Word level prepass

[borgholt]

Description

• Added word-level prepass: 2-3x speed-up (default behavior)
• Introduced to SubgraphMetadata dataclass to make beam search instantiation work for subspans which is required by the word-level pass.
• Minor optimizations (e.g., using ref_idx and hyp_idx instead of property index which avoids wrapping the indices in a tuple for every code reference)

[codecov]

Codecov Report

❌ Patch coverage is 88.07018% with 34 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.22%. Comparing base (4de4067) to head (ff4c499).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
src/error_align/error_align.py	91.25%	9 Missing and 12 partials ⚠️
src/error_align/utils.py	31.25%	5 Missing and 6 partials ⚠️
src/error_align/backtrace_graph.py	92.85%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main       #4      +/-   ##
==========================================
- Coverage   94.89%   91.22%   -3.67%     
==========================================
  Files           6        6              
  Lines         548      661     +113     
  Branches       90      114      +24     
==========================================
+ Hits          520      603      +83     
- Misses         10       25      +15     
- Partials       18       33      +15     

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[JakobHavtorn]

Left a single comment.

[lifeiteng]

@borgholt Is it ready to merge?