fix: deep-merge CLI agent-config with config file values

cecli/main.py

@@ -105,6 +105,31 @@ def convert_yaml_to_json_string(value):
     return value
 
 
+def merge_agent_config(cli_agent_config: str, file_agent_config) -> str:
+    """
+    Deep-merge the config-file agent-config into the CLI agent-config so CLI
+    values override individual keys while keys provided only by the config
+    files (e.g. skills_paths, skills_init) are preserved instead of being
+    discarded wholesale when --agent-config is passed on the CLI.
+
+    configargparse discards config-file values for options that are also given
+    on the command line, so without this merge a CLI --agent-config silently
+    drops every agent-config key that lives only in .cecli.conf.yml.
+    """
+    try:
+        from cecli.helpers.config_utils import deep_merge
+
+        file_ac = file_agent_config
+        if isinstance(file_ac, str):
+            file_ac = json.loads(file_ac)
+        cli_ac = json.loads(cli_agent_config)
+        if isinstance(file_ac, dict) and file_ac and isinstance(cli_ac, dict):
+            return json.dumps(deep_merge(file_ac, cli_ac, deep_merge_arrays=False))
+    except Exception:
+        pass
+    return cli_agent_config
+
+
 def check_config_files_for_yes(config_files):
     from cecli.decoding import safe_open
 
@@ -731,6 +756,11 @@ async def main_async(
 
     if hasattr(args, "agent_config") and args.agent_config is not None:
         args.agent_config = convert_yaml_to_json_string(args.agent_config)
+        # CLI --agent-config should deep-merge with (not replace) the
+        # agent-config from the merged config files so file-only keys
+        # (e.g. skills_paths, skills_init) are preserved.
+        file_agent_config = merged_config.get("agent-config") or merged_config.get("agent_config")
+        args.agent_config = merge_agent_config(args.agent_config, file_agent_config)
     if hasattr(args, "tui_config") and args.tui_config is not None:
         args.tui_config = convert_yaml_to_json_string(args.tui_config)
     if hasattr(args, "mcp_servers") and args.mcp_servers is not None:

tests/basic/test_agent_config_merge.py

@@ -0,0 +1,94 @@
+import json
+import os
+import tempfile
+
+import yaml
+
+from cecli.args import get_parser
+from cecli.helpers import config_utils
+from cecli.main import convert_yaml_to_json_string, merge_agent_config
+
+
+def test_cli_agent_config_merges_with_config_file():
+    """CLI --agent-config must deep-merge with the config-file agent-config
+    instead of replacing it wholesale (regression: file-only keys dropped)."""
+    file_ac = {
+        "command_timeout": 0,
+        "skip_cli_confirmations": True,
+        "tools_paths": ["/tmp/mytools"],
+        "skills_paths": ["/tmp/skills"],
+    }
+    cli = json.dumps({"command_timeout": 120})
+    merged = json.loads(merge_agent_config(cli, file_ac))
+    assert merged["command_timeout"] == 120  # CLI wins per-key
+    assert merged["skip_cli_confirmations"] is True  # file-only key preserved
+    assert merged["tools_paths"] == ["/tmp/mytools"]  # file-only key preserved
+    assert merged["skills_paths"] == ["/tmp/skills"]  # file-only key preserved
+
+
+def test_file_agent_config_given_as_json_string():
+    """Merged config from read_and_merge_all_configs holds agent-config as a
+    JSON string (YAML block scalar) - the helper must handle that form."""
+    file_ac = '{"command_timeout": 0, "skills_paths": ["/tmp/skills"]}'
+    merged = json.loads(merge_agent_config('{"skip_cli_confirmations": true}', file_ac))
+    assert merged["skip_cli_confirmations"] is True
+    assert merged["command_timeout"] == 0
+    assert merged["skills_paths"] == ["/tmp/skills"]
+
+
+def test_no_file_agent_config_returns_cli_unchanged():
+    """Without a config-file agent-config the merge must be a no-op."""
+    cli = '{"command_timeout": 120}'
+    assert merge_agent_config(cli, None) == cli
+    assert merge_agent_config(cli, {}) == cli
+    assert merge_agent_config(cli, "not json") == cli
+
+
+def test_nested_dict_keys_deep_merged():
+    """Nested dicts under agent-config are merged recursively, CLI wins."""
+    file_ac = {"nested": {"a": 1, "b": 2}}
+    merged = json.loads(merge_agent_config('{"nested": {"b": 9, "c": 3}}', file_ac))
+    assert merged["nested"] == {"a": 1, "b": 9, "c": 3}
+
+
+def test_cli_array_replaces_file_array():
+    """Arrays are not deep-merged: CLI list values win wholesale."""
+    file_ac = {"skills_paths": ["/tmp/file-skills"]}
+    merged = json.loads(merge_agent_config('{"skills_paths": ["/tmp/cli-skills"]}', file_ac))
+    assert merged["skills_paths"] == ["/tmp/cli-skills"]
+
+
+def test_main_async_pipeline_preserves_file_keys(tmp_path):
+    """Replicates main_async: merge config files -> temp yaml -> parser ->
+    CLI parse -> temp file deleted -> convert + merge against merged_config.
+
+    Guards against regressing to the broken baseline (re-parsing argv after
+    the temp config file was already unlinked yields no config-file values).
+    """
+    conf = tmp_path / ".cecli.conf.yml"
+    conf.write_text(
+        "agent-config: |\n"
+        '  {"skills_paths": ["./.cecli/skills"], "skills_init": ["android-cli"]}\n'
+    )
+    paths = [str(conf)]
+    merged_config = config_utils.read_and_merge_all_configs(paths, [], paths)
+
+    fd, tmp = tempfile.mkstemp(suffix=".yml", prefix="cecli_merged_")
+    os.close(fd)
+    with open(tmp, "w") as f:
+        yaml.dump(merged_config, f)
+    try:
+        parser = get_parser([tmp], None)
+        argv = ['--agent-config={"command_timeout": 0}']
+        args, _ = parser.parse_known_args(argv)
+    finally:
+        os.unlink(tmp)  # main_async deletes the temp file before the merge point
+
+    args.agent_config = convert_yaml_to_json_string(args.agent_config)
+    file_ac = merged_config.get("agent-config")
+    args.agent_config = merge_agent_config(args.agent_config, file_ac)
+
+    merged = json.loads(args.agent_config)
+    assert merged["command_timeout"] == 0
+    assert merged["skills_paths"] == ["./.cecli/skills"]
+    assert merged["skills_init"] == ["android-cli"]