fix(lightweight-extension): 输出前缀绑定、拖拽导入与前端入口修复

- runtime_binding: 验证时排除输入 sidecar 输出，目录参数跟随输出前缀重命名
- import-folder: 改 multipart 二进制上传，规避大文件 base64 报 Invalid string length
- main: 前端入口切回 index.html，conda 路径兜底

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

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 = {