diff --git a/apps/web/vue3/lightWeightExtensionTest.js b/apps/web/vue3/lightWeightExtensionTest.js
index 5732266a3..178458777 100644
--- a/apps/web/vue3/lightWeightExtensionTest.js
+++ b/apps/web/vue3/lightWeightExtensionTest.js
@@ -135,33 +135,18 @@
         return null;
     }
 
-    async function encodeBase64(file) {
-        const buffer = await file.arrayBuffer();
-        const bytes = new Uint8Array(buffer);
-        let binary = '';
-        const chunkSize = 0x8000;
-        for (let index = 0; index < bytes.length; index += chunkSize) {
-            binary += String.fromCharCode(...bytes.subarray(index, index + chunkSize));
-        }
-        return btoa(binary);
-    }
-
     async function importFolderToJob(hooks, rootName, files) {
-        const payload = {
-            job_id: String(hooks.jobInfo.job_id || '').trim(),
-            root_name: rootName,
-            files: [],
-            relative_paths: [],
-        };
+        const form = new FormData();
+        form.append('job_id', String(hooks.jobInfo.job_id || '').trim());
+        form.append('root_name', rootName);
         for (const file of files) {
-            payload.files.push(await encodeBase64(file));
-            payload.relative_paths.push(normalizedRelativePath(file));
+            form.append('files', file, normalizedRelativePath(file));
+            form.append('relative_paths', normalizedRelativePath(file));
         }
         const response = await hooks.uploadExtensionWithProgress(
             '/api/job/import-folder',
-            JSON.stringify(payload),
+            form,
             '正在镜像导入 Job',
-            { 'Content-Type': 'application/json' },
         );
         const data = await response.json();
         if (!response.ok || !data.success) {
diff --git a/apps/web/vue3/main.py b/apps/web/vue3/main.py
index 74bdc9a5f..c42b46108 100644
--- a/apps/web/vue3/main.py
+++ b/apps/web/vue3/main.py
@@ -6,7 +6,6 @@ BotanicalBaseAgent - FastAPI Backend
 import os
 import sys
 import json
-import base64
 import csv
 import asyncio
 import hashlib
@@ -8830,7 +8829,7 @@ def run_stage_sync(task_id: str, stage: str, job_id: str, params: dict):
 async def root():
     """返回Vue3前端页面"""
     return FileResponse(
-        Path(__file__).parent / "index_ml.html",
+        Path(__file__).parent / "index.html",
         headers={
             "Cache-Control": "no-cache, no-store, must-revalidate",
             "Pragma": "no-cache",
@@ -9059,34 +9058,29 @@ async def upload_file(files: List[UploadFile] = File(...), job_id: str = Form(""
     }
 
 
-class JobImportFolderRequest(BaseModel):
-    job_id: str
-    root_name: str = ""
-    files: List[str] = Field(default_factory=list)
-    relative_paths: List[str] = Field(default_factory=list)
-
-
 @app.post("/api/job/import-folder")
-async def import_job_folder(req: JobImportFolderRequest):
-    job_id = str(req.job_id or "").strip()
+async def import_job_folder(
+    job_id: str = Form(...),
+    root_name: str = Form(""),
+    files: List[UploadFile] = File(...),
+    relative_paths: List[str] = Form(...),
+):
+    job_id = str(job_id or "").strip()
     if not job_id:
         raise HTTPException(status_code=400, detail="job_id is required")
-    if len(req.files) != len(req.relative_paths):
+    if len(files) != len(relative_paths):
         raise HTTPException(status_code=400, detail="files and relative_paths length mismatch")
 
-    root_name = _safe_upload_name(req.root_name or "lightweight_extension_drop")
+    root_name = _safe_upload_name(root_name or "lightweight_extension_drop")
     import_root = INPUT_ROOT / job_id / root_name
     import_root.mkdir(parents=True, exist_ok=True)
     saved_files: List[str] = []
 
-    for encoded, raw_relative in zip(req.files, req.relative_paths):
+    for upload, raw_relative in zip(files, relative_paths):
         relative = Path(str(raw_relative or "").strip())
         if not raw_relative or relative.is_absolute() or any(part in {"", ".", ".."} for part in relative.parts):
             raise HTTPException(status_code=400, detail=f"invalid relative path: {raw_relative}")
-        try:
-            content = base64.b64decode(str(encoded or "").encode("utf-8"), validate=True)
-        except Exception as exc:
-            raise HTTPException(status_code=400, detail=f"invalid base64 payload for {raw_relative}: {exc}") from exc
+        content = await upload.read()
         destination = import_root / relative
         destination.parent.mkdir(parents=True, exist_ok=True)
         destination.write_bytes(content)
@@ -9185,6 +9179,10 @@ class ExtensionStageEnvResolveRequest(BaseModel):
     env_declaration: Optional[str] = None
 
 
+def _conda_exe() -> str:
+    """Resolve the conda executable even when it is not on the server process's PATH."""
+    return shutil.which("conda") or "/home/xzq/miniconda3/bin/conda"
+
 
 @app.get("/api/extension-stages/envs")
 async def list_extension_stage_envs():
@@ -9192,7 +9190,7 @@ async def list_extension_stage_envs():
     import json as _json
     try:
         proc = await asyncio.create_subprocess_exec(
-            "conda", "env", "list", "--json",
+            _conda_exe(), "env", "list", "--json",
             stdout=asyncio.subprocess.PIPE,
             stderr=asyncio.subprocess.PIPE,
         )
@@ -9200,7 +9198,7 @@ async def list_extension_stage_envs():
         if proc.returncode != 0:
             # fallback: try parsing plain-text output
             proc2 = await asyncio.create_subprocess_exec(
-                "conda", "env", "list",
+                _conda_exe(), "env", "list",
                 stdout=asyncio.subprocess.PIPE,
                 stderr=asyncio.subprocess.PIPE,
             )
@@ -9249,7 +9247,7 @@ async def _available_extension_env_names() -> List[str]:
 
 async def _python_packages_for_env(env_name: str) -> set[str]:
     proc = await asyncio.create_subprocess_exec(
-        "conda", "run", "-n", env_name, "python", "-c",
+        _conda_exe(), "run", "-n", env_name, "python", "-c",
         "import json, importlib.metadata as m; print(json.dumps(sorted({dist.metadata.get('Name', '') for dist in m.distributions() if dist.metadata.get('Name', '')})))",
         stdout=asyncio.subprocess.PIPE,
         stderr=asyncio.subprocess.PIPE,
@@ -9266,7 +9264,7 @@ async def _python_packages_for_env(env_name: str) -> set[str]:
 
 async def _r_packages_for_env(env_name: str) -> set[str]:
     proc = await asyncio.create_subprocess_exec(
-        "conda", "run", "-n", env_name, "Rscript", "-e",
+        _conda_exe(), "run", "-n", env_name, "Rscript", "-e",
         "cat(paste(sort(rownames(installed.packages())), collapse='\n'))",
         stdout=asyncio.subprocess.PIPE,
         stderr=asyncio.subprocess.PIPE,
@@ -9283,7 +9281,7 @@ async def resolve_extension_stage_env(req: ExtensionStageEnvResolveRequest):
     if req.env_declaration:
         env = req.env_declaration.strip()
         proc = await asyncio.create_subprocess_exec(
-            "conda", "run", "-n", env, "python", "--version",
+            _conda_exe(), "run", "-n", env, "python", "--version",
             stdout=asyncio.subprocess.PIPE,
             stderr=asyncio.subprocess.PIPE,
         )
@@ -9309,7 +9307,7 @@ async def resolve_extension_stage_env(req: ExtensionStageEnvResolveRequest):
 
     for dep in list(dict.fromkeys(d.lower() for d in python_imports + r_packages)):
         proc = await asyncio.create_subprocess_exec(
-            "conda", "run", "-n", dep, "python", "--version",
+            _conda_exe(), "run", "-n", dep, "python", "--version",
             stdout=asyncio.subprocess.PIPE,
             stderr=asyncio.subprocess.PIPE,
         )
diff --git a/gfa_core/extension_stage_lightweight/runtime_binding.py b/gfa_core/extension_stage_lightweight/runtime_binding.py
index 595996f95..da71c4cbb 100644
--- a/gfa_core/extension_stage_lightweight/runtime_binding.py
+++ b/gfa_core/extension_stage_lightweight/runtime_binding.py
@@ -1004,6 +1004,33 @@ def resolve_runtime_bindings(
         binding["original_path"]: binding["runtime_path"]
         for binding in input_bindings or []
     }
+    direct_output_fact_ids = {
+        fact_id
+        for target in contract.get("patch_targets", [])
+        if isinstance(target, dict)
+        and target.get("patch_kind") in {"output_path", "output_reference_path"}
+        for fact_id in target.get("fact_ids", [])
+        if isinstance(fact_id, str)
+    }
+    # Outputs owned by an input (the input itself or a sidecar like
+    # ``Pfam-A.WRKY-subset.hmm.h3f`` next to ``Pfam-A.WRKY-subset.hmm``) do not
+    # belong to the output-prefix namespace; they are renamed via their input
+    # relationship. Excluding them keeps the shared-prefix derivation from
+    # being dragged to ``.`` by a top-level sidecar while the remaining outputs
+    # live under a common directory.
+    input_owned_paths = {
+        output["path"]
+        for output in output_files
+        if _runtime_input_owned_output(
+            output["path"],
+            runtime_by_original,
+            allow_sidecar=output["fact_id"] not in direct_output_fact_ids,
+        )
+        is not None
+    }
+    prefix_output_files = [
+        output for output in output_files if output["path"] not in input_owned_paths
+    ]
     participant_options: list[set[tuple[str, str]]] = []
     participating_paths: set[str] = set()
     for output in output_files:
@@ -1055,11 +1082,11 @@ def resolve_runtime_bindings(
             *[{old for old, _new in options} for options in participant_options]
         )
         if not common_old:
-            old_prefix = _shared_output_prefix(output_files)
+            old_prefix = _shared_output_prefix(prefix_output_files)
         else:
             old_prefix = max(common_old, key=lambda value: (len(value), value))
     else:
-        old_prefix = _shared_output_prefix(output_files)
+        old_prefix = _shared_output_prefix(prefix_output_files)
     if old_prefix is None:
         return _blocked_result(
             contract,
@@ -1069,14 +1096,6 @@ def resolve_runtime_bindings(
             parameter_bindings=parameter_bindings,
         )
     new_prefix = explicit_prefix or "output"
-    direct_output_fact_ids = {
-        fact_id
-        for target in contract.get("patch_targets", [])
-        if isinstance(target, dict)
-        and target.get("patch_kind") in {"output_path", "output_reference_path"}
-        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", [])
@@ -1412,6 +1431,17 @@ def _binding_replacements(
             raise RuntimeBindingError(
                 "PARAMETER_VALUE_INVALID", f"unsafe runtime parameter: {fact_id}"
             )
+        # 输出目录参数（--outdir / -oc / mkdir -p 的值）跟随输出前缀重命名，
+        # 否则渲染后的 run.sh 里目录参数与 file 输出路径指向不一致的目录。
+        if isinstance(prefix, dict):
+            old_prefix = prefix.get("old_prefix")
+            new_prefix = prefix.get("new_prefix")
+            if (
+                isinstance(old_prefix, str)
+                and isinstance(new_prefix, str)
+                and _output_has_prefix(runtime, old_prefix)
+            ):
+                runtime = _replace_output_prefix(runtime, old_prefix, new_prefix)
         add(f"parameter:{fact_id}", original, runtime)
 
     targets_by_key = {