diff --git a/gitnexus/hooks/claude/gitnexus-hook.cjs b/gitnexus/hooks/claude/gitnexus-hook.cjs
index 7bfa150cd..ca7e89ca2 100755
--- a/gitnexus/hooks/claude/gitnexus-hook.cjs
+++ b/gitnexus/hooks/claude/gitnexus-hook.cjs
@@ -298,11 +298,12 @@ function handlePostToolUse(input) {
   // If HEAD matches last indexed commit, no reindex needed
   if (currentHead && currentHead === lastCommit) return;
 
-  const analyzeCmd = `npx gitnexus analyze${hadEmbeddings ? ' --embeddings' : ''}`;
+  const analyzeCmd = `gitnexus analyze${hadEmbeddings ? ' --embeddings' : ''}`;
+  const npxAnalyzeCmd = `npx gitnexus analyze${hadEmbeddings ? ' --embeddings' : ''}`;
   sendHookResponse(
     'PostToolUse',
     `GitNexus index is stale (last indexed: ${lastCommit ? lastCommit.slice(0, 7) : 'never'}). ` +
-      `Run \`${analyzeCmd}\` to update the knowledge graph.`,
+      `Run \`${analyzeCmd}\` to update the knowledge graph, or \`${npxAnalyzeCmd}\` if the CLI is not installed.`,
   );
 }
 
diff --git a/gitnexus/src/cli/ai-context.ts b/gitnexus/src/cli/ai-context.ts
index 41ba6c73e..d2e1ae4c8 100644
--- a/gitnexus/src/cli/ai-context.ts
+++ b/gitnexus/src/cli/ai-context.ts
@@ -119,7 +119,7 @@ function generateGitNexusContent(
 
 This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${stats.nodes || 0} symbols, ${stats.edges || 0} relationships, ${stats.processes || 0} execution flows)`}. Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
 
-> If any GitNexus tool warns the index is stale, run \`npx gitnexus analyze\` in terminal first.
+> If any GitNexus tool warns the index is stale, run \`gitnexus analyze\` in terminal first (or \`npx gitnexus analyze\` if the CLI is not installed).
 
 ## Always Do
 
diff --git a/gitnexus/src/mcp/resources.ts b/gitnexus/src/mcp/resources.ts
index 88e7a99cc..4a9fb8475 100644
--- a/gitnexus/src/mcp/resources.ts
+++ b/gitnexus/src/mcp/resources.ts
@@ -340,7 +340,9 @@ async function getContextResource(backend: LocalBackend, repoName?: string): Pro
   lines.push('  - cypher: Raw graph queries');
   lines.push('  - list_repos: Discover all indexed repositories');
   lines.push('');
-  lines.push('re_index: Run `npx gitnexus analyze` in terminal if data is stale');
+  lines.push(
+    're_index: Run `gitnexus analyze` in terminal if data is stale (or `npx gitnexus analyze` if the CLI is not installed)',
+  );
   lines.push('');
   lines.push('resources_available:');
   lines.push('  - gitnexus://repos: All indexed repositories');
@@ -581,7 +583,7 @@ async function getSetupResource(backend: LocalBackend): Promise<string> {
   const repos = await backend.listRepos();
 
   if (repos.length === 0) {
-    return '# GitNexus\n\nNo repositories indexed. Run: `npx gitnexus analyze` in a repository.';
+    return '# GitNexus\n\nNo repositories indexed. Run: `gitnexus analyze` in a repository (or `npx gitnexus analyze` if the CLI is not installed).';
   }
 
   const sections: string[] = [];
diff --git a/gitnexus/test/integration/hooks-e2e.test.ts b/gitnexus/test/integration/hooks-e2e.test.ts
index 6d3b79172..2afa852ea 100644
--- a/gitnexus/test/integration/hooks-e2e.test.ts
+++ b/gitnexus/test/integration/hooks-e2e.test.ts
@@ -77,7 +77,10 @@ describe.each(HOOKS)('hooks e2e ($name)', ({ name, path: hookPath }) => {
       const output = parseHookOutput(result.stdout);
       expect(output).not.toBeNull();
       expect(output!.additionalContext).toContain('stale');
-      expect(output!.additionalContext).toContain('npx gitnexus analyze');
+      expect(output!.additionalContext).toContain('Run `gitnexus analyze`');
+      expect(output!.additionalContext).toContain(
+        '`npx gitnexus analyze` if the CLI is not installed',
+      );
     });
 
     it('stays silent when meta.json lastCommit matches HEAD', () => {
diff --git a/gitnexus/test/unit/ai-context.test.ts b/gitnexus/test/unit/ai-context.test.ts
index bbaecb932..2620699d9 100644
--- a/gitnexus/test/unit/ai-context.test.ts
+++ b/gitnexus/test/unit/ai-context.test.ts
@@ -57,6 +57,8 @@ describe('generateAIContextFiles', () => {
     const content = await fs.readFile(path.join(tmpDir, 'CLAUDE.md'), 'utf-8');
 
     expect(content).toContain('If any GitNexus tool warns the index is stale');
+    expect(content).toContain('run `gitnexus analyze`');
+    expect(content).toContain('`npx gitnexus analyze` if the CLI is not installed');
     expect(content).toContain('## Always Do');
     expect(content).toContain('## Never Do');
     expect(content).toContain('## Resources');
diff --git a/gitnexus/test/unit/resources.test.ts b/gitnexus/test/unit/resources.test.ts
index ccd8461f1..86da22f58 100644
--- a/gitnexus/test/unit/resources.test.ts
+++ b/gitnexus/test/unit/resources.test.ts
@@ -188,6 +188,7 @@ describe('readResource', () => {
     const backend = createMockBackend({ repos: [] });
     const result = await readResource('gitnexus://repos', backend);
     expect(result).toContain('No repositories indexed');
+    expect(result).toContain('Run: gitnexus analyze');
   });
 
   it('routes gitnexus://setup to setup resource', async () => {
@@ -211,6 +212,8 @@ describe('readResource', () => {
     const backend = createMockBackend({ repos: [] });
     const result = await readResource('gitnexus://setup', backend);
     expect(result).toContain('No repositories indexed');
+    expect(result).toContain('Run: `gitnexus analyze`');
+    expect(result).toContain('`npx gitnexus analyze` if the CLI is not installed');
   });
 
   it('routes group contracts resource through backend', async () => {