mypy: fix type errors flagged by lint + packages jobs

- AbstractToolBox gains a no-op invalidate_index_cache (LazyToolBox
  overrides it); shed installs no longer depend on the subclass type.
- Annotate LazyToolboxSearch.build_index, ToolFileWatcher.observer,
  populator session cast, UUID key coercion in _register_lazy_entry,
  and drop stale type: ignore comments.

lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py

@@ -161,7 +161,9 @@ class ToolPanelManager:
 
                     populate_for_paths(
                         self.app.config,
-                        self.app.model.context,
+                        # Lazy mode implies a full Galaxy app, which carries
+                        # ``model`` beyond the InstallationTarget protocol.
+                        self.app.model.context,  # type: ignore[attr-defined]
                         paths=new_paths,
                         rebuild_whoosh=True,
                     )

lib/galaxy/tool_source_store/discover.py

@@ -134,7 +134,7 @@ def _resolve_file_template_kwds(root_dir: str | None) -> dict[str, str]:
     """
     try:
         # Lazy + optional: helper must still work outside a galaxy install.
-        from galaxy.tools import MODEL_TOOLS_PATH  # type: ignore[attr-defined]
+        from galaxy.tools import MODEL_TOOLS_PATH
     except Exception:
         if root_dir:
             MODEL_TOOLS_PATH = os.path.abspath(os.path.join(root_dir, "lib", "galaxy", "tools"))

lib/galaxy/tool_source_store/populator.py

@@ -41,6 +41,7 @@ from datetime import (
 from pathlib import Path
 from typing import (
     Any,
+    cast,
 )
 
 from galaxy.tool_source_store import (
@@ -65,6 +66,7 @@ from galaxy.config import GalaxyAppConfiguration
 from galaxy.datatypes.registry import Registry
 from galaxy.model import set_datatypes_registry
 from galaxy.model.mapping import init_models_from_config
+from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.queues import galaxy_exchange
 from galaxy.tool_source_store import build_tool_source_store
 from galaxy.tool_source_store.search import (
@@ -169,7 +171,9 @@ class ToolFileWatcher:
         self.verbose = verbose
         # Injected so tests can substitute a fake; default is the AMQP notifier.
         self._notify = notify_callable or send_reload_notification
-        self.observer = None
+        # ``watchdog`` observer; typed Any because watchdog is an optional
+        # dependency imported inside :meth:`start`.
+        self.observer: Any = None
         self._pending_changes: set[str] = set()
         self._lock = threading.Lock()
         self._debounce_timer: threading.Timer | None = None
@@ -862,7 +866,7 @@ def watch_mode(
 
     log.info(f"Building tool source store (backend: {config.tool_source_store})...")
 
-    store = build_tool_source_store(config, model.context)
+    store = build_tool_source_store(config, cast("galaxy_scoped_session", model.context))
 
     # Determine directories to watch from tool configurations
     tools_dirs_set: set[Path] = set()

lib/galaxy/tool_util/toolbox/base.py

@@ -894,6 +894,14 @@ class AbstractToolBox(ManagesIntegratedToolPanelMixin):
                 return [tool]
         return []
 
+    def invalidate_index_cache(self) -> None:
+        """Drop any cached tool-index state.
+
+        No-op for the eager toolbox — there is no external index to go
+        stale. ``LazyToolBox`` overrides this to re-read the persistent
+        ``ToolIndex`` after an out-of-band populator write.
+        """
+
     def tools(self):
         # Snapshot the id list so a concurrent shed install can't mutate
         # the dict mid-iteration.

lib/galaxy/tools/lazy_toolbox.py

@@ -972,11 +972,11 @@ class LazyToolBox(ToolBox):
             if not any(getattr(t, "id", None) == tool_id for t in bucket):
                 bucket.append(stub)  # type: ignore[arg-type]
         if entry.uuid:
-            self._tools_by_uuid[entry.uuid] = stub  # type: ignore[assignment]
+            self._tools_by_uuid[UUID(entry.uuid)] = stub  # type: ignore[assignment]
         # Lineage: LazyLineageMap builds it from entries_by_version, which the
         # populator wrote on the previous step, so .get() returns the right
         # ToolLineage; register() is the fallback for an as-yet-unseen id.
-        stub._lineage = self._lineage_map.get(tool_id) or self._lineage_map.register(stub)
+        stub._lineage = self._lineage_map.get(tool_id) or self._lineage_map.register(stub)  # type: ignore[arg-type]
         # Place into the panel. The populator stamped panel_section_id /
         # panel_section_name onto the entry; create the ToolSection if it
         # doesn't already exist (peer-process install of the first tool in
@@ -990,7 +990,7 @@ class LazyToolBox(ToolBox):
                 self._tool_panel[section_key] = section
             section.elems.append_tool(stub)
         else:
-            self._tool_panel[f"tool_{tool_id}"] = stub  # type: ignore[assignment]
+            self._tool_panel[f"tool_{tool_id}"] = stub
         return stub
 
     def _register_loaded_tool(self, tool: "Tool") -> None:

lib/galaxy/tools/search/__init__.py

@@ -30,6 +30,7 @@ import os
 import re
 import shutil
 from typing import (
+    Any,
     TYPE_CHECKING,
 )
 
@@ -149,7 +150,7 @@ class LazyToolboxSearch(ToolBoxSearch):
         self.panel_searches: dict[str, ToolPanelViewSearch] = {}
         self.index_count = -1
 
-    def build_index(self, tool_cache, toolbox, index_help: bool = True) -> None:
+    def build_index(self, tool_cache: Any, toolbox: Any, index_help: bool = True) -> None:
         # Populator side owns whoosh writes; bump the watermark so the
         # rebuild_toolbox_search_index control task observes "in sync".
         self.index_count += 1

lib/galaxy/webapps/galaxy/services/tools.py

@@ -689,7 +689,7 @@ class ToolsService(ServiceBase):
         for hit in self._search(query, view) or []:
             try:
                 tool = self._get_tool(trans, hit, user=trans.user)
-                if tool:
+                if tool and tool.id:
                     results.append(tool.id)
             except exceptions.AuthenticationFailed:
                 pass

test/unit/app/tools/test_lazy_tool.py

@@ -124,7 +124,7 @@ def test_to_panel_entry_does_not_materialise():
 
 
 def test_to_dict_materialises():
-    calls = []
+    calls: list[Any] = []
 
     class _Real:
         def to_dict(self, trans, link_details, tool_help, **kw):