Remove deprecated `include_custom` directive

When running the tests, there is a warning about include_custom:
```
Warning: 06 23:22:51,753] [WARNING] In layer s2_l2a: The 'include_custom' directive is deprecated and will be removed in version 1.9. Please refer to the documentation for information on how to migrate your configuration to the new 'custom_includes' directive.
```
