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

[devsoft-co-za]

OK here is the right one (I hope). Previously based PR off of experimental branch by mistake..

Recently I had an issue adding a skill to local cecli.conf.yml - it wasn't picked up. I asked Cecli to investigate and it ended up patching itself. Apparently the way the home directory and working directory configs are parsed was not working right when certain arguments were also included - resulted in my local skill not being recognized on startup.

Please have a look and see if this might help.

What I did:
Added a new skill to local directory

What happened:
The skill was not shown in "skills"

Command in question:
cecli --agent-config '{"command_timeout": 0, "skip_cli_confirmations": true}' --model deepseek/deepseek-v4-flash --editor-model deepseek/deepseek-v4-flash

My cecli.conf.yml for reference:

dark-mode: true
light-mode: false
agent: true
analytics: false
auto-commits: true
auto-save: true
auto-load: false
cache-prompts: true
check-update: true
debug: false
enable-context-compaction: true
multiline: false
preserve-todo-list: true
show-model-warnings: true
watch-files: false
tui: false

disable-playwright: true
yes-always: true

agent-config: |
  {
    "skills_paths": ["~/skills", "./.cecli/skills"],
    "skills_init": ["android-cli"],
    "large_file_token_threshold": 12500,
    "skip_cli_confirmations": true
  }

mcp-servers: |
  {
    "mcpServers": {
      "context7": {
        "type": "stdio",
        "command": "npx",
        "args": ["-y", "@upstash/context7-mcp"],
        "env": {
          "DEFAULT_MINIMUM_TOKENS": "6000"
        },
        "autoApprove": ["resolve-library-id", "get-library-docs"],
        "alwaysAllow": ["resolve-library-id", "get-library-docs"]
      },
      "fetch": {
        "type": "stdio",
        "command": "uvx",
        "args": ["--with", "mcp<2", "mcp-server-fetch"]
      },
      "brainfile": {
        "type": "stdio",
        "command": "npx",
        "args": ["@brainfile/cli", "mcp"]
      },
      "sequential-thinking": {
        "type": "stdio",
        "command": "npx",
        "args": [
            "-y",
            "@modelcontextprotocol/server-sequential-thinking"
        ]
        },
        "kitesurf": {
              "type": "stdio",
              "command": "npx",
              "args": [
                "-y",
                "chrome-devtools-mcp@latest",
                "--wsEndpoint=wss://kitesurf.cloudflare.app/devtools/browser"
              ],
              "enabled": true
            }
    }
  }

Skill is android-cli (in .cecli/skills)

Notification before patch:

cecli v1.0.5.dev+less
Models         deepseek-v4-flash (main)
Settings       agent (edit format)
Environment    no git repo • repo-map disabled
 ├─ Subagents  memorizer • worker
 └─ Servers    fetch • context7 • kitesurf • sequential-thinking • brainfile • Local

Notification after patch:

cecli v1.0.5.dev+less
Models         deepseek-v4-flash (main)
Settings       agent (edit format)
Environment    no git repo • repo-map disabled
 ├─ Subagents  memorizer • worker
 ├─ Skills     android-cli
 └─ Servers    kitesurf • sequential-thinking • context7 • fetch • brainfile • Local