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`codegraph upgrade [version]` detects how the CLI was installed — the standalone install.sh/install.ps1 bundle, npm-global, npx, or a source checkout — and updates in place: re-running the canonical install.sh on macOS/Linux, an in-place rename-and-extract swap on Windows (a running node.exe can't be deleted, only renamed, so the detached-helper approach is avoided), and npm/npx/source-specific guidance otherwise. Flags: `--check` (report only), `--force`, and a positional version to pin. Each full index is now stamped with the engine's EXTRACTION_VERSION in project_metadata; `codegraph status` (and `--json`) flags an index built by an older engine and recommends re-indexing, and `upgrade` prints the same reminder. Gated on EXTRACTION_VERSION so it never nags on extraction-neutral releases. Validated end-to-end on macOS (real bundle upgrade), Linux (Docker, real curl|sh) and Windows (Parallels VM, real in-place swap). 32 new unit tests. Closes #679 Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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