspace-snapshot.test.mjs
index 822e61f..80cd553 100644
--- a/test/workspace-snapshot.test.mjs
+++ b/test/workspace-snapshot.test.mjs
@@ -271,3 +271,36 @@ test('publishing a partial snapshot preserves excluded upstream paths and verifi
   assert.equal(writes.find(write=>write.path==='/git/commits').body.tree,expected);
   assert.equal(treeSha([file,...skipped]),expected);
 });
+
+// Publish a candidate through a GitHub double whose tree answers come from `trees` in order.
+async function publishTree(t,{files,snapshot,trees}){
+  const h=await emptyRepositoryFixture(t),branch='bot/issue-1-tree',source='d'.repeat(40),writes=[];
+  h.store.run('INSERT INTO bot_branches VALUES(?,?,?)','101',branch,h.taskId);
+  const expected=treeHash(files),answers=[...trees(expected)];
+  const github={defaultBranch:'main',path:path=>path,authorEmail:()=> '999+fixture-bot@users.noreply.github.com',ref:async()=>null,
+    async request(_method,path,body){writes.push({path,body});if(path==='/git/blobs')return {sha:body.sha||files.find(f=>f.base64===body.content).sha};
+      if(path==='/git/trees')return {sha:answers.shift()};if(path==='/git/commits')return {sha:'e'.repeat(40),tree:{sha:expected}};if(path==='/git/refs')return {object:{sha:'e'.repeat(40)}};assert.fail(path);}};
+  const candidate={branch,owner_task_id:h.taskId,files,skipped_files:[],snapshot_files:snapshot,source_tree:source,tree_sha:expected,base_sha:commit,date:new Date().toISOString(),
+    summary:'Update source',test_command:'true',validation:{source:'agent',skipped:true,command:'true'}};
+  await new Publisher(h.store,github,h.store.get('SELECT * FROM tasks WHERE id=?',h.taskId),async()=>{}).branch(candidate);
+  return {source,trees:writes.filter(write=>write.path==='/git/trees').map(write=>write.body)};
+}
+
+test('a change in a large repository sends GitHub only the changed paths on top of the source tree',async t=>{
+  const unchanged=Array.from({length:5000},(_,i)=>entry(`src/${i%50}/file-${i}.txt`,Buffer.from('same '+i)));
+  const old=entry('src/changed.txt',Buffer.from('old')),data=Buffer.from('new'),changed={...entry('src/changed.txt',data),base64:data.toString('base64')};
+  const removed=entry('docs/obsolete.md',Buffer.from('gone')),added={...entry('docs/new.md',data),base64:data.toString('base64')},executable={...unchanged[0],mode:'100755'};
+  const {source,trees}=await publishTree(t,{files:[executable,...unchanged.slice(1),changed,added],snapshot:[...unchanged,old,removed],trees:expected=>[expected]});
+  assert.equal(trees.length,1);assert.equal(trees[0].base_tree,source);
+  assert.deepEqual(trees[0].tree.map(e=>[e.path,e.mode,e.sha]).sort(),[[added.path,'100644',added.sha],[removed.path,'100644',null],[changed.path,'100644',changed.sha],[executable.path,'100755',executable.sha]].sort());
+});
+
+test('a path that turns from a file into a directory, or a tree GitHub builds differently, uses the complete listing',async t=>{
+  const data=Buffer.from('x'),readme={...entry('docs/readme.md',data),base64:data.toString('base64')},kept=entry('keep.txt',Buffer.from('k'));
+  let result=await publishTree(t,{files:[kept,readme],snapshot:[kept,entry('docs',Buffer.from('was a file'))],trees:expected=>[expected]});
+  assert.equal(result.trees.length,1);assert.equal(result.trees[0].base_tree,undefined);assert.deepEqual(result.trees[0].tree.map(e=>e.path).sort(),['docs/readme.md','keep.txt']);
+  const changed={...entry('keep.txt',data),base64:data.toString('base64')};
+  result=await publishTree(t,{files:[changed],snapshot:[kept],trees:expected=>['f'.repeat(40),expected]});
+  assert.equal(result.trees.length,2);assert.equal(result.trees[0].base_tree,result.source);assert.equal(result.trees[1].base_tree,undefined);
+  await assert.rejects(publishTree(t,{files:[changed],snapshot:[kept],trees:()=>['f'.repeat(40),'f'.repeat(40)]}),/github_tree_mismatch/);
+});