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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Add deep merge support for array fields in .cecli.conf.yml","articleBody":"## Feature Request\n\nAdd support for array fields in configuration files with different merge behaviors:\n- **`.cecli.conf.yml`**: Deep merge on array fields (merge entries into existing arrays)\n- **`.cecli/conf.yml`**: Shallow merge (existing behavior - replaces entire arrays)\n\n### Current Behavior\nBoth `.cecli.conf.yml` and `.cecli/conf.yml` perform shallow merges on array fields, meaning that when an array is specified in a config file, it completely replaces the existing array values rather than merging with them.\n\n### Problem\nUsers cannot additively extend configuration arrays (like `read`, `rules`, `skills_paths`, `mcp-servers-files`, `subagents_paths`, `tools_paths`, etc.) without completely overriding the defaults. This makes it difficult to incrementally add configuration entries.\n\n### Example Use Case\nIf the default configuration includes:\n```yaml\nread:\n  - \"src/**/*.py\"\n  - \"tests/**/*.py\"\n```\n\nA user who wants to add `docs/**/*.md` must currently specify ALL files:\n```yaml\nread:\n  - \"src/**/*.py\"\n  - \"tests/**/*.py\"\n  - \"docs/**/*.md\"  # Must remember to include defaults\n```\n\nWith deep merge, they could simply add:\n```yaml\nread:\n  - \"docs/**/*.md\"  # Automatically merged with defaults\n```\n\n### Proposed Solution\n\n1. **Configuration Hierarchy**: Maintain existing hierarchy where `.cecli.conf.yml` (in project root) has higher precedence than `.cecli/conf.yml` (in `.cecli` directory).\n\n2. **Merge Behavior**:\n   - `.cecli.conf.yml`: Perform **deep merge** on array fields. New entries are appended/merged with existing values rather than replacing them.\n   - `.cecli/conf.yml`: Maintain **shallow merge** (current behavior) for backward compatibility.\n\n3. **Array Field Detection**: Identify which configuration fields are arrays that should support deep merging:\n   - `read`\n   - `rules`\n   - `skills_paths`\n   - `mcp-servers-files`\n   - `subagents_paths`\n   - `tools_paths`\n   - Other array fields as needed\n\n4. **Implementation Strategy**:\n   - Modify the configuration loading/merging logic to detect the config file type.\n   - For `.cecli.conf.yml`, use a deep merge algorithm for arrays (append unique entries, preserve order).\n   - For `.cecli/conf.yml`, continue using shallow merge (replace).\n   - Ensure backward compatibility: existing configs continue to work unchanged.\n\n5. **Deduplication**: When deep merging arrays, deduplicate entries based on value to avoid duplicates.\n\n### Technical Considerations\n\n- **Order Preservation**: Deep merge should append new entries to the end of existing arrays, maintaining the order of both existing and new items.\n- **Deduplication**: Use value-based deduplication (not object identity) to prevent duplicate entries.\n- **Nested Arrays**: Determine if nested arrays should also be deep-merged (likely yes, but need to define scope).\n- **Performance**: Deep merge should be efficient even with large configuration arrays.\n- **Error Handling**: Handle malformed YAML gracefully with clear error messages.\n\n### Acceptance Criteria\n\n- [ ] Identify all array configuration fields that need deep merge support.\n- [ ] Implement deep merge algorithm for arrays in `.cecli.conf.yml`.\n- [ ] Maintain shallow merge behavior for `.cecli/conf.yml`.\n- [ ] Ensure backward compatibility - existing configs work without changes.\n- [ ] Add comprehensive tests for:\n  - Deep merge of arrays\n  - Shallow merge preservation\n  - Deduplication\n  - Nested array handling\n  - Error cases (malformed YAML, invalid arrays)\n- [ ] Update documentation to explain the new merge behavior and configuration options.\n- [ ] Add examples showing how to use the new feature.\n\n### Jira Task\n\nThis issue is aligned with Jira task [CLI-57](https://team-16702636586024.atlassian.net/browse/CLI-57).\n\n### Configuration File Precedence\n\nReminder of existing precedence (highest to lowest):\n1. Command-line arguments\n2. `.cecli.conf.yml` (project root) - **Will support deep merge on arrays**\n3. `.cecli/conf.yml` (in `.cecli` directory) - **Shallow merge (existing)**\n4. Default values","author":{"url":"https://github.com/szmania","@type":"Person","name":"szmania"},"datePublished":"2026-07-14T17:59:11.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":0},"url":"https://github.com/604/cecli/issues/604"}