fix(mcp): CLI readers no longer reopen include: [] as "all tools enabled"

The runtime already registers nothing for an explicit empty include list
(fb1ec36a4b), but every CLI reader still coerced `[]` to "no filter":
`hermes mcp list` printed "all", `hermes mcp configure` and `hermes tools`
pre-checked every tool (so confirming the picker silently re-enabled all of
them), and a catalog reinstall pre-checked the manifest defaults over the
user's zero-tool choice.

`_tool_filters` now returns the list whenever the key holds a list; only an
absent/non-list key is None. The pickers and list output branch on `is not
None`, matching `tools/mcp_tool_registration.py`.

Fixes #12865. Builds on #13096 (@dingn42) and #52874 (@Bartok9).

hermes_cli/mcp_catalog.py

@@ -576,7 +576,9 @@ def _apply_tool_selection(
         )
         return
 
-    pre_set = {n for n in (prior_selection or entry.tools.default_enabled or tool_names) if n in tool_names}
+    # A prior ``include: []`` (user chose zero tools) outranks manifest defaults, like the non-TTY path.
+    preferred = prior_selection if prior_selection is not None else (entry.tools.default_enabled or tool_names)
+    pre_set = {n for n in preferred if n in tool_names}
     pre_indices = {i for i, n in enumerate(tool_names) if n in pre_set}
     _say(f"  Found {len(probed)} tool(s). Pre-checked: {len(pre_indices)}.")