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>

src/bin/codegraph.ts

@@ -2351,6 +2351,7 @@ program
         method,
         resolveLatest: () => up.resolveLatestVersion(),
         run: up.defaultRun,
+        capture: up.defaultCapture,
         hasCommand: up.hasCommand,
         log: (m: string) => console.log(m),
         warn: (m: string) => warn(m),