source_store: discover per-conf stores from all_tool_config_files

Store discovery walked config.tool_configs, but in the standalone
populator CLI that list is never expanded to include shed_tool_config_file
(that expansion only happens during app boot). So a store declared with
store="..." on the shed tool_conf — the documented CVMFS pattern — was
invisible, and --target NAME failed with "not found; available:
[__default__]". Walk config.all_tool_config_files() in
_collect_per_conf_store_names, _build_stores, and _build_conf_to_store_map,
matching discover_tools. Regression test covers a store declared on the
shed conf.

Claude-Session: https://claude.ai/code/session_018L7ZmCv2ubKA3JNeSL8Pkr

lib/galaxy/tools/source_store/factory.py

@@ -81,10 +81,8 @@ def build_named_store(
 
 def _collect_per_conf_store_names(config: "GalaxyAppConfiguration") -> set[str]:
     """Walk configured tool_confs and collect referenced store names."""
-    if not config.tool_configs:
-        return set()
     names: set[str] = set()
-    for path in config.tool_configs:
+    for path in config.all_tool_config_files():
         try:
             parser = get_toolbox_parser(path)
         except Exception as e: