diff --git a/backend/local_rag.py b/backend/local_rag.py
index 0fa65fd..195e56f 100644
--- a/backend/local_rag.py
+++ b/backend/local_rag.py
@@ -180,6 +180,22 @@ def _collect_library_paths(slug: str) -> Dict[str, Path]:
     }
 
 
+def _cleanup_generated_artifacts(slug: str) -> None:
+    paths = _collect_library_paths(slug)
+    for key in (
+        "corpus",
+        "enhanced",
+        "shadow",
+        "shadow_index",
+        "shadow_store",
+        "content_index",
+        "content_store",
+    ):
+        target = paths[key]
+        if target.exists():
+            target.unlink()
+
+
 def library_payload(data: Dict[str, Any]) -> Dict[str, Any]:
     paths = _collect_library_paths(data["slug"])
     files = list(data.get("files", []))
@@ -315,6 +331,80 @@ def _mark_pipeline_stage(slug: str, stage: str, source_signature: Optional[str])
     write_library(slug, data)
 
 
+def _set_pending_prepare_signature(data: Dict[str, Any], source_signature: Optional[str]) -> None:
+    pipeline = data.get("pipeline")
+    if not isinstance(pipeline, dict):
+        pipeline = {}
+        data["pipeline"] = pipeline
+
+    if source_signature:
+        pipeline["pending_prepare_signature"] = source_signature
+        pipeline["pending_prepare_updated_at"] = now_iso()
+    else:
+        pipeline.pop("pending_prepare_signature", None)
+        pipeline.pop("pending_prepare_updated_at", None)
+
+
+def _clear_pending_prepare(slug: str) -> None:
+    path = lib_json(slug)
+    if not path.exists():
+        return
+
+    data = _read_json(path)
+    _set_pending_prepare_signature(data, None)
+    write_library(slug, data)
+
+
+async def _ensure_prepare_job(slug: str) -> Optional[str]:
+    path = lib_json(slug)
+    if not path.exists():
+        return None
+
+    lock = LIB_LOCKS.setdefault(slug, asyncio.Lock())
+    async with lock:
+        if _has_active_job(slug):
+            return None
+
+        data = read_library(slug)
+        payload = library_payload(data)
+        pipeline = _pipeline_meta(data)
+        pending_signature = pipeline.get("pending_prepare_signature")
+
+        if not payload["states"].get("has_files") or not pending_signature:
+            return None
+        if payload["states"].get("is_indexed") and payload.get("source_signature") == pending_signature:
+            _clear_pending_prepare(slug)
+            return None
+
+        return _start_job(slug, "prepare")
+
+
+async def _handle_post_job_state(slug: str, job_type: str, status: str) -> None:
+    path = lib_json(slug)
+    if not path.exists():
+        return
+
+    data = read_library(slug)
+    payload = library_payload(data)
+    pipeline = _pipeline_meta(data)
+    pending_signature = pipeline.get("pending_prepare_signature")
+
+    if not payload["states"].get("has_files"):
+        _clear_pending_prepare(slug)
+        _cleanup_generated_artifacts(slug)
+        return
+
+    if pending_signature and payload["states"].get("is_indexed") and payload.get("source_signature") == pending_signature:
+        _clear_pending_prepare(slug)
+        return
+
+    if status != "succeeded":
+        return
+
+    if pending_signature and not payload["states"].get("is_indexed"):
+        await _ensure_prepare_job(slug)
+
+
 def _scaled_progress(on_progress, start: float, end: float, prefix: str):
     def wrapped(phase: str, pct: float, detail: str):
         clamped = min(1.0, max(0.0, float(pct)))
@@ -431,6 +521,10 @@ async def _run_job(job_id: str, fn_name: str, **kwargs):
         job["error"] = f"{type(exc).__name__}: {exc}"
     finally:
         job["finished_at"] = now_iso()
+        try:
+            await _handle_post_job_state(job["slug"], fn_name, job["status"])
+        except Exception:
+            pass
 
 
 def _start_job(slug: str, job_type: str, **kwargs) -> str:
@@ -537,7 +631,7 @@ def delete_library(slug: str):
 
 
 @router.post("/libraries/{slug}/files/register")
-def register_paths(slug: str, req: RegisterPathsRequest):
+async def register_paths(slug: str, req: RegisterPathsRequest):
     data = read_library(slug)
     stage = stage_dir(slug)
     existing = {entry.get("sha256"): entry for entry in data.get("files", [])}
@@ -566,26 +660,44 @@ def register_paths(slug: str, req: RegisterPathsRequest):
         added.append(entry)
         existing[sha] = entry
 
+    job_id = None
+    if added:
+        _set_pending_prepare_signature(data, _source_signature(data.get("files", [])))
     write_library(slug, data)
+    if added:
+        job_id = await _ensure_prepare_job(slug)
     return {
         "added": added,
         "skipped": skipped,
+        "job_id": job_id,
         "library": library_payload(data),
     }
 
 
 @router.delete("/libraries/{slug}/files")
-def remove_file(slug: str, req: RemoveFileRequest):
+async def remove_file(slug: str, req: RemoveFileRequest):
     data = read_library(slug)
-    before = len(data.get("files", []))
-    data["files"] = [entry for entry in data.get("files", []) if entry.get("rel") != req.rel]
+    files = list(data.get("files", []))
+    removed = next((entry for entry in files if entry.get("rel") == req.rel), None)
+    if not removed:
+        raise HTTPException(status_code=404, detail="File not found")
+
+    data["files"] = [entry for entry in files if entry.get("rel") != req.rel]
     symlink_path = stage_dir(slug) / req.rel
     if symlink_path.exists():
         symlink_path.unlink()
+
+    source_signature = _source_signature(data.get("files", []))
+    _set_pending_prepare_signature(data, source_signature)
     write_library(slug, data)
-    if len(data["files"]) == before:
-        raise HTTPException(status_code=404, detail="File not found")
-    return {"ok": True, "library": library_payload(data)}
+
+    job_id = None
+    if source_signature:
+        job_id = await _ensure_prepare_job(slug)
+    else:
+        _cleanup_generated_artifacts(slug)
+
+    return {"ok": True, "job_id": job_id, "library": library_payload(data)}
 
 
 @router.post("/libraries/{slug}/jobs/build")