fix(core): empty code files, multi-source cycle sync, root-level entity refs

Three community-PR takeovers rebased onto master:

- import-file (#840): importCodeFile skips empty (0-byte) code files instead
  of writing a page with empty compiled_truth that fails every reindex-code
  pass. When a previously-imported file BECOMES empty, the stale page is
  deleted (chunks cascade) instead of ghosting in search — mirrors the
  markdown importer's empty-content branch.

- cycle (#1079): runPhaseSync now enumerates every registered, non-archived,
  sync-enabled source with a local checkout instead of syncing only the
  single brainDir-matched source. Preserves the SyncLockBusyError per-source
  skip (#1794), keeps the legacy brainDir fallback when no source covers it,
  and respects explicit --source scoping (#1503) so a scoped cycle stays
  single-source. Single-target result shape is unchanged.

- link-extraction (#1101): ENTITY_REF_RE gains a root-level branch so
  [Name](action-tracker.md) resolves to slug 'action-tracker'. The bare
  branch requires the .md suffix and excludes '#', '/', ':' so anchors,
  non-markdown assets, and URLs don't emit bogus refs; the capture's .md is
  stripped in extractEntityRefs and dir is '' (not the filename).
  LINK_EXTRACTOR_VERSION_TS bumped so stamped pages re-extract.

Takeover of #840, #1079, #1101 (rebased; flaws named in review fixed).

Co-authored-by: nightlaro <nightlaro@users.noreply.github.com>
Co-authored-by: samvilian <samvilian@users.noreply.github.com>
Co-authored-by: essexcanning <essexcanning@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

test/import-empty-code-file.test.ts

@@ -0,0 +1,64 @@
+/**
+ * Regression test for `importCodeFile` skipping empty (0-byte) code files (#840).
+ *
+ * Before this guard, an empty file produced a page row with empty
+ * compiled_truth, which then failed every subsequent `gbrain reindex-code`
+ * pass with `missing compiled_truth`. Empty files are legitimate in real
+ * repos (stub/placeholder files committed during refactors); the importer
+ * skips them the same way it skips files over MAX_FILE_SIZE — and when a
+ * previously-imported file BECOMES empty, the stale page is deleted (chunks
+ * cascade) instead of ghosting in search, mirroring the markdown importer's
+ * empty-content branch.
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { importCodeFile } from '../src/core/import-file.ts';
+
+let engine: PGLiteEngine;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+describe('importCodeFile — empty file guard (#840)', () => {
+  test('zero-byte content is skipped, not inserted', async () => {
+    const result = await importCodeFile(engine, 'src/empty.ts', '', { noEmbed: true });
+
+    expect(result.status).toBe('skipped');
+    expect(result.chunks).toBe(0);
+    expect(result.error).toBe('empty code file');
+
+    // The skip must short-circuit before any page row is written, otherwise
+    // reindex-code will still trip on the missing compiled_truth.
+    const page = await engine.getPage(result.slug);
+    expect(page).toBeNull();
+  });
+
+  test('file that BECOMES empty deletes the stale page instead of ghosting', async () => {
+    const first = await importCodeFile(engine, 'src/becomes-empty.ts', 'export const x = 1;\n', { noEmbed: true });
+    expect(first.status).toBe('imported');
+    expect(await engine.getPage(first.slug)).not.toBeNull();
+
+    const second = await importCodeFile(engine, 'src/becomes-empty.ts', '', { noEmbed: true });
+    expect(second.status).toBe('skipped');
+    expect(second.error).toBe('empty code file');
+
+    // Stale page (and its chunks, via FK cascade) must be gone.
+    expect(await engine.getPage(first.slug)).toBeNull();
+    expect(await engine.getChunks(first.slug)).toEqual([]);
+  });
+
+  test('non-empty content still imports normally', async () => {
+    const result = await importCodeFile(engine, 'src/non-empty.ts', 'export const x = 1;\n', { noEmbed: true });
+
+    expect(result.status).toBe('imported');
+    expect(result.chunks).toBeGreaterThan(0);
+  });
+});