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fix(index): prevent triple indexing when non-git parent contains git repos (#81)

* fix(index): prevent triple indexing when non-git parent contains git repos

When a non-git parent directory contains independent git subdirectories,
indexing the parent would include all files from nested repos. Then
indexing a sub-repo separately created a duplicate index with the same
files.

This change:
- Skips nested git repo directories during merkle walk when the project
  root is not itself a git repository
- Auto-discovers and indexes each nested git repo separately when
  running `lumen index` on a non-git parent
- Normalizes projectPath to the git repository root in both `cmd/index.go`
  and `cmd/hook.go` so DB paths are consistent

Closes #71

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix(test): use git-initialized sample project in CLI E2E tests

The RepoRoot normalization added in 8d4065b resolves subdirectories to
their enclosing git repo root. Since testdata/sample-project has no .git,
it was being resolved to the lumen repo root, causing the CLI tests to
index the entire codebase and exceed the embedding model's context length.

Fix by copying the sample project to a temp dir with `git init` so
RepoRoot resolves to the temp dir itself.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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