materialise data manager tools with their conf id

DataManagerTool resolves the registry by the <data_manager id> conf id,
which may differ from the tool XML id
(test_data_manager_async_submission_with_mismatched_conf_id). Eager
threads it through load_hidden_tool(data_manager_id=...); lazy
materialisation built the tool from the stored source alone, so
DataManagerTool.__init__ fell back to the tool id and
exec_after_process failed with 'Invalid data manager requested'.

Discovery now records the conf id, the index entry carries it, and
_create_tool_from_stored_source restores it at materialise time. Also
stamp is_local from the discovered guid — it defaulted True, which kept
the ToolConfRepository branch of the shed materialise path dead even
with repository metadata present.

lib/galaxy/tool_source_store/index.py

@@ -66,6 +66,12 @@ class ToolIndexEntry:
     # User-facing tags from ``<tool>`` config (distinct from ``labels``).
     # Surfaced for custom tool filters that bucket tools by tag.
     tags: list[str] = field(default_factory=list)
+    # ``<data_manager id="...">`` from the data manager conf that references
+    # this tool. The conf id and the tool XML id may differ;
+    # ``DataManagerTool.exec_after_process`` resolves the registry by conf
+    # id, so materialise must restore it (eager threads it through
+    # ``load_hidden_tool``).
+    data_manager_id: str | None = None
 
     # === Tests (for /api/tools/tests_summary) ===
     test_count: int = 0
@@ -159,6 +165,7 @@ class ToolIndexEntry:
             "require_login": self.require_login,
             "tool_type": self.tool_type,
             "tags": self.tags,
+            "data_manager_id": self.data_manager_id,
             "test_count": self.test_count,
             "requirements": self.requirements,
             "container_requirements": self.container_requirements,
@@ -202,6 +209,7 @@ class ToolIndexEntry:
             require_login=data.get("require_login", False),
             tool_type=data.get("tool_type", "default"),
             tags=data.get("tags", []),
+            data_manager_id=data.get("data_manager_id"),
             test_count=data.get("test_count", 0),
             requirements=data.get("requirements", []),
             container_requirements=data.get("container_requirements", []),

lib/galaxy/tools/lazy_toolbox.py

@@ -965,6 +965,13 @@ class LazyToolBox(ToolBox):
         # eager toolbox does and what callers consult via ``has_tool``
         # / ``get_tool`` and the ``_tools_by_id`` registry.
         kwds: dict[str, Any] = {"tool_dir": stored.tool_dir}
+        if entry and entry.data_manager_id:
+            # The registry is keyed by the ``<data_manager id>`` conf id,
+            # which may differ from the tool XML id.
+            # ``DataManagerTool.__init__`` falls back to the tool id when
+            # the kwd is missing and ``exec_after_process`` then can't find
+            # the manager — eager threads this through ``load_hidden_tool``.
+            kwds["data_manager_id"] = entry.data_manager_id
         if stored.tool_id and "/repos/" in stored.tool_id:
             kwds["guid"] = stored.tool_id
             # ``ToolConfRepository`` (lib/galaxy/tool_util/toolbox/base.py:87)