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>

lib/code-intelligence/selection.ts

@@ -18,9 +18,11 @@ export interface Selection {
   provider: CodeProviderId | null;
   /** Absolute repo path → consented. */
   consents: Record<string, boolean>;
+  /** Provider id → the absolute repo path it last indexed (so search finds it). */
+  roots: Record<string, string>;
 }
 
-const EMPTY: Selection = { provider: null, consents: {} };
+const EMPTY: Selection = { provider: null, consents: {}, roots: {} };
 
 function storePath(env: NodeJS.ProcessEnv = process.env): string {
   const home = env.GSTACK_HOME || join(env.HOME || homedir(), ".gstack");
@@ -35,6 +37,7 @@ export function readSelection(env: NodeJS.ProcessEnv = process.env): Selection {
     return {
       provider: raw.provider ?? null,
       consents: raw.consents && typeof raw.consents === "object" ? raw.consents : {},
+      roots: raw.roots && typeof raw.roots === "object" ? raw.roots : {},
     };
   } catch {
     return { ...EMPTY };
@@ -66,3 +69,15 @@ export function setConsent(repoPath: string, consented: boolean, env: NodeJS.Pro
 export function hasConsent(repoPath: string, env: NodeJS.ProcessEnv = process.env): boolean {
   return readSelection(env).consents[resolve(repoPath)] === true;
 }
+
+/** Record the repo path a provider last indexed, so search reads the same graph. */
+export function setRoot(provider: CodeProviderId, repoPath: string, env: NodeJS.ProcessEnv = process.env): Selection {
+  const current = readSelection(env);
+  const next: Selection = { ...current, roots: { ...current.roots, [provider]: resolve(repoPath) } };
+  write(next, env);
+  return next;
+}
+
+export function getRoot(provider: CodeProviderId, env: NodeJS.ProcessEnv = process.env): string | undefined {
+  return readSelection(env).roots[provider];
+}