fix: persist indexed repo per provider and detect installs honestly

search was running in cwd and missing the repo you indexed. Persist the indexed
path per provider in the selection store and resolve it back so `search` reads
the same graph `index` built. Graphify availability now checks `graphify --version`
(installed = selectable) instead of "a graph already exists here", and the CLI
keys Graphify sources on the repo path.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

bin/gstack-code-intelligence

@@ -29,6 +29,7 @@ import {
   resolveSelectedProvider,
   setConsent,
   setProvider,
+  setRoot,
   type CodeProviderId,
 } from "../lib/code-intelligence";
 
@@ -98,11 +99,15 @@ async function cmdIndex(pathArg: string | undefined): Promise<void> {
   if (!provider!.local && !consented) {
     fail(`${provider!.label} would send this repo's content off the machine. Run \`gstack-code-intelligence consent ${repoPath}\` first.`);
   }
-  const repo = { id: basename(repoPath), path: repoPath };
+  // Graphify keys sources on the repo path; GBrain/Sourcebot on a short id.
+  const sourceId = provider!.id === "graphify" ? repoPath : basename(repoPath);
+  const repo = { id: sourceId, path: repoPath };
   try {
     const registered = await provider!.registerSource(repo, { consented });
     out(`registered ${repo.id} with ${provider!.label} (${registered.state})`);
     const refreshed = await provider!.refresh({ id: registered.id }, { consented });
+    // Remember which repo this provider indexed so `search` reads the same graph.
+    setRoot(provider!.id, repoPath);
     out(`indexed: ${refreshed.state}${refreshed.itemCount != null ? ` (${refreshed.itemCount} items)` : ""}`);
   } catch (err) {
     handleProviderError(err, provider!.label);