Apply template exclusions when combining schemas

[Copilot]

When combining multiple templates (e.g., ms-proteomics + metaproteomics), exclusions declared by any template were ignored. The metaproteomics template explicitly excludes sample-metadata, but columns from that excluded template were still required when combined with ms-proteomics.

Changes

• Model Updates: Added excludes field to SchemaDefinition to represent template exclusions from YAML
• Exclusion Resolution: Implemented _get_excluded_templates() to collect all excluded templates from schemas being combined
• Column Filtering: Added _get_template_columns() to recursively identify columns defined by a template (including inherited columns)
• Schema Combination: Modified combine_schemas() to filter out columns belonging to excluded templates before returning the combined schema

Example exclusion in YAML:

name: metaproteomics
excludes:
  templates:
    - sample-metadata

When combine_schemas(['ms-proteomics', 'metaproteomics']) is called, columns from sample-metadata (such as characteristics[organism], characteristics[organism part]) are now properly excluded from the combined schema.

• Fixes Metaproteomics exclusions are ignored when combining templates #333

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