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>

README.md

@@ -57,6 +57,8 @@ npm i -g @colbymchenry/codegraph
 
 <sub>CodeGraph bundles its own runtime — nothing to compile, no native build, works the same everywhere. The installer puts `codegraph` on your PATH but **doesn't change your current shell** — open a new terminal before the next step so the command resolves.</sub>
 
+<sub>**Upgrade any time** with `codegraph upgrade` — it detects how you installed (bundle, npm, or npx) and updates in place. Add `--check` to see if an update is available, or `codegraph upgrade <version>` to pin one.</sub>
+
 ### 2. Wire up your agent(s)
 
 In a **new terminal**, run the installer to connect CodeGraph to the agents you use:
@@ -465,6 +467,7 @@ codegraph callees <symbol>        # Find what a function/method calls (--limit,
 codegraph impact <symbol>         # Analyze what code is affected by changing a symbol (--depth, --json)
 codegraph affected [files...]     # Find test files affected by changes (see below)
 codegraph serve --mcp             # Start MCP server
+codegraph upgrade [version]       # Update to the latest release (--check, --force)
 ```
 
 ### `codegraph affected`