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feat: discover files with `git ls-files` (respect .gitignore, skip nested worktrees) - #4

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Kevinrob wants to merge 3 commits into

ThinkyMiner:mainfrom

qoqa:feat/git-file-discovery

Commits on Oct 1, 2026
- fix: delete a file's edges by exact, indexed prefix match
  
  Kevinrob
  and
  claude
  committed
  94d13b5
- perf: memoize tree-sitter queries and remove quadratic graph build steps
  
  Kevinrob
  and
  claude
  committed
  2c89469
- feat: discover files with git ls-files and skip nested worktrees
  
  Kevinrob
  and
  claude
  committed
  866acb6