docs(cli): fix includeDirectories nesting in configuration.md

[maru0804]

Update docs/cli/configuration.md to reflect the V2 schema structure where includeDirectories is nested under context object. This aligns the documentation with the actual implementation in packages/cli/src/config/settings.ts.

Changes:

• Update setting names from includeDirectories to context.includeDirectories
• Update setting names from loadMemoryFromIncludeDirectories to context.loadMemoryFromIncludeDirectories
• Update example settings.json to use nested structure

Fixes #14973

Summary

The documentation in docs/cli/configuration.md was still showing the deprecated V1 format for includeDirectories and loadMemoryFromIncludeDirectories settings. This PR updates the documentation to reflect the current V2 nested schema structure under the context object, which was introduced in PR #7244.

Details

• The codebase migrates includeDirectories to context.includeDirectories (confirmed in packages/cli/src/config/settings.ts MIGRATION_MAP)
• Updated three instances in the documentation:
  1. Setting definition for includeDirectories
  2. Setting definition for loadMemoryFromIncludeDirectories
  3. Example settings.json at the bottom of the configuration guide
• Other documentation files (docs/get-started/configuration.md, docs/cli/enterprise.md) already use the correct V2 format
• docs/get-started/configuration-v1.md intentionally maintains the old format as it documents the legacy V1 schema

Related Issues

Fixes #14973

How to Validate

1. Review the changes in docs/cli/configuration.md
2. Verify that the examples now match the V2 schema structure with nested context object
3. Confirm consistency with other documentation files that use the same settings
4. (Optional) Test that the nested format works correctly:

   Create a test settings.json with the nested format

   echo '{ "context": { "includeDirectories": ["../test-dir"] } }' > .gemini/settings.json gemini --help

   Pre-Merge Checklist

• [x] Updated relevant documentation and README (if needed)
• [x] Added/updated tests (if needed) - N/A for documentation-only changes
• [ ] Noted breaking changes (if any) - No breaking changes, documentation fix only
• [ ] Validated on required platforms/methods - N/A for documentation-only changes
  • Documentation changes do not require platform-specific validation