index reload: refresh the entries behind already-registered stubs

_register_new_index_entries_as_stubs skipped every tool already in
_tools_by_id, so a stub minted from an install-time ad-hoc entry kept
serving that metadata-poor entry after the conf-driven populate
enriched the index — the fastp panel payload was missing
tool_shed_repository (test_only_latest_version_in_panel_fastp).

Swap the entry behind the existing stub instead: the panel and
registries hold the stub object, and _overrides survive.

lib/galaxy/tools/lazy_toolbox.py

@@ -1052,7 +1052,17 @@ class LazyToolBox(ToolBox):
         if self._tool_index is None:
             return
         for tool_id, entry in self._tool_index.entries.items():
-            if tool_id in self._tools_by_id:
+            # ``Any``: the registry is typed for real Tools but holds
+            # LazyTool stubs on this toolbox (same duck-typing as create_tool).
+            existing: Any = self._tools_by_id.get(tool_id)
+            if existing is not None:
+                if isinstance(existing, LazyTool) and existing._entry is not entry:
+                    # Refresh the stub in place — the panel and registries
+                    # hold this object, and the reloaded index may carry an
+                    # enriched entry (e.g. the conf-driven populate after a
+                    # shed install adds repository metadata the install-time
+                    # ad-hoc entry lacked). ``_overrides`` survive.
+                    existing._entry = entry
                 continue
             try:
                 self._register_lazy_entry(entry)

test/unit/app/tools/test_lazy_tool.py

@@ -366,6 +366,18 @@ def test_create_tool_stamps_data_manager_conf_id_on_entry():
     box._store.update_index_entry.assert_called_once_with(e)
 
 
+def test_index_reload_refreshes_existing_stub_entries():
+    box = _seam_box()
+    stale = _entry(id="fastp_guid")
+    stub = _stub(stale)
+    box._tools_by_id = {"fastp_guid": stub}
+    enriched = _entry(id="fastp_guid", tool_shed="toolshed.example.com", repository_name="fastp")
+    box._tool_index.entries["fastp_guid"] = enriched
+    box._register_new_index_entries_as_stubs()
+    assert stub._entry is enriched
+    assert stub.to_panel_entry()["tool_shed_repository"]["name"] == "fastp"
+
+
 def test_create_tool_raises_on_index_miss():
     # The populator owns the index — including the Galaxy-internal lib
     # tools listed in ``galaxy.tools.special_tools.hidden_lib_tool_paths``.