# Diagnose Config

> Diagnose MegaLinter .mega-linter.yml configuration issues. Use when linters aren't running as expected or configuration seems wrong.

- Skill: `oxsecurity/diagnose-config` (Agent Skill)
- Install (CLI): `npx skillmds@latest add oxsecurity/diagnose-config`
- Raw SKILL.md: https://api.skillmd.com/api/skills/oxsecurity/diagnose-config/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: oxsecurity (https://skillmd.com/u/oxsecurity)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/oxsecurity/diagnose-config

---


Diagnose MegaLinter configuration. Read the `.mega-linter.yml` (or path provided in `$ARGUMENTS`) and check for:

1. **Configuration hierarchy**: Env vars override `.mega-linter.yml`, which overrides descriptor defaults. Both `.mega-linter.yml` and `.megalinter.yml` are recognized.
2. **ENABLE/DISABLE conflicts**: `ENABLE_LINTERS`/`DISABLE_LINTERS` take precedence over `ENABLE`/`DISABLE` (descriptor-level). You can't enable a linter if its descriptor is disabled.
3. **Filter patterns**: Validate `FILTER_REGEX_INCLUDE`/`FILTER_REGEX_EXCLUDE` regex syntax
4. **Linter variable naming**: Must be UPPERCASE with `_` separator matching the generated name `DESCRIPTOR_LINTERNAME` (e.g., `PYTHON_PYLINT_ARGUMENTS`, not `pylint_arguments`)
5. **Flavor compatibility**: If using a flavor image, verify the enabled linters exist in that flavor by checking `flavors/<flavor>/flavor.json`
6. **EXTENDS**: If using remote config inheritance via HTTPS URLs, verify they're accessible
7. **APPLY_FIXES**: Check the fix mode is compatible with the CI system — auto-commit requires write access to the branch
8. **Pre/Post commands**: Validate `PRE_COMMANDS` and `POST_COMMANDS` syntax (each needs `command` and `cwd` fields, `cwd` is `root` or `workspace`)
9. **Common mistakes**:
   - Using lowercase linter names (must be UPPERCASE)
   - Missing `_` separator in linter-specific vars
   - Setting `VALIDATE_ALL_CODEBASE=true` in CI (slow — usually want diff-only)
   - Forgetting `{LINTER}_FILTER_REGEX_INCLUDE/EXCLUDE` overrides global filters

Reference `megalinter/config.py` for the full resolution logic.