Sam Morrow 1777da6eba Add feature-flagged compare_file_contents tool with semantic diffs ...

Add a new compare_file_contents MCP tool that compares two versions of a
file across refs (branches, tags, or SHAs). For structured data formats
(JSON, YAML, CSV, TOML), it produces semantic diffs that show only
meaningful changes, ignoring formatting differences. For unsupported
formats, it falls back to unified diff.

Key features:
- Semantic diffs for JSON, YAML, CSV, TOML files
- Unified diff fallback for code and other text files
- Handles new files (base not found) and deleted files (head not found)
- 1MB max file size to prevent excessive server-side processing
- Gated behind 'compare_file_contents' feature flag

This helps AI models by:
- Reducing token usage (formatting noise eliminated)
- Providing unambiguous before/after semantics
- Enabling self-verification of edits to config/data files

Refs: #1973

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