diff --git a/.runechoguardignore b/.runechoguardignore
index b14dc0d..e37380f 100644
--- a/.runechoguardignore
+++ b/.runechoguardignore
@@ -3,3 +3,4 @@ fn
 promisify
 execFileAsync
 parseArgs
+MAX_CODEGRAPH_BUFFER
diff --git a/USAGE.md b/USAGE.md
index c94f0fe..357c3a5 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -98,6 +98,7 @@ fall back to a raw byte-compare, which does require CI to use the same
 ## What to Do When Something Breaks
 
 - **"codeshot: 'codegraph' not found on PATH"** — Install CodeGraph and make sure it's on your PATH, then try again.
+- **"codeshot: codegraph has no index for '...' yet"** — CodeGraph is installed but this repo has never been indexed. Run the exact command the message gives you (`codegraph init <path>`), then rerun codeshot. Codeshot reads CodeGraph's index; it deliberately doesn't build one for you (indexing is a heavy, persistent operation and CodeGraph's call to make).
 - **"codeshot: 'dot' not found on PATH"** — Install Graphviz (`brew install graphviz` on Mac, `apt install graphviz` on Ubuntu/WSL), then try again.
 - **The command runs but the diagram is empty or missing edges** — The repo probably hasn't been indexed yet, or the index is stale. Run `codegraph init` (or re-run indexing) in the target repo first. Codeshot no longer draws a blank picture silently: it warns on stderr in the two cases below.
 - **"codeshot: '...' has no callers or callees in codegraph's index"** — The symbol exists but nothing calls it and it calls nothing, so the diagram is just that one box. It may be genuinely unused (dead code) or a top-level entry point — or codegraph's index is incomplete for its file (see the sparse-diagram note below). The image is still written; the warning just explains why it's a lone box.
diff --git a/render/callgraph.js b/render/callgraph.js
index d75cfbc..8bff508 100755
--- a/render/callgraph.js
+++ b/render/callgraph.js
@@ -68,6 +68,40 @@ function matchSymbolNotFound(out) {
   return m ? m[1] : null;
 }
 
+// codegraph prints "✗ CodeGraph not initialized in <path> — Run 'codegraph init'
+// first" (plain text, not JSON) when --path points at a repo it has never
+// indexed — the single most common first-run failure. Without special-casing it,
+// the JSON.parse fallback wraps that message in a confusing "did not return JSON"
+// line; here it earns its own clean, actionable message instead. Sibling of
+// matchSymbolNotFound. Deliberately does NOT auto-run 'codegraph init' — building
+// an index is a heavy, persistent side effect and codegraph's call to make, not
+// codeshot's (same detect-and-instruct stance as requireOnPath).
+function matchNotInitialized(out) {
+  return /CodeGraph\s+not\s+initialized/i.test(String(out));
+}
+
+// The repo path codeshot passed to codegraph, recovered from the arg array so an
+// error message can name it. Every codegraph invocation includes '--path <p>'.
+function argRepoPath(args) {
+  const i = args.indexOf('--path');
+  return i !== -1 && args[i + 1] !== undefined ? args[i + 1] : '.';
+}
+
+// Shared clean exit for the unindexed-repo case. Reached ONLY from runCodegraph's
+// catch, matched against codegraph's STDERR on a non-zero exit — never against a
+// successful command's stdout. That distinction is load-bearing: codegraph's
+// enumerate query (`query -- ''`) returns every indexed node, whose content can
+// legitimately include the literal phrase "CodeGraph not initialized" (e.g. this
+// file's own source describing the message). Scanning stdout for it would false-
+// positive on a repo that is perfectly well indexed. Returns null for non-fatal
+// callers, exits 1 otherwise — same contract as the matchSymbolNotFound branch.
+function exitNotInitialized(args, fatal) {
+  if (!fatal) return null;
+  const repoPath = argRepoPath(args);
+  console.error(`codeshot: codegraph has no index for '${repoPath}' yet — build one first with 'codegraph init ${repoPath}', then rerun. (codeshot reads codegraph's index; it doesn't create it.)`);
+  process.exit(1);
+}
+
 // `fatal` (default true) matches every existing call site's behavior. Pass
 // `fatal: false` when calling this in a loop that probes many symbols and
 // must survive an individual bad one (e.g. --architecture's enumeration) —
@@ -80,6 +114,10 @@ function parseCodegraphOutput(out, args, { fatal = true } = {}) {
     console.error(`codeshot: symbol '${notFound}' not found in codegraph's index — check the spelling/casing, or confirm --path points at the repo that contains it.`);
     process.exit(1);
   }
+  // NOTE: the "not initialized" case is deliberately NOT handled here on stdout —
+  // see exitNotInitialized. A successful codegraph response can contain that
+  // phrase as indexed source content; it's only a real signal on stderr with a
+  // non-zero exit, which runCodegraph handles.
   try {
     return JSON.parse(out);
   } catch {
@@ -95,8 +133,20 @@ function parseCodegraphOutput(out, args, { fatal = true } = {}) {
 // single codegraph response this tool realistically produces.
 const MAX_CODEGRAPH_BUFFER = 64 * 1024 * 1024;
 async function runCodegraph(args, { fatal = true } = {}) {
-  const { stdout } = await execFileAsync('codegraph', args, { encoding: 'utf8', maxBuffer: MAX_CODEGRAPH_BUFFER });
-  return parseCodegraphOutput(stdout, args, { fatal });
+  let result;
+  try {
+    result = await execFileAsync('codegraph', args, { encoding: 'utf8', maxBuffer: MAX_CODEGRAPH_BUFFER });
+  } catch (err) {
+    // codegraph exits NON-ZERO for an unindexed repo, printing "CodeGraph not
+    // initialized" to STDERR. Match only stderr — never err.stdout — because a
+    // partial stdout on some other failure could contain that phrase as indexed
+    // source content and false-positive (the same trap that stdout scanning in
+    // parseCodegraphOutput would be). Surface this known first-run state cleanly;
+    // re-throw anything else so a genuine codegraph failure isn't misreported.
+    if (matchNotInitialized(`${err.stderr || ''}`)) return exitNotInitialized(args, fatal);
+    throw err;
+  }
+  return parseCodegraphOutput(result.stdout, args, { fatal });
 }
 
 // `codegraph status` warns when an index was left mid-build ("N references from
@@ -974,4 +1024,5 @@ module.exports = {
   applyEmbed, embedMarkers, embedRelLink, parseUnresolvedRefs,
   svgStructure, decodeXmlEntities,
   emptyGraphWarning, emptyArchitectureWarning,
+  matchNotInitialized, argRepoPath, parseCodegraphOutput,
 };
diff --git a/test/run.js b/test/run.js
index f7b0386..58c82ba 100644
--- a/test/run.js
+++ b/test/run.js
@@ -10,6 +10,7 @@ const {
   applyEmbed, embedMarkers, embedRelLink, parseUnresolvedRefs,
   svgStructure, decodeXmlEntities,
   emptyGraphWarning, emptyArchitectureWarning,
+  matchNotInitialized, argRepoPath, parseCodegraphOutput,
 } = require('../render/callgraph.js');
 
 let passed = 0;
@@ -250,6 +251,31 @@ test('matchSymbolNotFound extracts the symbol name from codegraph\'s plain-text
   assert.strictEqual(matchSymbolNotFound('{"symbol":"Foo","callers":[]}'), null, 'a real JSON response should never match');
 });
 
+test('matchNotInitialized detects codegraph\'s unindexed-repo message, not JSON or other errors', () => {
+  const esc = String.fromCharCode(27);
+  assert.strictEqual(matchNotInitialized(`${esc}[31m✗${esc}[0m CodeGraph not initialized in /repo\n Run "codegraph init" first`), true);
+  assert.strictEqual(matchNotInitialized('codegraph not initialized'), true, 'case-insensitive');
+  assert.strictEqual(matchNotInitialized('[{"node":{}}]'), false, 'a real JSON response must not match');
+  assert.strictEqual(matchNotInitialized('Symbol "Foo" not found'), false, 'the not-found message is a different case');
+  assert.strictEqual(matchNotInitialized(''), false);
+});
+
+test('argRepoPath recovers the --path value codeshot passed, defaulting to "."', () => {
+  assert.strictEqual(argRepoPath(['query', '--path', '/repo/x', '--json', '--', 'Foo']), '/repo/x');
+  assert.strictEqual(argRepoPath(['callers', '--json']), '.', 'no --path → cwd default');
+});
+
+test('parseCodegraphOutput does NOT treat a successful JSON response as "not initialized" just because a node\'s content mentions the phrase', () => {
+  // Regression: codegraph's enumerate query returns indexed node content, and
+  // this very file's source contains "CodeGraph not initialized" in a comment.
+  // Scanning stdout for that phrase falsely reported a well-indexed repo as
+  // uninitialized (the CI diagrams job caught it). The phrase is a real signal
+  // only on stderr with a non-zero exit (runCodegraph), never on stdout.
+  const stdout = JSON.stringify([{ node: { name: 'matchNotInitialized', content: 'detects "CodeGraph not initialized"' } }]);
+  const parsed = parseCodegraphOutput(stdout, ['query', '--path', '.', '--json', '--', ''], { fatal: false });
+  assert.deepStrictEqual(parsed, [{ node: { name: 'matchNotInitialized', content: 'detects "CodeGraph not initialized"' } }]);
+});
+
 test('buildDot styles a "kind":"file" caller/callee distinctly from a real function call', () => {
   const dot = buildDot('Target', [{ name: 'some.js', kind: 'file', filePath: 'src/some.js' }], [{ name: 'other.js', kind: 'file', filePath: 'src/other.js' }]);
   assert.match(dot, /"some\.js" -> "Target" \[style=dotted, color="#9ca3af", label="file"\];/);
@@ -790,6 +816,39 @@ test('CLI --embed into a nonexistent doc is rejected (refresh, not create)', ()
   assert.strictEqual(threw, true, 'expected --embed into a missing doc to be rejected');
 });
 
+test('CLI on an unindexed repo prints a clean "no index" message, not a raw codegraph error', () => {
+  const { execFileSync } = require('child_process');
+  const path = require('path');
+  const fs = require('fs');
+  const os = require('os');
+  const callgraphJs = path.join(__dirname, '..', 'render', 'callgraph.js');
+
+  // Needs codegraph on PATH to produce the real non-zero "not initialized" exit.
+  try {
+    execFileSync('codegraph', ['--version'], { stdio: 'pipe' });
+  } catch {
+    console.log('  # skipped: `codegraph` not on PATH');
+    return;
+  }
+
+  // A fresh dir under tmp with no .codegraph anywhere above it → codegraph
+  // reports "not initialized" rather than resolving a parent index.
+  const dir = fs.mkdtempSync(path.join(os.tmpdir(), 'codeshot-unindexed-'));
+  fs.writeFileSync(path.join(dir, 'app.py'), 'def hello():\n    pass\n', 'utf8');
+  let threw = false;
+  try {
+    execFileSync('node', [callgraphJs, 'hello', '--path', dir], { encoding: 'utf8', stdio: 'pipe' });
+  } catch (err) {
+    threw = true;
+    assert.match(err.stderr, /has no index for/);
+    assert.match(err.stderr, /codegraph init/);
+    assert.doesNotMatch(err.stderr, /did not return JSON|Command failed/, 'must be the clean message, not the raw thrown error');
+  } finally {
+    fs.rmSync(dir, { recursive: true, force: true });
+  }
+  assert.strictEqual(threw, true, 'expected exit 1 on an unindexed repo');
+});
+
 // --- svgStructure: version-independent --check comparison -------------
 
 test('decodeXmlEntities undoes the entities graphviz emits in a <title>', () => {