fix: score removed source files with tree diff

[volcano303]

Summary

• Route removed source files with available base content through tree-diff scoring instead of skipping before content lookup.
• Preserve skip behavior for removed non-code files, missing base content, oversized files, and unsupported extensions.
• Add pipeline-level regression coverage for removed source files with and without old content.

Related Issues

Fixes #1268

Type of Change

• Bug fix
• New feature
• Refactor
• Documentation
• Other (describe below)

Testing

• Tests added/updated
• Manually tested

Commands run:

.venv312/bin/python -m pytest tests/validator/test_token_scoring_integration.py -q
.venv312/bin/python -m ruff check gittensor/validator/utils/tree_sitter_scoring.py tests/validator/test_token_scoring_integration.py
.venv312/bin/python -m ruff format --check gittensor/validator/utils/tree_sitter_scoring.py tests/validator/test_token_scoring_integration.py

Note: uv run pytest tests/validator/test_token_scoring_integration.py -q could not complete in this workspace because uv selected Python 3.14 and failed building bittensor-wallet while bootstrapping Rust/cargo.

Checklist

• Code follows project style guidelines
• Self-review completed
• Changes are documented (if applicable)