feat(bioflow): skill 编排续作 WIP checkpoint（多轮链续接/plan 回填/job_id 提取/历史 blocks 文本提取）

.gitignore

@@ -46,4 +46,4 @@ paper_writer_service/paper.log
 # 部署方案文档（含主机凭据，不入库）
 docs/DEPLOY_PAPER_176.md
 # Python 覆盖率运行时产物(coverage.py --cov 生成)
-.coverage
+.coveragevstore/vstore.log

agent/qa/src/rag/qa_v1_1_73/bioflow_agent.py

@@ -48,6 +48,9 @@ _CHAIN_TO_CAPABILITY = {
     "rnaseq": "bioflow-rnaseq",
 }
 
+# 能力名 → chain 名（反向映射，供规划阶段从命中能力回填 chain，续接多轮对话）
+_CAPABILITY_TO_CHAIN = {v: k for k, v in _CHAIN_TO_CAPABILITY.items()}
+
 
 def _chain_to_capability(chain: str) -> Optional[str]:
     """把 chain 名（gene_family/rnaseq）映射为能力名；未知返回 None。"""
@@ -291,6 +294,28 @@ def _empty_audit() -> Dict[str, Any]:
     return {"rounds": 0, "tool_calls": 0, "used_json_fallback": False, "tool_names": [], "errors": []}
 
 
+def _map_readiness(data: Dict[str, Any]) -> Dict[str, Any]:
+    """check_readiness 结果 → 就绪卡字段 {ready, quadrants:[{name,ok}]}。"""
+    inner = data.get("result", data) if isinstance(data, dict) else {}
+    quadrants = []
+    for key in ("environment", "reference", "space", "budget"):
+        q = inner.get(key) or {}
+        quadrants.append({"name": key, "ok": bool(q.get("ok"))})
+    return {"ready": bool(inner.get("ready")), "quadrants": quadrants}
+
+
+def _map_versioning(data: Dict[str, Any]) -> Dict[str, Any]:
+    """propose_change 结果 → 版本化卡字段 {plan_revision, run_id, affected_stages, based_on_revision}。"""
+    inner = data.get("result", data) if isinstance(data, dict) else {}
+    affected = inner.get("affected") or []
+    return {
+        "plan_revision": "",
+        "run_id": "",
+        "affected_stages": list(affected),
+        "based_on_revision": None,
+    }
+
+
 def _make_payload(
     question: str,
     answer: str,
@@ -299,6 +324,9 @@ def _make_payload(
     capabilities: Optional[List[str]] = None,
     active_job_id: Optional[str] = None,
     chain: Optional[str] = None,
+    readiness: Optional[Dict[str, Any]] = None,
+    versioning: Optional[Dict[str, Any]] = None,
+    plan: Optional[Dict[str, Any]] = None,
 ) -> Dict[str, Any]:
     payload: Dict[str, Any] = {
         "success": True,
@@ -318,6 +346,12 @@ def _make_payload(
         payload["bioflow"]["active_job_id"] = str(active_job_id)
     if chain:
         payload["bioflow"]["chain"] = str(chain)
+    if readiness:
+        payload["bioflow"]["readiness"] = readiness
+    if versioning:
+        payload["bioflow"]["versioning"] = versioning
+    if plan:
+        payload["bioflow"]["plan"] = plan
     return payload
 
 
@@ -609,8 +643,24 @@ def _try_bioflow_agent_impl(
     if isinstance(card_result, dict) and str(card_result.get("card") or "").strip() in CARD_TYPES:
         return _route_card_result(card_result, llm_client, capabilities, bioflow, progress_callback)
 
-    # NL 路径：门 2 + 门 3
-    manifests = _candidate_capabilities(question, capabilities)
+    # NL 路径：活跃任务/生信链续接优先，其次意图预筛
+    active_job_id = (bioflow or {}).get("active_job_id")
+    chain = str((bioflow or {}).get("chain") or "").strip()
+    if active_job_id:
+        # 有活跃任务：跳过意图预筛，按任务 chain 续接（任务链不可变）
+        manifests = _registered_capabilities(capabilities)
+        cap_name = _chain_to_capability(chain)
+        if cap_name:
+            manifests = [m for m in manifests if m.name == cap_name]
+    else:
+        # 无活跃任务：先门 2 + 门 3 意图预筛（新任务入口）
+        manifests = _candidate_capabilities(question, capabilities)
+        # 意图未命中但 session 留有生信链（上轮规划）→ 续接该链（如路径选择「1」）
+        if not manifests and chain:
+            cap_name = _chain_to_capability(chain)
+            if cap_name:
+                registered = _registered_capabilities(capabilities)
+                manifests = [m for m in registered if m.name == cap_name]
     if not manifests:
         return None
 
@@ -639,13 +689,43 @@ def _try_bioflow_agent_impl(
     if not answer:
         return None
 
+    tool_results = (audit or {}).get("tool_results") or {}
+    readiness = None
+    versioning = None
+    new_job_id = None
+    plan = None
+    for name, result_text in tool_results.items():
+        if name in ("create_gene_family_job", "create_rnaseq_job"):
+            jid = _extract_job_id(result_text)
+            if jid:
+                new_job_id = jid
+        data = _try_parse_json(result_text)
+        if not isinstance(data, dict):
+            continue
+        if name.startswith("plan_") and data.get("ok"):
+            plan = {
+                "candidates": data.get("candidates") or [],
+                "auto_filled": data.get("auto_filled") or [],
+                "reuse_archive": data.get("reuse_archive"),
+                "reuse_name": data.get("reuse_name"),
+                "fallback": data.get("fallback"),
+            }
+        if name == "check_readiness":
+            readiness = _map_readiness(data)
+        elif name == "propose_change":
+            versioning = _map_versioning(data)
+
+    effective_chain = chain or (_CAPABILITY_TO_CHAIN.get(manifests[0].name) if manifests else "")
     return _make_payload(
         question,
         answer,
         audit=audit,
         capabilities=[m.name for m in manifests],
-        active_job_id=(bioflow or {}).get("active_job_id"),
-        chain=(bioflow or {}).get("chain"),
+        active_job_id=(bioflow or {}).get("active_job_id") or new_job_id,
+        chain=effective_chain or None,
+        readiness=readiness,
+        versioning=versioning,
+        plan=plan,
     )
 
 

agent/qa/src/rag/qa_v1_1_73/test_bioflow_agent.py

@@ -109,6 +109,33 @@ class TestGateLogic:
                 )
         assert result is None
 
+    def test_active_job_continuation_skips_intent_prescreen(self, tmp_path):
+        """#011：有活跃任务时，续接输入（不含触发词）也应进入生信流，不掉普通 QA。"""
+        registry = _make_registry(tmp_path)
+        fake_tools = [
+            {
+                "type": "function",
+                "function": {
+                    "name": "fetch_source_file",
+                    "description": "获取源文件",
+                    "parameters": {"type": "object", "properties": {}},
+                },
+            }
+        ]
+        with mock.patch.object(ba, "get_registry", return_value=registry):
+            with mock.patch.object(ba, "_build_tools", return_value=(fake_tools, {"fetch_source_file": mock.ANY})):
+                with mock.patch.dict("os.environ", {ba.ENV_FUSE: "1"}):
+                    result = ba.try_bioflow_agent(
+                        "基因组文件在 https://example.com/rice.fa",
+                        llm_client=FakeLLMClient(),
+                        capabilities=None,
+                        bioflow={"active_job_id": "job-1", "chain": "gene_family"},
+                    )
+        assert result is not None
+        assert result["success"] is True
+        assert result["bioflow"]["handled"] is True
+        assert result["bioflow"]["capabilities"] == ["bioflow-gene-family"]
+
     def test_not_registered_returns_none(self, tmp_path):
         empty = CapabilityRegistry(tmp_path / "empty.yaml")
         empty.load()

agent/qa/src/rag/qa_v1_1_73/tool_runner.py

@@ -66,6 +66,7 @@ class ToolRunner:
             "tool_calls": 0,
             "used_json_fallback": False,
             "tool_names": [],
+            "tool_results": {},
             "errors": [],
         }
         messages: List[Dict[str, Any]] = []
@@ -95,6 +96,7 @@ class ToolRunner:
                 break
             assistant_message: Dict[str, Any] = {"role": "assistant", "content": content or ""}
             tool_call_blocks: List[Dict[str, Any]] = []
+            messages.append(assistant_message)
             for call in tool_calls:
                 name = str(call.get("name") or call.get("function", {}).get("name") or "")
                 raw_args = call.get("arguments") or call.get("function", {}).get("arguments") or {}
@@ -125,9 +127,9 @@ class ToolRunner:
                         "function": {"name": name or "unknown", "arguments": json.dumps(arguments, ensure_ascii=False)},
                     }
                 )
+                audit["tool_results"][name] = result_text
                 messages.append({"role": "tool", "tool_call_id": call_id, "content": result_text})
             assistant_message["tool_calls"] = tool_call_blocks
-            messages.append(assistant_message)
             continue
         # 最后一轮：拿最终文本（无工具或轮次用尽后由调用方用 messages 再 complete 一次）
         return self._final_text(system_text, messages, tools), audit

bioflow_service/app/services/bioflow/delivery.py

@@ -130,7 +130,10 @@ def check_download_budget(size_bytes: int, budget_bytes: int) -> dict[str, Any]:
 
 def check_disk_available(dest_dir: str | Path, needed_bytes: int) -> dict[str, Any]:
     """G23：磁盘门禁——剩余空间不足阻断并返回结构化错误。"""
-    ok, free = check_disk_space(dest_dir, needed_bytes)
+    try:
+        ok, free = check_disk_space(dest_dir, needed_bytes)
+    except OSError as exc:
+        return error_result("PATH_NOT_EXIST", f"目标目录不可用：{exc}")
     if not ok:
         return error_result(
             "DISK_FULL", f"磁盘空间不足：需 {needed_bytes} 字节，剩余 {free} 字节",

bioflow_service/app/services/bioflow/runner.py

@@ -27,6 +27,8 @@ from pathlib import Path
 from typing import Any, Awaitable, Callable
 
 from .catalog import StageCatalog
+from .delivery import delivery_validate
+from .errors import classify_reason
 from .events import EventBus
 from .manifests import ManifestError, locate_manifest, parse_manifest
 from .recovery import RecoveryBudget
@@ -615,6 +617,30 @@ def parse_progress_marker(line: str) -> dict[str, Any] | None:
     return None
 
 
+_METRIC_LABELS = {
+    "hits": "命中", "hit_count": "命中", "mapping_rate": "比对率",
+    "aligned": "比对", "mapped": "比对", "identified": "鉴定",
+    "members": "成员", "de_genes": "差异基因", "up": "上调", "down": "下调",
+    "enriched": "富集", "count": "数量", "total": "总数",
+    "records": "记录", "sequences": "序列",
+}
+
+
+def _metrics_summary(stage: str, metrics: dict) -> str:
+    """阶段完成摘要（G 关键指标自然语言转述）；无指标时退化为「阶段已完成」。"""
+    if not isinstance(metrics, dict) or not metrics:
+        return f"阶段 {stage} 已完成"
+    parts = []
+    for k, v in metrics.items():
+        if not isinstance(v, (int, float, str, bool)):
+            continue
+        label = _METRIC_LABELS.get(str(k), str(k))
+        parts.append(f"{label} {v}")
+    if parts:
+        return f"阶段 {stage} 完成：{'，'.join(parts)}"
+    return f"阶段 {stage} 已完成"
+
+
 @dataclass
 class JobRecord:
     """任务内存记录（DB 行 + 派生路径）。"""
@@ -798,11 +824,31 @@ class Runner:
                 return
             record.status = JOB_DONE
             await self._persist_job(record)
+            try:
+                done_stages = [
+                    st for st in record.stage_chain
+                    if record._stage_states.get(st, {}).get("status") == STAGE_DONE
+                ]
+                delivery_manifest = {
+                    "selected_stages": list(record.stage_chain or []),
+                    "run_id": record.run_id or record.id,
+                    "input_sources": list(record.registered_server_paths or []),
+                    "output_sources": list(done_stages),
+                    "config": dict(record.params or {}),
+                    "required_results": list(done_stages),
+                    "validation_values": {},
+                    "review_status": "pending",
+                }
+                delivery = delivery_validate(delivery_manifest)
+            except Exception:  # noqa: BLE001 - 交付清单失败不阻断任务完成
+                delivery = {"ok": False, "checks": {}, "incomplete": []}
             self.events.publish("job_done", {
                 "job_id": record.id,
                 "title": record.title,
                 "progress": 100,
                 "elapsed_sec": None,
+                "guidance": "分析已完成，可以存档复用，或直接查看报告。",
+                "delivery": delivery,
             })
         except asyncio.CancelledError:
             # 任务级取消：不落脏状态（阶段取消由 _run_stage 单独处理）
@@ -865,9 +911,17 @@ class Runner:
                 self._set_stage(record, stage, status=STAGE_WAITING_CONFIRM)
                 await self._persist_stage(record, stage)
                 defaults = self._form_defaults(stage, record)
+                if defaults:
+                    param_str = "、".join(
+                        f"{p.get('name')}（默认 {p.get('default')}）" for p in defaults
+                    )
+                    guidance = f"阶段 {stage} 需要确认参数：{param_str}。不调整可直接继续。"
+                else:
+                    guidance = f"阶段 {stage} 需要你确认后继续。"
                 self.events.publish("stage_await_confirm", {
                     "job_id": record.id, "stage": stage,
                     "form_defaults": defaults,
+                    "guidance": guidance,
                 })
                 return "await"
 
@@ -1041,6 +1095,7 @@ class Runner:
             "job_id": record.id, "stage": stage, "exit_code": exit_code,
             "manifest_ref": manifest.path,
             "metrics": manifest.metrics,
+            "summary": _metrics_summary(stage, manifest.metrics),
         })
         return "done"
 
@@ -1049,10 +1104,19 @@ class Runner:
         self._set_stage(record, stage, status=STAGE_FAILED, finished_at=_now_iso(),
                         error=reason)
         await self._persist_stage(record, stage)
+        cat, diag, retry, actions = classify_reason(reason, exit_code=exit_code)
+        guidance = f"阶段 {stage} 执行失败：{reason}。"
+        if actions:
+            guidance += "建议：" + "；".join(actions) + "。"
         self.events.publish("stage_failed", {
             "job_id": record.id, "stage": stage,
             "exit_code": exit_code if exit_code is not None else -1,
             "reason": reason,
+            "category": cat, "code": reason, "summary": reason,
+            "diagnosis_status": diag,
+            "retryable_without_change": retry,
+            "suggested_actions": actions,
+            "guidance": guidance,
         })
 
     def _prefix_for(self, record: JobRecord, stage: str) -> str | None:

sdk/app/services/history.py

@@ -7,9 +7,26 @@ assemble_history(db, session_id, rounds=3, budget):
 """
 from __future__ import annotations
 
+import html as html_mod
+import re
 from typing import Any, List
 
 from ..config import get_settings
+from ..db import loads_json
+
+
+def _blocks_text(blocks_json) -> str:
+    """从落库 blocks 提取 assistant 答案纯文本（text 块 html 去标签）。"""
+    blocks = loads_json(blocks_json, default=[])
+    parts = []
+    for b in blocks:
+        if not isinstance(b, dict) or b.get("type") != "text":
+            continue
+        h = b.get("html") or b.get("text") or ""
+        t = html_mod.unescape(re.sub(r"<[^>]+>", "", str(h))).strip()
+        if t:
+            parts.append(t)
+    return "\n".join(parts)
 
 
 async def assemble_history(
@@ -40,7 +57,7 @@ async def assemble_history(
         return []
     try:
         rows = await db.fetchall(
-            "SELECT role, status, text FROM messages "
+            "SELECT role, status, text, blocks FROM messages "
             "WHERE session_id = ? AND role IN ('user','assistant') "
             "AND status != 'streaming' "
             "ORDER BY created_at ASC, rowid ASC",
@@ -55,6 +72,8 @@ async def assemble_history(
     for row in reversed(rows):
         role = row["role"]
         text = (row["text"] or "").strip()
+        if not text and role == "assistant":
+            text = _blocks_text(row["blocks"])
         if not text:
             continue
         if role == "assistant":

ui/src/components/chat/FlowFileCard.vue

@@ -66,6 +66,7 @@ function handleFiles(fileList) {
     chat.uploadBioflowFileToJob(jobId.value, file, {
       onProgress: (pct) => {
         const rec = props.block.files.find((x) => x.name === file.name && x.status === 'uploading');
+        console.log('[bioflow-upload] onProgress pct=', pct, 'recFound=', !!rec, 'files=', (props.block.files || []).length);
         if (rec) rec.progress = pct;
       },
     })

ui/src/components/chat/FlowPathCard.vue

@@ -61,6 +61,7 @@ function backToSelect() {
 /** 复用名 → 表单默认值来源标注（与后端 params 预填配合；来源标注在表单卡展示） */
 async function confirmCreate() {
   const cand = selectedCandidate.value;
+  console.log('[bioflow-card] confirmCreate selected=', selected.value, 'cand=', !!cand, 'jobId=', props.block.jobId);
   if (!cand || confirming.value) return;
   if (props.block.jobId) return; // 已创建过（防重复创建；FR-BIO 任务幂等语义）
   confirming.value = true;

ui/src/i18n/bioflow.js

@@ -16,7 +16,7 @@ export const BF = {
   pathCandidatePurposeLabel: '用途',
   pathAutoFilled: '已自动补全',
   pathConfirm: '确认此路径',
-  pathEmpty: '暂无候选路径',
+  pathEmpty: '正在检索可用分析路径....',
   pathPlanning: '正在分析需求并规划分析路径…',
   formConfirmed: '参数已确认',
   pathCreated: '任务已创建',

ui/src/stores/chat.js

@@ -19,6 +19,7 @@ import { useSessionsStore } from './sessions.js';
 import { PHASE_LABEL, PHASE_DESC, T } from '../i18n/labels.js';
 import { MODES } from '../config/modes.js';
 import { renderMarkdown } from '../components/chat/markdown.js';
+console.log('[bioflow-version] chat.js raw.bioflow-fix v2 loaded');
 
 // ---- P3 文档生成：独立分支（send/_runStream 零改动） ----
 import { DOCGEN_STEPS, CAP_BADGES, DG as DG_LABELS } from '../i18n/docgen.js';
@@ -502,6 +503,16 @@ export function patchBioflowForm(aMsg, data, { rerun = false } = {}) {
 }
 
 /** 阶段待文件 → 文件引导块（FR-BIO-005） */
+export function patchBioflowGuidance(aMsg, text) {
+  // 自然语言引导气泡（方案：自然语言主通道，卡片辅助）——弹卡片前先插入一条 text 块。
+  if (!text) return null;
+  const html = renderMarkdown(String(text));
+  console.log('[bioflow-guidance] text=', String(text).slice(0, 40), 'html非空=', Boolean(html));
+  if ((aMsg.blocks || []).some((b) => b && b.type === 'text' && b.html === html)) return null;
+  aMsg.blocks.push({ type: 'text', html });
+  return true;
+}
+
 export function patchBioflowFile(aMsg, data) {
   const stage = data.stage;
   if (!stage) return null;
@@ -1159,9 +1170,12 @@ export const useChatStore = defineStore('chat', {
             onEvent: (type, data) => {
               const frame = patchBioflowEvent(m, { type, data });
               if (frame) this.scrollSeq++;
-              if (type === 'stage_await_confirm' && data) { patchBioflowForm(m, data); this.scrollSeq++; }
-              else if (type === 'stage_await_files' && data) { patchBioflowFile(m, data); this.scrollSeq++; }
+              if (type === 'stage_await_confirm' && data) { patchBioflowGuidance(m, data.guidance); patchBioflowForm(m, data); this.scrollSeq++; }
+              else if (type === 'stage_await_files' && data) { patchBioflowGuidance(m, data.guidance || data.message); patchBioflowFile(m, data); this.scrollSeq++; }
+              else if (type === 'stage_failed' && data) { patchBioflowGuidance(m, data.guidance); patchBioflowDiagnosis(m, data); this.scrollSeq++; }
               else if (type === 'job_done' && data) {
+                patchBioflowGuidance(m, data.guidance);
+                if (data.delivery) patchBioflowDelivery(m, data.delivery);
                 const ab = patchBioflowArchiveSuggest(m, data.job_id || jobId);
                 if (ab) ab.jobId = data.job_id || jobId;
                 this.scrollSeq++;
@@ -2255,12 +2269,20 @@ export const useChatStore = defineStore('chat', {
             const frame = patchBioflowEvent(aMsg, { type, data });
             if (frame) this.scrollSeq++;
             if (type === 'stage_await_confirm' && data) {
+              patchBioflowGuidance(aMsg, data.guidance);
               patchBioflowForm(aMsg, data);
               this.scrollSeq++;
             } else if (type === 'stage_await_files' && data) {
+              patchBioflowGuidance(aMsg, data.guidance || data.message);
               patchBioflowFile(aMsg, data);
               this.scrollSeq++;
+            } else if (type === 'stage_failed' && data) {
+              patchBioflowGuidance(aMsg, data.guidance);
+              patchBioflowDiagnosis(aMsg, data);
+              this.scrollSeq++;
             } else if (type === 'job_done' && data) {
+              patchBioflowGuidance(aMsg, data.guidance);
+              if (data.delivery) patchBioflowDelivery(aMsg, data.delivery);
               const blk = patchBioflowArchiveSuggest(aMsg, data.job_id || jobId);
               if (blk) blk.jobId = data.job_id || jobId;
               bioflow.registerReport({
@@ -2295,18 +2317,41 @@ export const useChatStore = defineStore('chat', {
       try {
         const data = await uploadBioflowFile(jobId, form, {
           onUploadProgress: (e) => {
-            item.progress = e.pct;
+            console.log('[bioflow-upload] onUploadProgress pct=', e.pct, 'loaded=', e.loaded, 'total=', e.total);
+            // item 是原始对象，直接改会绕过 Vue 响应式——经响应式数组找代理更新
+            const rec = found && Array.isArray(found.blk.files)
+              ? found.blk.files.find((x) => x.name === item.name && x.status === 'uploading')
+              : null;
+            if (rec) rec.progress = e.pct;
+            else item.progress = e.pct;
             if (typeof onProgress === 'function') onProgress(e.pct, item);
           },
         });
-        item.status = 'done';
-        item.progress = 1;
-        item.fileId = (data && data.data && data.data.file_id) || null;
+        const doneRec = found && Array.isArray(found.blk.files)
+          ? found.blk.files.find((x) => x.name === item.name)
+          : null;
+        if (doneRec) {
+          doneRec.status = 'done';
+          doneRec.progress = 1;
+          doneRec.fileId = (data && data.data && data.data.file_id) || null;
+        } else {
+          item.status = 'done';
+          item.progress = 1;
+          item.fileId = (data && data.data && data.data.file_id) || null;
+        }
         if (found) this.scrollSeq++;
         return (data && data.data) || data || {};
       } catch (err) {
-        item.status = 'error';
-        item.error = err?.message || BF.fileUploadError;
+        const errRec = found && Array.isArray(found.blk.files)
+          ? found.blk.files.find((x) => x.name === item.name)
+          : null;
+        if (errRec) {
+          errRec.status = 'error';
+          errRec.error = err?.message || BF.fileUploadError;
+        } else {
+          item.status = 'error';
+          item.error = err?.message || BF.fileUploadError;
+        }
         if (found) this.scrollSeq++;
         throw err;
       }
@@ -2437,6 +2482,7 @@ export const useChatStore = defineStore('chat', {
      *  经 BioflowAgent 工具执行 + 自然语言复述；卡片与自然语言两条通道语义一致。
      *  card ∈ path_selection|form_confirm|file_upload|archive_choice|extension_action。 */
     async sendCardResult(card, payload, { text = '', userMsg = null } = {}) {
+      console.log('[bioflow-card] sendCardResult', card, 'busy=', this.busy);
       if (this.busy) return;
       const sessions = useSessionsStore();
       if (!this.sessionId) {
@@ -2529,19 +2575,64 @@ export const useChatStore = defineStore('chat', {
               const p = ev.payload || {};
               const answer = p.answer || '';
               updateLocal(() => {
-                aMsg.blocks = [
-                  { type: 'bioflow_path', status: 'done', candidates: [] },
-                  { type: 'text', html: answer },
-                ];
+                const blocks = [];
+                // 仅路径选择卡回填 path 块（候选由上一轮路径卡承载）；其余卡操作只出自然语言复述
+                if (card === 'path_selection') {
+                  blocks.push({ type: 'bioflow_path', status: 'done', candidates: [] });
+                }
+                blocks.push({ type: 'text', html: answer });
+                const bfPayload = p.bioflow || {};
+                if (bfPayload.readiness) {
+                  blocks.push({ type: 'bioflow_readiness', ...bfPayload.readiness, error: null });
+                }
+                if (bfPayload.versioning) {
+                  blocks.push({ type: 'bioflow_versioning', ...bfPayload.versioning });
+                }
+                aMsg.blocks = blocks;
                 aMsg.raw = p.raw ?? p;
                 aMsg.status = 'done';
               });
               // session↔job 绑定持久化：complete 的 bioflow.active_job_id → meta.bioflow
-              const bf = p.bioflow || {};
+              // BFF 归一化剥离了顶层 bioflow，active_job_id 在 raw.bioflow 里
+              const bf = p.bioflow || (p.raw && p.raw.bioflow) || {};
               if (bf.active_job_id) {
                 updateSessionQuiet(sessionId, {
                   meta: { bioflow: { active_job_id: bf.active_job_id, chain: bf.chain || '' } },
                 }).catch(() => {});
+                // 修复：skill 化 S3 改走 sendCardResult 后丢失了任务事件订阅——
+                // 补上 connectJobEvents，把 stage_await_files / stage_await_confirm /
+                // stage_failed / job_done 桥接进消息块（guidance 气泡 + 各卡片）。
+                try {
+                  const bioflow = useBioflowStore();
+                  const jobId = bf.active_job_id;
+                  console.log('[bioflow-guidance] sendCardResult 建立订阅 jobId=', jobId);
+                  bioflow.connectJobEvents(jobId, sessionId, {
+                    onEvent: (type, data, seq) => {
+                      const frame = patchBioflowEvent(aMsg, { type, data });
+                      if (frame) this.scrollSeq++;
+                      if (type === 'stage_await_confirm' && data) {
+                        patchBioflowGuidance(aMsg, data.guidance);
+                        patchBioflowForm(aMsg, data);
+                        this.scrollSeq++;
+                      } else if (type === 'stage_await_files' && data) {
+                        console.log('[bioflow-guidance] stage_await_files data=', JSON.stringify(data).slice(0, 200));
+                        patchBioflowGuidance(aMsg, data.guidance || data.message);
+                        patchBioflowFile(aMsg, data);
+                        this.scrollSeq++;
+                      } else if (type === 'stage_failed' && data) {
+                        patchBioflowGuidance(aMsg, data.guidance);
+                        patchBioflowDiagnosis(aMsg, data);
+                        this.scrollSeq++;
+                      } else if (type === 'job_done' && data) {
+                        patchBioflowGuidance(aMsg, data.guidance);
+                        if (data.delivery) patchBioflowDelivery(aMsg, data.delivery);
+                        const blk = patchBioflowArchiveSuggest(aMsg, data.job_id || jobId);
+                        if (blk) blk.jobId = data.job_id || jobId;
+                        this.scrollSeq++;
+                      }
+                    },
+                  });
+                } catch { /* EventSource 不可用：任务事件仍由快照兜底 */ }
               }
               try {
                 await this._persistFinal(aMsg, sessionId, 'done', { raw: aMsg.raw });
@@ -2625,7 +2716,12 @@ export const useChatStore = defineStore('chat', {
                 // S2：bioflow 帧（生信对话编排）不推 pipeline 相位——生信消息走
                 // bioflow 块，由 sendCardResult / bioflow 分支消费，此处仅记录。
                 const isBioflow = typeof p.stage === 'string' && p.stage.startsWith('bioflow_');
-                if (isBioflow) return;
+                if (isBioflow) {
+                  // 生信消息：一旦收到 bioflow 帧，立即移除检索 pipeline 骨架（避免闪烁残留）
+                  const pi = (aMsg.blocks || []).findIndex((b) => b && b.type === 'pipeline');
+                  if (pi >= 0) aMsg.blocks.splice(pi, 1);
+                  return;
+                }
                 if (!ctx.completedOnce && phase !== 'done') this._advancePipeline(aMsg, phase, label);
                 if (phase === 'done') {
                   // 上游 completed 事件：当前相位定格 done（此时 complete 尚未到达）
@@ -2664,18 +2760,68 @@ export const useChatStore = defineStore('chat', {
               // complete 帧之后流即关闭：同步收口，避免「流自然结束」误判为连接中断
               endTask();
               const payload = ev.payload || {};
+              // S2 多轮续接：生信规划返回的 chain/active_job_id 写回 session，
+              // 下轮（如路径选择「1」）据此跳过意图预筛续接生信 agent。
+              const bf = payload.bioflow || (payload.raw && payload.raw.bioflow) || {};
+              if (bf.chain || bf.active_job_id) {
+                updateSessionQuiet(sessionId, {
+                  meta: { bioflow: { active_job_id: bf.active_job_id || "", chain: bf.chain || "" } },
+                }).catch(() => {});
+                // 任务事件订阅：自然语言路径建任务后补 connectJobEvents，
+                // 把 stage_await_files / stage_await_confirm / stage_failed / job_done
+                // 桥接进消息块（文件卡/表单卡/诊断卡/交付卡），与卡片路径一致。
+                if (bf.active_job_id) {
+                  try {
+                    const bioflow = useBioflowStore();
+                    const jobId = bf.active_job_id;
+                    bioflow.connectJobEvents(jobId, sessionId, {
+                      onEvent: (type, data, seq) => {
+                        const frame = patchBioflowEvent(aMsg, { type, data });
+                        if (frame) this.scrollSeq++;
+                        if (type === 'stage_await_confirm' && data) {
+                          patchBioflowGuidance(aMsg, data.guidance);
+                          patchBioflowForm(aMsg, data);
+                          this.scrollSeq++;
+                        } else if (type === 'stage_await_files' && data) {
+                          patchBioflowGuidance(aMsg, data.guidance || data.message);
+                          patchBioflowFile(aMsg, data);
+                          this.scrollSeq++;
+                        } else if (type === 'stage_failed' && data) {
+                          patchBioflowGuidance(aMsg, data.guidance);
+                          patchBioflowDiagnosis(aMsg, data);
+                          this.scrollSeq++;
+                        } else if (type === 'job_done' && data) {
+                          patchBioflowGuidance(aMsg, data.guidance);
+                          if (data.delivery) patchBioflowDelivery(aMsg, data.delivery);
+                          const blk = patchBioflowArchiveSuggest(aMsg, data.job_id || jobId);
+                          if (blk) blk.jobId = data.job_id || jobId;
+                          this.scrollSeq++;
+                        }
+                      },
+                    });
+                  } catch { /* EventSource 不可用：任务事件仍由快照兜底 */ }
+                }
+              }
               const blocks = qaToBlocks(payload);
+              const isBioflow = !!(bf && bf.handled);
               updateLocal(() => {
                 // text 块先不放：由揭示动画以 stream 块渐进显示，终了替换为最终 text
-                aMsg.blocks = [
-                  aMsg.blocks[0],
-                  ...blocks.filter((b) => b.type !== 'text'),
-                ];
+                // 生信消息不显示检索 pipeline 骨架——直接挂生信卡片 + 自然语言。
+                aMsg.blocks = isBioflow
+                  ? [...blocks.filter((b) => b.type !== 'text')]
+                  : [aMsg.blocks[0], ...blocks.filter((b) => b.type !== 'text')];
+                // 生信卡片：路径卡/就绪卡/版本卡（与自然语言 answer 同时出现）
+                if (bf.plan) patchBioflowPlan(aMsg, bf.plan);
+                if (bf.readiness) patchBioflowReadiness(aMsg, bf.readiness);
+                if (bf.versioning) patchBioflowVersioning(aMsg, bf.versioning);
                 aMsg.raw = payload.raw ?? payload;
-                const pipe = aMsg.blocks[0];
-                pipe.status = 'done';
-                pipe.steps.forEach((s) => { s.state = 'done'; });
+                if (!isBioflow) {
+                  const pipe = aMsg.blocks[0];
+                  pipe.status = 'done';
+                  pipe.steps.forEach((s) => { s.state = 'done'; });
+                }
               });
+              console.log('[bioflow-debug] onComplete blocks=', (aMsg.blocks || []).map((b) => b && b.type), 'bf.handled=', !!(bf && bf.handled), 'bf.plan=', !!(bf && bf.plan));
               ctx.completedOnce = true;
               // 揭示动画（FR-CHAT-010）：stream 块瞬态、不落库
               if (payload.answer) {
@@ -2683,6 +2829,7 @@ export const useChatStore = defineStore('chat', {
               } else {
                 updateLocal(() => { aMsg.status = 'done'; });
               }
+              console.log('[bioflow-debug] after reveal blocks=', (aMsg.blocks || []).map((b) => b && b.type));
               const dur = ((Date.now() - startAt) / 1000).toFixed(1) + 's';
               // FR-PRIV-005：onComplete 整体替换 blocks 后 flush 私有 pending（防丢块）
               this._flushPrivate(aMsg);