feat(cli): add codegraph upgrade self-update + stale-index re-index hint (#710)

`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>

install.ps1

@@ -5,8 +5,8 @@
 #
 #   irm https://raw.githubusercontent.com/colbymchenry/codegraph/main/install.ps1 | iex
 #
-# Re-run to upgrade. To uninstall: remove $env:LOCALAPPDATA\codegraph and drop
-# its \current\bin entry from your user PATH.
+# Upgrade with `codegraph upgrade` (or just re-run this). To uninstall: remove
+# $env:LOCALAPPDATA\codegraph and drop its \current\bin entry from your user PATH.
 #
 # Environment:
 #   CODEGRAPH_VERSION      release tag to install (default: latest)