fix: optimization issues #125, #127, #126#441
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- #125: Eliminate process-per-call and quadratic scans — HashMap indexes + graph cache with mtime invalidation - #127: Replace global mutable state in cache.zig with injected CacheState struct - #126: Decompose tools.zig — extract repo.zig and graph_tools.zig, fix runChainStep 9-arg signature Co-authored-by: trilokagent <275208033+trilokagent@users.noreply.github.com>
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Summary
Co-authored-by: trilokagent 275208033+trilokagent@users.noreply.github.com
Closes #125, Closes #127, Closes #126