fix(config): preserve YAML lists in hermes config set (#17876)

_set_nested unconditionally replaced any non-dict value with an empty
dict when walking the dotted path, which silently destroyed list-typed
config nodes the moment someone set a value with a numeric index
(e.g. 'hermes config set custom_providers.0.api_key NEW'). Any sibling
entries and any fields inside the targeted entry that the user didn't
write were lost.

Fix:
- _set_nested now detects list nodes and navigates by numeric index,
  and preserves both dicts AND lists at intermediate positions (scalars
  are still replaced so bare-scalar -> nested overrides keep working).
- set_config_value drops its duplicated navigation logic and calls
  _set_nested instead -- single source of truth for the rules.

Regression tests (tests/hermes_cli/test_set_config_value.py):
- test_indexed_set_preserves_sibling_list_entries -- exact #17876 repro
- test_indexed_set_preserves_non_targeted_fields -- inner-dict fields survive
- test_deeper_nesting_through_list -- dict -> list -> dict -> scalar path

35/35 existing + new tests pass.

E2E-verified with the issue's repro against a real on-disk config.yaml --
list stays a list, entry 0 updated, entry 1 intact.

Closes #17876

hermes_cli/config.py

@@ -2305,19 +2305,55 @@ def get_missing_env_vars(required_only: bool = False) -> List[Dict[str, Any]]:
     return missing
 
 
-def _set_nested(config: dict, dotted_key: str, value):
+def _set_nested(config, dotted_key: str, value):
     """Set a value at an arbitrarily nested dotted key path.
 
-    Creates intermediate dicts as needed, e.g. ``_set_nested(c, "a.b.c", 1)``
-    ensures ``c["a"]["b"]["c"] == 1``.
+    Supports both dict and list navigation:
+      _set_nested(c, "a.b.c", 1)     → c["a"]["b"]["c"] = 1
+      _set_nested(c, "a.0.b", 1)     → c["a"][0]["b"] = 1
+      _set_nested(c, "providers.1", "x") → c["providers"][1] = "x"
+
+    Intermediate dicts are created on demand.  List indices are parsed
+    from numeric path segments; the referenced index must already exist
+    (we do not grow lists — the user is navigating into structure they
+    wrote themselves).  If a segment targets a non-container leaf
+    (scalar), the leaf is replaced with a fresh dict so the write can
+    proceed — this preserves the pre-existing behavior for bare scalar
+    overrides (e.g. setting ``a.b.c`` where ``a.b`` was previously a
+    string).
+
+    Guards against #17876: before this fix the code unconditionally
+    replaced any non-dict value (including lists) with ``{}``, silently
+    destroying list-typed config like ``custom_providers`` whenever a
+    caller used an indexed path.
     """
     parts = dotted_key.split(".")
     current = config
     for part in parts[:-1]:
-        if part not in current or not isinstance(current.get(part), dict):
-            current[part] = {}
-        current = current[part]
-    current[parts[-1]] = value
+        if isinstance(current, list):
+            try:
+                idx = int(part)
+            except (TypeError, ValueError):
+                raise TypeError(
+                    f"Cannot navigate into list at key {dotted_key!r}: "
+                    f"segment {part!r} is not a numeric index"
+                )
+            current = current[idx]
+        elif isinstance(current, dict):
+            existing = current.get(part)
+            # Preserve dicts and lists; replace missing/scalar with a fresh dict.
+            if part not in current or not isinstance(existing, (dict, list)):
+                current[part] = {}
+            current = current[part]
+        else:
+            raise TypeError(
+                f"Cannot navigate into {type(current).__name__} at key {dotted_key!r}"
+            )
+    last = parts[-1]
+    if isinstance(current, list):
+        current[int(last)] = value
+    else:
+        current[last] = value
 
 
 def get_missing_config_fields() -> List[Dict[str, Any]]:
@@ -4421,15 +4457,11 @@ def set_config_value(key: str, value: str):
         except Exception:
             user_config = {}
     
-    # Handle nested keys (e.g., "tts.provider")
-    parts = key.split('.')
-    current = user_config
-    
-    for part in parts[:-1]:
-        if part not in current or not isinstance(current.get(part), dict):
-            current[part] = {}
-        current = current[part]
-    
+    # Handle nested keys (e.g., "tts.provider") including numeric list
+    # indices (e.g., "custom_providers.0.api_key").  Delegates to
+    # _set_nested which preserves list-typed nodes; before #17876 the
+    # inline navigation here silently overwrote lists with dicts.
+
     # Convert value to appropriate type
     if value.lower() in ('true', 'yes', 'on'):
         value = True
@@ -4439,8 +4471,8 @@ def set_config_value(key: str, value: str):
         value = int(value)
     elif value.replace('.', '', 1).isdigit():
         value = float(value)
-    
-    current[parts[-1]] = value
+
+    _set_nested(user_config, key, value)
     
     # Write only user config back (not the full merged defaults)
     ensure_hermes_home()