Begin breaking up the 13,837-line Core class by lifting seven self-
contained, low-coupling helpers into TypeScript modules. The pattern
matches the existing composed siblings (Dependencies.js, ParameterStack):
each module is constructed with a `core` back-reference, and Core retains
a thin delegating wrapper for every method/property that was previously
on the class so external callers (CoreWorker, tests, components, and
`coreFunctions`-bound references) continue to work unchanged.

Modules extracted:
- DiagnosticsManager.ts       — diagnostics queue + source-location walk
- StateVariableNameResolver.ts — pure-function name resolution utilities
- VisibilityTracker.ts        — visibility state and save/suspend timers
- StatePersistence.ts         — save to localStorage / database
- AutoSubmitManager.ts        — debounced answer-submit queue
- NavigationHandler.ts        — handleNavigatingToComponent, navigateToTarget
- ResolverAdapter.ts          — adapter to the external Rust name resolver

No behavior change. Core.js drops from 13,837 to 12,909 lines.

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

Address 9 Copilot review comments on PR Doenet#1036. All flagged code (the
.primitive.number bug, six fire-and-forget Promises, the typo, four
TS errors) pre-existed in Core.js and was either copied verbatim or
exposed when the JS was converted to TS during extraction.

- ResolverAdapter: fix latent createComponentIdx.primitive.number access
  (should be .value, with a primitive.type === "number" guard) — same
  pattern as utils/resolver.ts:220-224 and utils/componentIndices.ts:725.
- ResolverAdapter: add type: "flatFragment" and parentSourceSequence
  fields to two FlatFragment literals; tighten gatherDiagnosticsAnd-
  AssignDoenetMLRange signature so position/sourceDoc match assign-
  DoenetMLRange's required arguments.
- Add reportTimerError helper and attach .catch() handlers to six
  fire-and-forget Promises in setTimeout callbacks across
  StatePersistence (2), AutoSubmitManager (1), and VisibilityTracker
  (3), per AGENTS.md convention. Also clear submitAnswersTimeout when
  it fires.
- Fix typo "case-senstitive" -> "case-sensitive" in
  StateVariableNameResolver.

Documentation: merge CLAUDE.md into AGENTS.md as the single source of
truth (project conventions, architecture, build commands, testing,
common tasks). Reduce CLAUDE.md to a one-line pointer so Claude Code
auto-context still finds the project guide while eliminating drift.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Address the in-scope findings from the second-round review of the
Core.js helper extraction:

- DiagnosticsManager: replace local Diagnostic type with the existing
  DiagnosticRecord discriminated union from @doenet/utils; preliminary
  diagnostics now type-narrow via NonErrorDiagnosticRecord, addDiagnostic
  pushes the record directly, and the dedup check uses explicit branches.
- DiagnosticsManager: add markPending() and route the one external
  setter (Core.js error-component path) through it; drop the
  set hasPendingDiagnostics accessor on Core.
- Core.js: replace five aliased imports with a single
  import * as nameResolver namespace import.
- Core.js: remove six near-duplicate wrapper-block preambles; replace
  with one file-level explanation and short // → managerName markers.
- DiagnosticsManager: tighten getDiagnostics docstring (was misleading
  about the codebase accumulating messages); correct addDiagnostic
  return-value docstring (Core.js does inspect it for the rethrow path).
- StatePersistence: drop the "slated for Phase 4" reference.
- AGENTS.md: clarify Layer 2 Rust phrasing; expand the "Add a new
  component type" step about schema registration.

Defer the structural items (typing core: any, reducing stateless
managers to plain functions, moving getSourceLocationForComponent,
TimerLabels const, regression test for the .primitive.value fix)
to CORE_REFACTOR_DEFERRED.md for the next refactor pass.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

… and fix stale reference

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Adds a deferred-items entry listing three intentionally unawaited Promise
calls (Core.js:410, 11160, and 449-452) that pre-date Phase 1 and violate
the AGENTS.md fire-and-forget convention, with a suggested fix using the
reportTimerError helper added in this PR.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>