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);

lib/code-intelligence/index.ts

@@ -12,6 +12,8 @@ export {
   setProvider,
   setConsent,
   hasConsent,
+  setRoot,
+  getRoot,
   type Selection,
 } from "./selection";
 export {

lib/code-intelligence/picker.ts

@@ -15,9 +15,9 @@
 
 import { localEngineStatus } from "../gbrain-local-status";
 import { GbrainProvider } from "./gbrain-adapter";
-import { GraphifyProvider, type GraphifyOptions } from "./graphify-adapter";
+import { GraphifyProvider, graphifyInstalled, type GraphifyOptions } from "./graphify-adapter";
 import { SourcebotProvider, type SourcebotOptions } from "./sourcebot-adapter";
-import { readSelection } from "./selection";
+import { readSelection, getRoot } from "./selection";
 import type { CodeProvider, CodeProviderId } from "./contract";
 
 /** Recommendation order — GBrain first. */
@@ -34,8 +34,12 @@ export function providerById(id: CodeProviderId, opts: PickerOptions = {}): Code
   switch (id) {
     case "gbrain":
       return new GbrainProvider();
-    case "graphify":
-      return new GraphifyProvider({ env: opts.env, ...opts.graphify });
+    case "graphify": {
+      // Default the graph root to the repo Graphify last indexed, so `search`
+      // reads the same graph `index` built (not whatever cwd happens to be).
+      const root = opts.graphify?.root ?? getRoot("graphify", opts.env);
+      return new GraphifyProvider({ env: opts.env, ...opts.graphify, ...(root ? { root } : {}) });
+    }
     case "sourcebot":
       return new SourcebotProvider({ env: opts.env, ...opts.sourcebot });
   }
@@ -65,14 +69,17 @@ export async function detectAvailable(opts: PickerOptions = {}): Promise<Availab
   const gbrainStatus = localEngineStatus({ env: opts.env });
   const gbrainOk = gbrainStatus === "ok" || gbrainStatus === "timeout";
 
-  let graphifyOk = false;
-  let graphifyDetail = "graphify CLI not installed";
-  try {
-    const s = await new GraphifyProvider({ env: opts.env, ...opts.graphify }).status();
-    graphifyOk = s.state === "ready";
-    graphifyDetail = graphifyOk ? "graph indexed in this repo" : "installed; no graph in this repo yet";
-  } catch {
-    graphifyOk = false;
+  // Available = the CLI is installed and selectable (NOT "a graph already exists
+  // here"). A freshly installed Graphify with no graph yet is still available.
+  const graphifyOk = graphifyInstalled(opts.env);
+  let graphifyDetail = "graphify CLI not installed (pip install graphifyy, Python >= 3.10)";
+  if (graphifyOk) {
+    try {
+      const s = await new GraphifyProvider({ env: opts.env, ...opts.graphify }).status();
+      graphifyDetail = s.state === "ready" ? "installed; graph built in this repo" : "installed; run `index` to build a graph";
+    } catch {
+      graphifyDetail = "installed";
+    }
   }
 
   let sourcebotOk = false;

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];
+}