diff --git a/bin/gstack-code-intelligence b/bin/gstack-code-intelligence
index 9bcca08ef..e9ea163f4 100755
--- a/bin/gstack-code-intelligence
+++ b/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);
diff --git a/lib/code-intelligence/index.ts b/lib/code-intelligence/index.ts
index 0c69719c8..6b387ff8c 100644
--- a/lib/code-intelligence/index.ts
+++ b/lib/code-intelligence/index.ts
@@ -12,6 +12,8 @@ export {
   setProvider,
   setConsent,
   hasConsent,
+  setRoot,
+  getRoot,
   type Selection,
 } from "./selection";
 export {
diff --git a/lib/code-intelligence/picker.ts b/lib/code-intelligence/picker.ts
index 0d31d1c28..56573bc91 100644
--- a/lib/code-intelligence/picker.ts
+++ b/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;
diff --git a/lib/code-intelligence/selection.ts b/lib/code-intelligence/selection.ts
index c6657aa06..22d98a69d 100644
--- a/lib/code-intelligence/selection.ts
+++ b/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];
+}