fix(upgrade): stop npm installs self-shadowing on upgrade; verify the resolved version after every upgrade (#1238, #1071) (#1245)

Two fixes to make `codegraph upgrade` trustworthy in the terminal it ran in:

1. detectInstallMethod checked the bundle layout before the node_modules
   path check, but the npm thin-installer's per-platform package IS a
   complete bundle inside node_modules — so every npm install misdetected
   as a standalone bundle, and upgrade curled install.sh into ~/.codegraph:
   a second install that never wins the PATH race against npm's shim,
   leaving `codegraph -v` permanently on the old version. Path-based
   checks (_npx, node_modules) now win over layout sniffing, so npm
   installs upgrade through npm again, in place.

2. After a successful swap, runUpgrade now probes the PATH-resolved
   `codegraph --version` and reports the real outcome: a green
   confirmation that this terminal already serves the new version, a
   loud shadow warning naming the fix (`which -a codegraph`) on
   mismatch, or the old soft new-terminal hint only when the probe is
   inconclusive. Replaces the unconditional "open a new terminal if the
   version looks unchanged" hedge. Skipped for npm-local installs, whose
   binary PATH never serves.

Companion to #1239: the misdetection also broke its post-upgrade
`install --refresh` for npm users (the spawn resolved the stale shim).

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

CHANGELOG.md

@@ -11,6 +11,8 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
+- `codegraph upgrade` on an npm install now upgrades through npm again instead of quietly creating a second copy that never wins the PATH race — previously `codegraph --version` kept reporting the old version forever, no matter how many times you upgraded. (#1238)
+- After every upgrade, CodeGraph now checks that the `codegraph` command your terminal resolves actually serves the freshly installed version — confirming you don't need a new terminal, or telling you exactly which stale install is shadowing the new one. (#1071)
 - The safety watchdog no longer kills a healthy index on severely degraded storage. It used to judge liveness purely by the event loop, so one long database write on a struggling disk looked identical to a hung process and could get a valid, in-progress index terminated. During `codegraph index`/`codegraph init` the watchdog now also checks whether the index files on disk are advancing before it acts: slow-but-progressing work is left alone (bounded by a hard cap), while a genuinely hung process is still killed exactly as fast as before. (#1231)
 
 ## [1.4.0] - 2026-07-10