feat(core): add first-class Pi session indexing (#23)

Pi cannot be read as another linear JSONL stream. Its history is a tree with
a durable leaf, orphan roots, branch summaries, and two compaction forms, so
the active context is something the format states rather than something line
order implies. The adapter keeps those semantics inside itself and projects
the result into the existing canonical tables.

Sessions are keyed by (normalized header cwd, header id) rather than by path,
because Pi's --session-id lookup is project-local: two projects may reuse an
id, while a move or an identical copy is still one session. Discovery covers
both layouts Pi writes and fingerprints each file by mtime, ctime, size and
inode, so a rewrite that preserves mtime is not read as unchanged.

Abandoned branches are preserved rather than dropped. Visibility becomes
three-state -- visible, inactive, hidden -- and helpers return only visible
rows until includeInactive asks for the superseded path, labeling every row
so a caller knows which it holds. Usage counts all three, because an
abandoned call still spent tokens; message_count reports only the visible
transcript.

A committed MIT-licensed oracle transcribed from Pi 0.83.0 pins the context
algorithms, and a fixed-seed differential runs 512 generated sessions against
it on every test run. Schema changes are additive.

tests/runtime.test.mjs

@@ -31,6 +31,44 @@ test('runtime query scripts cannot call attune helpers', () => {
   });
 });
 
+test('malformed Obelisk settings skip refresh without disabling provider-backed queries', () => {
+  const home = tempHome();
+  const projectDir = join(home, '.claude', 'projects', '-tmp-settings-recovery');
+  const transcriptPath = join(projectDir, 'settings-recovery.jsonl');
+  const scriptPath = join(home, 'query.mjs');
+  mkdirSync(projectDir, { recursive: true });
+  writeFileSync(transcriptPath, `${JSON.stringify({
+    uuid: 'settings-recovery-user',
+    type: 'user',
+    timestamp: '2026-08-04T10:00:00.000Z',
+    cwd: '/tmp/settings-recovery',
+    message: { role: 'user', content: 'settings recovery evidence' },
+  })}\n`);
+  writeFileSync(scriptPath, `
+    const hit = search('settings recovery evidence', { limit: 1 })[0];
+    return {
+      uuid: hit?.message.uuid ?? null,
+      raw: hit ? raw(hit.message.uuid)?.text ?? null : null
+    };
+  `);
+
+  const indexed = runRuntime(['--query', scriptPath], { home });
+  assert.equal(indexed.status, 0, indexed.stderr || indexed.stdout);
+  assert.equal(JSON.parse(indexed.stdout).uuid, 'settings-recovery-user');
+
+  writeFileSync(join(home, '.obelisk', 'settings.json'), '{broken');
+  const recovered = runRuntime(['--query', scriptPath], { home });
+  assert.equal(recovered.status, 0, recovered.stderr || recovered.stdout);
+  assert.match(recovered.stderr, /index refresh skipped/);
+  assert.equal(JSON.parse(recovered.stdout).uuid, 'settings-recovery-user');
+  assert.match(JSON.parse(recovered.stdout).raw, /settings recovery evidence/);
+
+  const rebuild = runRuntime(['--build'], { home });
+  assert.equal(rebuild.status, 1);
+  assert.match(JSON.parse(rebuild.stdout).error, /settings_unavailable/);
+  assert.match(JSON.parse(rebuild.stdout).error, /Unable to read Obelisk settings/);
+});
+
 test('runtime attune scripts expose only memory mutation helpers', () => {
   const home = tempHome();
   const memoryPath = join(home, 'memory.md');
@@ -208,6 +246,76 @@ test('runtime indexes Codex root sessions into the shared query helpers', () =>
   assert.ok(payload.overviewSources.some(s => s.source === 'codex' && s.session_count === 1));
 });
 
+test('runtime raw lookup uses the configured Codex root for child sessions', () => {
+  const home = tempHome();
+  const codexDir = join(home, 'custom-codex');
+  const codexSessionDir = join(codexDir, 'sessions', '2026', '08', '04');
+  const parentId = '019ec6ee-cebd-7431-9c93-ceec89a98a5f';
+  const childId = '019ec739-9f75-7a02-ba2a-371986e23823';
+  mkdirSync(codexSessionDir, { recursive: true });
+  mkdirSync(join(home, '.obelisk'), { recursive: true });
+  writeFileSync(join(home, '.obelisk', 'settings.json'), JSON.stringify({
+    providerRoots: { codex: codexDir },
+  }));
+  writeFileSync(join(codexSessionDir, `a-parent-${parentId}.jsonl`), [
+    JSON.stringify({
+      timestamp: '2026-08-04T10:00:00.000Z',
+      type: 'session_meta',
+      payload: {
+        id: parentId,
+        timestamp: '2026-08-04T10:00:00.000Z',
+        cwd: '/tmp/custom-codex-runtime',
+        source: 'cli',
+      },
+    }),
+    '',
+  ].join('\n'));
+  writeFileSync(join(codexSessionDir, `b-child-${childId}.jsonl`), [
+    JSON.stringify({
+      timestamp: '2026-08-04T10:00:01.000Z',
+      type: 'session_meta',
+      payload: {
+        id: childId,
+        timestamp: '2026-08-04T10:00:01.000Z',
+        cwd: '/tmp/custom-codex-runtime',
+        source: {
+          subagent: {
+            thread_spawn: {
+              parent_thread_id: parentId,
+              agent_nickname: 'Plato',
+              agent_role: 'worker',
+            },
+          },
+        },
+      },
+    }),
+    JSON.stringify({
+      timestamp: '2026-08-04T10:00:02.000Z',
+      type: 'event_msg',
+      payload: {
+        type: 'user_message',
+        message: 'custom Codex child raw sentinel',
+        images: [],
+        local_images: [],
+        text_elements: [],
+      },
+    }),
+    '',
+  ].join('\n'));
+  const scriptPath = join(home, 'query.mjs');
+  writeFileSync(
+    scriptPath,
+    `return raw(${JSON.stringify(`codex:${childId}:000002`)}, { limit: 1000 });`,
+  );
+
+  const result = runRuntime(['--query', scriptPath], { home });
+
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  const raw = JSON.parse(result.stdout);
+  assert.match(raw.text, /custom Codex child raw sentinel/);
+  assert.equal(raw.visibility, 'visible');
+});
+
 test('runtime skips Codex guardian review threads', () => {
   const home = tempHome();
   const codexSessionDir = join(home, '.codex', 'sessions', '2026', '06', '15');