fix(lightweight-extension): 环境激活、前缀重命名、数据复制与上传进度

- service.py: _make_env 用 conda run 激活环境（执行 activate.d，补 PYTHONPATH）
- index_ml.html: 环境下拉框动态加载 + 补传 runtime_env
- runtime_binding.py: 前缀误判修复、放宽 ambiguous、can_rename 判断、子目录数据复制补 mkdir
- api.py: 缺输出目录时友好提示
- main.py + lightWeightExtensionTest.js: run.sh 环境声明 # lightweight-env
- index.html/index_ml.html: 拖拽上传进度条

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

apps/web/vue3/index.html

@@ -1422,6 +1422,12 @@
                                 placeholder="大文件可直接引用；每行填写一个绝对路径">
                             </el-input>
                         </div>
+                        <div v-if="lightweightUploadProgress.active" style="margin-top:9px;">
+                            <el-progress :percentage="lightweightUploadProgress.percent" :stroke-width="8"></el-progress>
+                            <div style="font-size:11px;color:#909399;margin-top:4px;">
+                                {{ lightweightUploadProgress.label }} · {{ formatBytes(lightweightUploadProgress.loaded) }} / {{ formatBytes(lightweightUploadProgress.total) }} · {{ formatBytes(lightweightUploadProgress.speed) }}/s
+                            </div>
+                        </div>
                         <div style="display:flex; gap:6px; margin-top:9px; align-items:center; justify-content:space-between; flex-wrap:nowrap;">
                             <el-button
                                 type="primary"
@@ -9148,6 +9154,14 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                     statusEvents: []
                 });
                 const extensionEnvOptions = ref(['test4py311', 'rnaseq', 'rnaR']);
+                const lightweightUploadProgress = reactive({
+                    active: false,
+                    percent: 0,
+                    loaded: 0,
+                    total: 0,
+                    speed: 0,
+                    label: '',
+                });
                 const lightweightExtensions = ref([]);
                 const lightweightExtensionConversation = reactive({
                     cards: [],
@@ -19508,6 +19522,13 @@ compare: [[flesh, peel]]`;
                     ElMessage.error('上传失败: ' + err.message);
                 };
 
+                const formatBytes = (bytes) => {
+                    if (!Number.isFinite(bytes) || bytes <= 0) return '0 B';
+                    const units = ['B', 'KB', 'MB', 'GB', 'TB'];
+                    const i = Math.min(Math.floor(Math.log(bytes) / Math.log(1024)), units.length - 1);
+                    const v = bytes / Math.pow(1024, i);
+                    return `${v >= 10 || i === 0 ? v.toFixed(0) : v.toFixed(1)} ${units[i]}`;
+                };
                 const extensionFileKey = (file) => `${file?.name || ''}::${file?.size || 0}::${file?.lastModified || 0}`;
                 const extensionUploadPath = (file) => {
                     const relative = String(file?.lightweightRelativePath || '').trim().replace(/^\/+/, '');
@@ -19623,6 +19644,36 @@ compare: [[flesh, peel]]`;
                     return port ? `${window.location.protocol}//${host}:${port}${value}` : `${window.location.protocol}//${host}${value}`;
                 };
                 const extensionApiFetch = async (path, options = {}) => fetch(extensionApiUrl(path), options);
+                const uploadExtensionWithProgress = (path, body, label, headers = {}) => {
+                    let lastLoaded = 0, lastTime = Date.now();
+                    const p = lightweightUploadProgress;
+                    p.active = true; p.percent = 0; p.loaded = 0; p.total = 0; p.speed = 0; p.label = label;
+                    return new Promise((resolve, reject) => {
+                        const xhr = new XMLHttpRequest();
+                        xhr.open('POST', extensionApiUrl(path));
+                        Object.entries(headers).forEach(([k, v]) => xhr.setRequestHeader(k, v));
+                        xhr.upload.onprogress = (e) => {
+                            if (!e.lengthComputable) return;
+                            const now = Date.now(), dt = now - lastTime;
+                            if (dt >= 200) { p.speed = (e.loaded - lastLoaded) / (dt / 1000); lastLoaded = e.loaded; lastTime = now; }
+                            p.loaded = e.loaded; p.total = e.total;
+                            p.percent = e.total > 0 ? Math.min(100, Math.round((e.loaded / e.total) * 100)) : 0;
+                        };
+                        xhr.onload = () => {
+                            p.active = false;
+                            resolve({
+                                ok: xhr.status >= 200 && xhr.status < 300,
+                                status: xhr.status,
+                                statusText: xhr.statusText,
+                                json: () => Promise.resolve().then(() => JSON.parse(xhr.responseText)),
+                                text: () => Promise.resolve(xhr.responseText),
+                            });
+                        };
+                        xhr.onerror = () => { p.active = false; reject(new Error('上传失败：网络错误')); };
+                        xhr.onabort = () => { p.active = false; reject(new Error('上传已取消')); };
+                        xhr.send(body);
+                    });
+                };
                 const pushExtensionStatus = (message, type = 'info', showDialog = false) => {
                     const text = String(message || '');
                     extensionBuild.statusText = text;
@@ -19985,7 +20036,7 @@ compare: [[flesh, peel]]`;
                         extensionBuild.dataFiles.forEach(file => form.append('raw_data_files', file, extensionUploadPath(file)));
                         if (hasDataPaths) form.append('raw_data_paths', extensionBuild.dataPaths);
                         form.append('runtime_env', extensionBuild.runtimeEnv);
-                        const response = await extensionApiFetch('/api/lightweight-extension-stages/upload', { method: 'POST', body: form });
+                        const response = await uploadExtensionWithProgress('/api/lightweight-extension-stages/upload', form, '正在上传拓展包');
                         if (!response.ok) throw new Error(await extensionApiError(response, '原始包可复现检查提交失败'));
                         ElMessage.success('文件上传成功，已开始生成并验收');
                         rememberLightweightOperation(extensionId, 'upload', token, card.card_id);
@@ -23805,6 +23856,7 @@ compare: [[flesh, peel]]`;
                     uploadedFiles,
                     extensionBuild,
                     extensionEnvOptions,
+                    lightweightUploadProgress,
                     extensionStages,
                     extensionCompletedStages,
                     lightweightExtensionConversation,
@@ -23821,6 +23873,7 @@ compare: [[flesh, peel]]`;
                     cancelExtensionRunParameters,
                     confirmExtensionRunParameters,
                     extensionFileKey,
+                    formatBytes,
                     onExtensionCodeFilesChange,
                     onExtensionDataFilesChange,
                     handleLightweightExtensionFolderDrop,
@@ -23971,6 +24024,7 @@ compare: [[flesh, peel]]`;
                         appendExtensionFiles,
                         buildLightweightExtensionStage,
                         lightweightExtensionTestStatus,
+                        uploadExtensionWithProgress,
                     }, event),
                     handleLightweightExtensionFolderPick: (event) => window.LightWeightExtensionTest && window.LightWeightExtensionTest.handlePick({
                         jobInfo,
@@ -23979,6 +24033,7 @@ compare: [[flesh, peel]]`;
                         appendExtensionFiles,
                         buildLightweightExtensionStage,
                         lightweightExtensionTestStatus,
+                        uploadExtensionWithProgress,
                     }, event),
                     openLightweightExtensionFolderPicker: () => window.LightWeightExtensionTest && window.LightWeightExtensionTest.openPicker(),
                     // Working DirectorySelect

apps/web/vue3/index_ml.html

@@ -1397,10 +1397,8 @@
                             <span>{{ t('名称') }}</span><el-input v-model="extensionBuild.displayName" size="small" placeholder="例如 HMMER hmmsearch"></el-input>
                             <span>{{ t('原始命令') }}</span><el-input v-model="extensionBuild.command" size="small" placeholder="例如 bash run.sh input.fa"></el-input>
                             <span>{{ t('环境') }}</span>
-                            <el-select v-model="extensionBuild.runtimeEnv" size="small">
-                                <el-option label="test4py311" value="test4py311"></el-option>
-                                <el-option label="rnaseq" value="rnaseq"></el-option>
-                                <el-option label="rnaR" value="rnaR"></el-option>
+                            <el-select v-model="extensionBuild.runtimeEnv" size="small" filterable>
+                                <el-option v-for="env in extensionEnvOptions" :key="env" :label="env" :value="env"></el-option>
                             </el-select>
                             <span>{{ t('原始代码') }}</span><input type="file" multiple @change="onExtensionCodeFilesChange" style="font-size:12px; min-width:0;">
                             <span v-if="extensionBuild.codeFiles.length"></span>
@@ -1426,6 +1424,12 @@
                                 placeholder="大文件可直接引用；每行填写一个绝对路径">
                             </el-input>
                         </div>
+                        <div v-if="lightweightUploadProgress.active" style="margin-top:9px;">
+                            <el-progress :percentage="lightweightUploadProgress.percent" :stroke-width="8"></el-progress>
+                            <div style="font-size:11px;color:#909399;margin-top:4px;">
+                                {{ lightweightUploadProgress.label }} · {{ formatBytes(lightweightUploadProgress.loaded) }} / {{ formatBytes(lightweightUploadProgress.total) }} · {{ formatBytes(lightweightUploadProgress.speed) }}/s
+                            </div>
+                        </div>
                         <div style="display:flex; gap:6px; margin-top:9px; align-items:center; justify-content:space-between; flex-wrap:nowrap;">
                             <el-button
                                 type="primary"
@@ -9200,6 +9204,15 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                     statusDialogVisible: false,
                     statusEvents: []
                 });
+                const extensionEnvOptions = ref(['test4py311', 'rnaseq', 'rnaR']);
+                const lightweightUploadProgress = reactive({
+                    active: false,
+                    percent: 0,
+                    loaded: 0,
+                    total: 0,
+                    speed: 0,
+                    label: '',
+                });
                 const lightweightExtensions = ref([]);
                 const lightweightExtensionConversation = reactive({
                     cards: [],
@@ -9252,6 +9265,18 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                     extensionBuild.runtimeEnv = (item.runtime && item.runtime.env) || extensionBuild.runtimeEnv || 'test4py311';
                     extensionBuild.nlTriggersText = (item.nl_triggers || []).join(', ');
                 };
+                const loadExtensionEnvOptions = async () => {
+                    try {
+                        const response = await extensionApiFetch('/api/extension-stages/envs');
+                        if (!response.ok) return;
+                        const data = await response.json();
+                        if (data.success && Array.isArray(data.envs) && data.envs.length) {
+                            extensionEnvOptions.value = data.envs;
+                        }
+                    } catch (err) {
+                        console.warn('[extension env options] load failed', err);
+                    }
+                };
                 const extensionRuns = ref([]);
                 const extensionResultDialogVisible = ref(false);
                 const extensionRun = reactive({
@@ -19325,6 +19350,13 @@ compare: [[flesh, peel]]`;
                     ElMessage.error('上传失败: ' + err.message);
                 };
 
+                const formatBytes = (bytes) => {
+                    if (!Number.isFinite(bytes) || bytes <= 0) return '0 B';
+                    const units = ['B', 'KB', 'MB', 'GB', 'TB'];
+                    const i = Math.min(Math.floor(Math.log(bytes) / Math.log(1024)), units.length - 1);
+                    const v = bytes / Math.pow(1024, i);
+                    return `${v >= 10 || i === 0 ? v.toFixed(0) : v.toFixed(1)} ${units[i]}`;
+                };
                 const extensionFileKey = (file) => `${file?.name || ''}::${file?.size || 0}::${file?.lastModified || 0}`;
                 const extensionUploadPath = (file) => {
                     const relative = String(file?.lightweightRelativePath || '').trim().replace(/^\/+/, '');
@@ -19439,6 +19471,36 @@ compare: [[flesh, peel]]`;
                     return `${window.location.protocol}//${host}:${window.location.port}${value}`;
                 };
                 const extensionApiFetch = async (path, options = {}) => fetch(extensionApiUrl(path), options);
+                const uploadExtensionWithProgress = (path, body, label, headers = {}) => {
+                    let lastLoaded = 0, lastTime = Date.now();
+                    const p = lightweightUploadProgress;
+                    p.active = true; p.percent = 0; p.loaded = 0; p.total = 0; p.speed = 0; p.label = label;
+                    return new Promise((resolve, reject) => {
+                        const xhr = new XMLHttpRequest();
+                        xhr.open('POST', extensionApiUrl(path));
+                        Object.entries(headers).forEach(([k, v]) => xhr.setRequestHeader(k, v));
+                        xhr.upload.onprogress = (e) => {
+                            if (!e.lengthComputable) return;
+                            const now = Date.now(), dt = now - lastTime;
+                            if (dt >= 200) { p.speed = (e.loaded - lastLoaded) / (dt / 1000); lastLoaded = e.loaded; lastTime = now; }
+                            p.loaded = e.loaded; p.total = e.total;
+                            p.percent = e.total > 0 ? Math.min(100, Math.round((e.loaded / e.total) * 100)) : 0;
+                        };
+                        xhr.onload = () => {
+                            p.active = false;
+                            resolve({
+                                ok: xhr.status >= 200 && xhr.status < 300,
+                                status: xhr.status,
+                                statusText: xhr.statusText,
+                                json: () => Promise.resolve().then(() => JSON.parse(xhr.responseText)),
+                                text: () => Promise.resolve(xhr.responseText),
+                            });
+                        };
+                        xhr.onerror = () => { p.active = false; reject(new Error('上传失败：网络错误')); };
+                        xhr.onabort = () => { p.active = false; reject(new Error('上传已取消')); };
+                        xhr.send(body);
+                    });
+                };
                 const pushExtensionStatus = (message, type = 'info', showDialog = false) => {
                     const text = String(message || '');
                     extensionBuild.statusText = text;
@@ -19800,7 +19862,8 @@ compare: [[flesh, peel]]`;
                         extensionBuild.codeFiles.forEach(file => form.append('raw_code_files', file, extensionUploadPath(file)));
                         extensionBuild.dataFiles.forEach(file => form.append('raw_data_files', file, extensionUploadPath(file)));
                         if (hasDataPaths) form.append('raw_data_paths', extensionBuild.dataPaths);
-                        const response = await extensionApiFetch('/api/lightweight-extension-stages/upload', { method: 'POST', body: form });
+                        form.append('runtime_env', extensionBuild.runtimeEnv);
+                        const response = await uploadExtensionWithProgress('/api/lightweight-extension-stages/upload', form, '正在上传拓展包');
                         if (!response.ok) throw new Error(await extensionApiError(response, t('原始包可复现检查提交失败')));
                         ElMessage.success(t('文件上传成功，已开始生成并验收'));
                         rememberLightweightOperation(extensionId, 'upload', token, card.card_id);
@@ -23225,6 +23288,7 @@ compare: [[flesh, peel]]`;
                     startAgentTaskPolling();
                     startRuntimeMonitor();
                     loadExtensionStages();
+                    loadExtensionEnvOptions();
                     loadLightweightExtensionStages();
                     resumeLightweightOperation();
                     loadExtensionRuns();
@@ -23556,6 +23620,8 @@ compare: [[flesh, peel]]`;
                     intentHistory,
                     uploadedFiles,
                     extensionBuild,
+                    extensionEnvOptions,
+                    lightweightUploadProgress,
                     extensionStages,
                     extensionCompletedStages,
                     lightweightExtensionConversation,
@@ -23572,6 +23638,7 @@ compare: [[flesh, peel]]`;
                     cancelExtensionRunParameters,
                     confirmExtensionRunParameters,
                     extensionFileKey,
+                    formatBytes,
                     onExtensionCodeFilesChange,
                     onExtensionDataFilesChange,
                     removeExtensionFile,
@@ -23593,6 +23660,7 @@ compare: [[flesh, peel]]`;
                     validateExtensionStage,
                     publishExtensionStage,
                     loadExtensionStages,
+                    loadExtensionEnvOptions,
                     loadExtensionRuns,
                     runExtensionStage,
                     runExtensionStageFromIntent,
@@ -23607,6 +23675,7 @@ compare: [[flesh, peel]]`;
                         appendExtensionFiles,
                         buildLightweightExtensionStage,
                         lightweightExtensionTestStatus,
+                        uploadExtensionWithProgress,
                     }, event),
                     handleLightweightExtensionFolderPick: (event) => window.LightWeightExtensionTest && window.LightWeightExtensionTest.handlePick({
                         jobInfo,
@@ -23615,6 +23684,7 @@ compare: [[flesh, peel]]`;
                         appendExtensionFiles,
                         buildLightweightExtensionStage,
                         lightweightExtensionTestStatus,
+                        uploadExtensionWithProgress,
                     }, event),
                     openLightweightExtensionFolderPicker: () => window.LightWeightExtensionTest && window.LightWeightExtensionTest.openPicker(),
                     methodologyPaperId,

apps/web/vue3/lightWeightExtensionTest.js

@@ -124,6 +124,17 @@
         };
     }
 
+    async function extractEnvDeclaration(files) {
+        for (const file of files) {
+            const path = normalizedRelativePath(file).toLowerCase();
+            if (!path.endsWith('.sh')) continue;
+            const content = await file.text();
+            const m = content.match(/^\s*#\s*lightweight-env\s*:\s*([A-Za-z0-9_.-]+)/m);
+            if (m) return m[1];
+        }
+        return null;
+    }
+
     async function encodeBase64(file) {
         const buffer = await file.arrayBuffer();
         const bytes = new Uint8Array(buffer);
@@ -146,11 +157,12 @@
             payload.files.push(await encodeBase64(file));
             payload.relative_paths.push(normalizedRelativePath(file));
         }
-        const response = await fetch('/api/job/import-folder', {
-            method: 'POST',
-            headers: { 'Content-Type': 'application/json' },
-            body: JSON.stringify(payload),
-        });
+        const response = await hooks.uploadExtensionWithProgress(
+            '/api/job/import-folder',
+            JSON.stringify(payload),
+            '正在镜像导入 Job',
+            { 'Content-Type': 'application/json' },
+        );
         const data = await response.json();
         if (!response.ok || !data.success) {
             throw new Error(data.detail || data.error || data.message || 'Job 导入失败');
@@ -160,6 +172,8 @@
 
     async function resolveRuntimeEnv(files) {
         const dependencies = await extractDependencies(files);
+        const envDeclaration = await extractEnvDeclaration(files);
+        if (envDeclaration) dependencies.env_declaration = envDeclaration;
         console.log('[lightWeightExtensionTest] 提取的依赖:', JSON.stringify(dependencies), '| 扫描文件数:', files.length);
         try {
             const response = await fetch('/api/extension-stages/envs/resolve', {

apps/web/vue3/main.py

@@ -8919,6 +8919,7 @@ class ExtensionStageResolveIntentRequest(BaseModel):
 class ExtensionStageEnvResolveRequest(BaseModel):
     python_imports: List[str] = Field(default_factory=list)
     r_packages: List[str] = Field(default_factory=list)
+    env_declaration: Optional[str] = None
 
 
 
@@ -9015,6 +9016,24 @@ async def _r_packages_for_env(env_name: str) -> set[str]:
 
 @app.post("/api/extension-stages/envs/resolve")
 async def resolve_extension_stage_env(req: ExtensionStageEnvResolveRequest):
+    # 工具显式声明的环境优先（run.sh 里 # lightweight-env: <env>）
+    if req.env_declaration:
+        env = req.env_declaration.strip()
+        proc = await asyncio.create_subprocess_exec(
+            "conda", "run", "-n", env, "python", "--version",
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+        )
+        await proc.communicate()
+        if proc.returncode == 0:
+            return {
+                "success": True,
+                "runtime_env": env,
+                "reason": "explicit_env_declaration",
+                "dependency": env,
+                "fallback": False,
+            }
+
     python_imports = _normalized_dependency_names(req.python_imports)
     r_packages = _normalized_dependency_names(req.r_packages)
     if not python_imports and not r_packages:

gfa_core/extension_stage_lightweight/api.py

@@ -278,12 +278,29 @@ def _operation_run(record: dict[str, Any], operation: dict[str, Any]) -> tuple[d
     return None, "runtime" if action == "run" else "validation"
 
 
+def _missing_output_dir_hint(record: dict[str, Any], token: str) -> str | None:
+    """当 stderr 提示输出目录不存在时，给出更明确的提示。"""
+    for log_path in _logs_for(record, token):
+        try:
+            text = Path(log_path).read_text(encoding="utf-8", errors="replace")
+        except OSError:
+            continue
+        if "No such file or directory" in text and "outputs/" in text:
+            return (
+                "输出目录不存在：工具把输出写入 outputs/ 子目录但未创建该目录"
+                "（hmmsearch/diamond 等不会自动建目录），请在 run.sh 开头添加 mkdir -p 对应目录"
+            )
+    return None
+
+
 def _run_error(record: dict[str, Any], token: str, run: dict[str, Any], phase: str) -> dict[str, Any]:
     details = run.get("error") if isinstance(run.get("error"), dict) else {}
     binding = run.get("binding") if isinstance(run.get("binding"), dict) else {}
     binding_error = binding.get("error") if isinstance(binding.get("error"), dict) else {}
+    hint = _missing_output_dir_hint(record, token)
     message = (
-        details.get("message")
+        hint
+        or details.get("message")
         or binding_error.get("message")
         or ("runtime binding was not resolved" if binding.get("status") != "resolved" else "execution did not satisfy the output contract")
     )

gfa_core/extension_stage_lightweight/runtime_binding.py

@@ -349,15 +349,14 @@ def _locate_patch_targets(
             for anchor in anchors
         }
         if reason is None:
-            if len(source_matches) > 1 or len(anchor_identities) != len(anchors):
-                reason = "source_literal_ambiguous"
-            elif (
-                len(source_matches) == 1
-                and source_matches[0][1] != len(anchors)
-            ):
-                reason = "source_literal_ambiguous"
-            elif not source_matches:
+            if not source_matches:
                 reason = "source_literal_not_found_in_raw_shell"
+            elif len(source_matches) > 1:
+                # 字面量跨多个脚本，无法唯一定位
+                reason = "source_literal_ambiguous"
+            elif len(anchors) != 1 or len(anchor_identities) != 1:
+                # 需要唯一 anchor 才能安全 patch
+                reason = "source_literal_ambiguous"
 
         clean_candidate = {
             key: value
@@ -782,9 +781,21 @@ def _shared_output_prefix(outputs: list[dict[str, Any]]) -> str | None:
 _DIR_OVERRIDE_SWITCHES = ("-oc", "-o")  # tools that accept a writable output directory
 
 
-def _is_dir_prefix(prefix: str) -> bool:
-    """Return True when *prefix* looks like a directory rather than a filename stem."""
-    return "/" not in prefix and "." not in prefix and _PREFIX_TOKEN.fullmatch(prefix) is not None
+def _prefix_targets_directory(paths: list[str], prefix: str) -> bool:
+    """Return True when *prefix* matches a directory component of any path.
+
+    Checks the actual output paths rather than guessing from the prefix string:
+    ``meme_out/logo1.png`` has ``meme_out`` as a directory component, while
+    ``input_qc.tsv`` and ``Ft.blast`` do not — so filename stems are not mistaken
+    for directory prefixes.
+    """
+    for path in paths:
+        for part in PurePosixPath(path).parts[:-1]:  # 排除文件名
+            if part.startswith(prefix) and (
+                len(part) == len(prefix) or part[len(prefix)] in _PREFIX_DELIMITERS
+            ):
+                return True
+    return False
 
 
 def _replace_positional_prefix(command: str, old: str, new: str) -> str:
@@ -1066,7 +1077,16 @@ def resolve_runtime_bindings(
         for fact_id in target.get("fact_ids", [])
         if isinstance(fact_id, str)
     }
+    unpatchable_fact_ids = {
+        fact_id
+        for target in contract.get("unpatchable_targets", [])
+        if isinstance(target, dict)
+        for fact_id in target.get("fact_ids", [])
+        if isinstance(fact_id, str)
+    }
     output_bindings = []
+    output_paths = [output["path"] for output in output_files]
+    prefix_targets_dir = _prefix_targets_directory(output_paths, old_prefix)
     for output in output_files:
         original_path = output["path"]
         runtime_path = _runtime_input_owned_output(
@@ -1075,9 +1095,17 @@ def resolve_runtime_bindings(
             allow_sidecar=output["fact_id"] not in direct_output_fact_ids,
         )
         if runtime_path is None:
+            # 可重命名当且仅当：input-derived 前缀 / 目录前缀 / 有可 patch 的
+            # 输出字面量。只有三者都不满足（硬编码且无法 patch，如
+            # input_qc.tsv 动态拼接）才保持原名。
+            can_rename = (
+                bool(participating_paths)
+                or prefix_targets_dir
+                or output["fact_id"] not in unpatchable_fact_ids
+            )
             runtime_path = (
                 _replace_output_prefix(original_path, old_prefix, new_prefix)
-                if _output_has_prefix(original_path, old_prefix)
+                if can_rename and _output_has_prefix(original_path, old_prefix)
                 else original_path
             )
         output_bindings.append(
@@ -1781,43 +1809,39 @@ def render_runtime_package(
     ):
         old = prefix["old_prefix"]
         new = prefix["new_prefix"]
-        # Only rewrite when the prefix looks like a directory being renamed.
-        # Check: every output whose runtime path differs has the prefix in
-        # a directory component (not the filename).  When that holds the
-        # tool is writing into a fixed directory name and we can inject a
-        # post-command rename.
         if any(
             b.get("transformed") for b in resolved.get("output_bindings", [])
         ):
-            # Prepend an output-dir override when the tool supports
-            # ``-oc`` (MEME family) and the old prefix is a plain
-            # single-segment directory.
-            if _is_dir_prefix(old):
+            # 目录前缀（如 meme_out/logo1.png 的 meme_out）→ -oc 注入。
+            # 文件名 stem（如 input_qc.tsv）不是目录，不能注入 -oc。
+            transformed_paths = [
+                b["original_path"]
+                for b in resolved.get("output_bindings", [])
+                if b.get("transformed")
+            ]
+            is_dir_prefix = _prefix_targets_directory(transformed_paths, old)
+            if is_dir_prefix:
                 actual_command = _inject_dir_prefix_override(
                     command, old, new
                 )
-                # Also rewrite the inner command inside wrapper scripts
-                # (e.g. ``bash run.sh`` wraps ``MCScanX ./Ft``).
-                # Try positional-prefix replacement (for tools that take
-                # the output prefix as a positional argument), then -oc/-o
-                # injection (for MEME-family tools).
-                for script in sorted(source_hashes):
-                    script_path = raw_code / script
-                    inner = script_path.read_text(
-                        encoding="utf-8", errors="replace"
+            # 改写 shell 脚本里的命令（位置参数替换 / -oc 注入）。
+            # 只处理 .sh 脚本：代码文件（.py 等）的输出路径由
+            # _render_script_updates 负责，shlex 会破坏它们的语法。
+            for script in sorted(source_hashes):
+                if not script.endswith(".sh"):
+                    continue
+                script_path = raw_code / script
+                inner = script_path.read_text(
+                    encoding="utf-8", errors="replace"
+                )
+                rewritten = _replace_positional_prefix(inner, old, new)
+                if rewritten == inner and is_dir_prefix:
+                    rewritten = _inject_dir_prefix_override(inner, old, new)
+                if rewritten != inner:
+                    source_script_updates[script] = rewritten
+                    _symlink_prefix_data_files(
+                        old, new, work_dir, set(source_hashes)
                     )
-                    rewritten = _replace_positional_prefix(inner, old, new)
-                    if rewritten == inner:
-                        rewritten = _inject_dir_prefix_override(inner, old, new)
-                    if rewritten != inner:
-                        source_script_updates[script] = rewritten
-                        # When positional-prefix rewrite changes a tool command
-                        # (e.g. MCScanX ./Ft → MCScanX ./output), some tools
-                        # expect data files matching the new prefix.  Create
-                        # symlinks so the tool finds its inputs.
-                        _symlink_prefix_data_files(
-                            old, new, work_dir, set(source_hashes)
-                        )
 
     for relative in sorted(source_hashes):
         destination = work_dir / relative
@@ -1860,6 +1884,7 @@ def render_runtime_package(
         src = raw_data_root / relative
         dst = work_dir / relative
         if src.is_file() and not dst.exists():
+            dst.parent.mkdir(parents=True, exist_ok=True)
             shutil.copy2(src, dst)
 
     # When a prefix rename is active, create symlinks so tools that

gfa_core/extension_stage_lightweight/service.py

@@ -9,6 +9,7 @@ import json
 import os
 from pathlib import Path
 import shutil
+import subprocess
 import tempfile
 from typing import Any, Callable, Iterator
 from uuid import uuid4
@@ -41,6 +42,34 @@ def _copy_tree(source: Path, destination: Path) -> None:
     shutil.copytree(source, destination, symlinks=True)
 
 
+def _conda_activated_env(runtime_env: str) -> dict[str, str]:
+    """Return the full environment after ``conda run -n <env>`` activation.
+
+    ``conda run`` runs the env's activate.d/*.sh scripts (which set
+    PYTHONPATH/LD_LIBRARY_PATH and may prepend PATH) in addition to the
+    normal PATH/CONDA_* bookkeeping — more complete than just pointing
+    PATH at env/bin.
+    """
+    try:
+        proc = subprocess.run(
+            ["conda", "run", "-n", runtime_env, "python", "-c",
+             "import os,json;print(json.dumps(dict(os.environ)))"],
+            capture_output=True, text=True, timeout=20,
+        )
+    except Exception:
+        return {}
+    if proc.returncode != 0:
+        return {}
+    try:
+        data = json.loads(proc.stdout.strip())
+    except ValueError:
+        return {}
+    if not isinstance(data, dict):
+        return {}
+    data.pop("_", None)
+    return data
+
+
 class LightweightExtensionService:
     """A small state machine that delegates all conversion/runtime facts to Phase A."""
 
@@ -119,6 +148,9 @@ class LightweightExtensionService:
         env["PATH"] = f"{conda_bin}:{existing_path}" if existing_path else conda_bin
         env["CONDA_PREFIX"] = conda_prefix
         env["CONDA_DEFAULT_ENV"] = runtime_env
+        # 用 conda run 的官方激活结果覆盖：activate.d 设置的 PYTHONPATH/LD_LIBRARY_PATH
+        # 以及 PATH 前置（如 MCScanX）都会被正确带进来；失败时保留上面的手动设置作为兜底。
+        env.update(_conda_activated_env(runtime_env))
         return env
 
     def _deepseek_candidate(self, facts: dict[str, Any], raw_code: Path) -> tuple[dict[str, Any], dict[str, Any]]: