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rows until includeInactive asks for the superseded path, labeling every row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/app-indexer-service.test.mjs

@@ -1,7 +1,7 @@
 import { test } from 'node:test';
 import assert from 'node:assert/strict';
 import { createRequire } from 'node:module';
-import { mkdtempSync } from 'node:fs';
+import { mkdirSync, mkdtempSync, writeFileSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 
@@ -101,6 +101,33 @@ test('indexer service reschedules a writer-lease deferral without publishing a h
   assert.equal(heartbeats, 1);
 });
 
+test('a deferred full-inventory build stays full when retried', async () => {
+  const timers = manualTimers();
+  const calls = [];
+  const service = createIndexerService({
+    buildIndex: async (args) => {
+      calls.push(args);
+      return calls.length === 1 ? { deferred: true } : { deferred: false };
+    },
+    watchProjects: () => null,
+    writeHeartbeat: () => {},
+    timers,
+    stabilityMs: 0,
+  });
+
+  service.scheduleBuild('root-appeared');
+  timers.flush();
+  await service.idle();
+  service.scheduleBuild('ordinary-change', '/tmp/later.jsonl');
+  timers.flush();
+  await service.idle();
+
+  assert.deepEqual(calls, [
+    { reason: 'root-appeared', changedPaths: undefined },
+    { reason: 'ordinary-change', changedPaths: undefined },
+  ]);
+});
+
 test('indexer service does not log a build cancelled by a service stop', async () => {
   const timers = manualTimers();
   const warnings = [];
@@ -143,6 +170,59 @@ test('indexer service logs a build that fails while running', async () => {
   assert.match(warnings[0], /Obelisk index build failed: disk on fire/);
 });
 
+test('indexer service reports partial inventory paths on ordinary builds', async () => {
+  const warnings = [];
+  const service = createIndexerService({
+    buildIndex: async () => ({
+      deferred: false,
+      complete: false,
+      inventoryIssues: [{
+        provider: 'pi',
+        path: '/tmp/pi/locked',
+        error: 'EACCES: permission denied',
+      }],
+    }),
+    watchProjects: () => null,
+    writeHeartbeat: () => {},
+    logger: { warn: (msg) => warnings.push(msg) },
+    stabilityMs: 0,
+  });
+
+  await service.runBuildNow('startup');
+
+  assert.deepEqual(warnings, [
+    'Obelisk indexed a partial pi inventory at /tmp/pi/locked: EACCES: permission denied',
+  ]);
+});
+
+test('indexer service reports partial inventory paths before a deferred retry', async () => {
+  const timers = manualTimers();
+  const warnings = [];
+  const service = createIndexerService({
+    buildIndex: async () => ({
+      deferred: true,
+      complete: false,
+      inventoryIssues: [{
+        provider: 'pi',
+        path: '/tmp/pi/locked',
+        error: 'EACCES: permission denied',
+      }],
+    }),
+    watchProjects: () => null,
+    writeHeartbeat: () => {},
+    logger: { warn: (msg) => warnings.push(msg) },
+    timers,
+    stabilityMs: 0,
+  });
+
+  await service.runBuildNow('startup');
+  service.stop();
+
+  assert.deepEqual(warnings, [
+    'Obelisk indexed a partial pi inventory at /tmp/pi/locked: EACCES: permission denied',
+  ]);
+});
+
 test('indexer service waits for a stability window before building', async () => {
   const timers = manualTimers();
   const calls = [];
@@ -345,3 +425,53 @@ test('indexer service watches Claude projects and Codex sessions for app-side in
     join(codexSessionsDir, '2026/06/15/rollout-2026-06-15T00-00-00-codex.jsonl'),
   ]);
 });
+
+test('indexer service starts watching a configured root that appears after startup', async () => {
+  const existingRoot = mkdtempSync(join(tmpdir(), 'obelisk-watch-existing-'));
+  const parent = mkdtempSync(join(tmpdir(), 'obelisk-watch-late-parent-'));
+  const lateRoot = join(parent, 'nested', 'sessions');
+  const timers = manualTimers();
+  const calls = [];
+  const watchArgs = [];
+  const chokidar = {
+    watch(root) {
+      watchArgs.push(root);
+      const watcher = {
+        on() {
+          return watcher;
+        },
+        close() {},
+      };
+      return watcher;
+    },
+  };
+  const service = createIndexerService({
+    watchDirs: [existingRoot, lateRoot],
+    buildIndex: async (args) => calls.push(args),
+    chokidar,
+    writeHeartbeat: () => {},
+    timers,
+    stabilityMs: 0,
+    debounceMs: 0,
+    watchRetryMs: 0,
+  });
+
+  try {
+    service.start({ buildOnStart: false });
+    assert.deepEqual(watchArgs, [existingRoot]);
+
+    mkdirSync(lateRoot, { recursive: true });
+    writeFileSync(join(lateRoot, 'pre-existing.jsonl'), '{}\n');
+    timers.flush();
+    assert.deepEqual(watchArgs, [existingRoot, lateRoot]);
+
+    timers.flush();
+    await service.idle();
+    assert.deepEqual(calls, [{
+      reason: 'watch',
+      changedPaths: undefined,
+    }]);
+  } finally {
+    service.stop();
+  }
+});