docs: Add missing configuration options to configurations.md (#1186)
- Add disabled_commands section with available commands
- Add comment_checker configuration (custom_prompt)
- Add notification configuration (force_enable)
- Add sisyphus tasks & swarm configuration sections
- Add staleTimeoutMs to background_task section
- Add dynamic_context_pruning to experimental section with full documentation
- Extend skills configuration with advanced options (sources, custom skills)
- Extend agents configuration with missing options (category, variant, maxTokens, thinking, reasoningEffort, textVerbosity, providerOptions)
- Extend categories configuration with missing options (description, is_unstable_agent)
- Extend LSP configuration with missing server options (env, initialization, disabled) and detailed examples
- Add missing hooks (auto-slash-command, sisyphus-junior-notepad, start-work) to hooks list
- Update available agents list to include all agents from schema
Co-authored-by: GitHub Actions <actions@github.com>
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