feat: implement solution for #58

[crashfrog]

Summary

Implemented CLI strategy routing with --strategy flag for the torchbase run command. This allows users to select typing strategies with different speed/accuracy tradeoffs.

Implementation Details

CLI Changes

• Added --strategy flag to torchbase run with choices: fast, balanced, sensitive
• Default strategy is balanced (MinHash with alignment fallback)
• Strategy is only used for torches without embedded workflows
• Clear error message if user specifies --strategy with torch-embedded workflows

Built-in Workflows

Created three new workflow files in torchbase/workflows/builtin/:

• fast_typing.wdl - MinHash-only pipeline (fastest)
• balanced_typing.wdl - MinHash with conditional alignment (default)
• sensitive_typing.wdl - Full alignment-based calling (most accurate)

Routing Logic

• If torch has embedded workflow: use it (ignore --strategy)
• If --strategy specified and torch has no workflow: use matching built-in workflow
• If no --strategy and torch has no workflow: fallback to fetching default workflow (backward compatible)

Help Text

• Explains all strategy options with descriptions
• Notes speed/accuracy tradeoffs
• Warns about restriction with embedded workflows

Test Coverage

All 32 acceptance tests pass:

• Strategy flag presence tests (accepts fast/balanced/sensitive, rejects invalid)
• Default strategy tests (balanced is default)
• Routing tests (correct workflow selected for each strategy)
• Error handling tests (clear messages when strategy used with embedded workflows)
• Help text tests (all required information present)
• Integration tests (works with multi-scheme torches)

Backward Compatibility

Maintains backward compatibility:

• When --strategy not specified and torch has no workflow, falls back to default workflow fetch
• Existing torches with embedded workflows continue to work without --strategy

Co-Authored-By: Claude Sonnet 4.5 noreply@anthropic.com