#493 (sqlite): route _initialize() through the _connect() contextmanager
(the one remaining raw sqlite3.connect FD leak); document the auto-commit
contract so the redundant explicit commits are understood.

#529 (book):
- _strip_thinking_preamble: guard `{ not in text` before rindex() so plain
  prose (refusals/errors) no longer raises ValueError -> ERROR block;
  hoist json import to module top.
- llm_json: honor caller max_tokens as max(max_tokens, 2600) instead of
  discarding it; bump default to 2600; fix stale 'minimal' docstring -> 'low'.
- engine.compile_page: rebuild OVERVIEW pages deterministically via
  _materialize_overview_page on force, instead of running the generic LLM
  compiler over hand-built intro/concept-graph/index blocks.
- kb_health.scan_log_health: key repeated-failure detection on the op, not
  the free-text message, removing false positives/negatives + dead block_error.
- services/__init__: drop orphaned notebook_manager lazy-import + __all__ entry.
- PageReader.tsx: restore t() i18n on regenerate buttons; add 'Regenerating…'.
- remove PATCHES.md (developer-local scratch notes).

#484 (zulip): also match the disambiguated @**Name|user_id** mention form;
make the docstring truthful; add coverage.

#500: remove stray PR_DESCRIPTION.md committed to repo root.

Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>

Security/correctness:
- Stop leaking diagnostic answers: persist a _sanitize_diagnostic() snapshot
  (drops top-level answers + inline answer keys) into progress.diagnostic,
  which is returned verbatim by the /progress endpoints. Grading is unaffected
  (authoritative answers live in LearningStore).
- _safe_json_parse + generate_from_notebook now use the shared fence-stripping
  parse_json_response instead of bare json.loads, so the common fenced/lightly
  -malformed LLM output is recovered instead of silently dropped / 500'd.

Decoupling:
- unified_ws change_module: move module lookup + PRETEST reset into
  LearningService.switch_module(); router keeps only the WS ordering
  (module_changed before cancel) and no longer imports learning.models.
- unified_ws check_active_turn: use new public TurnRuntimeManager
  .has_live_execution() instead of reaching into _lock/_executions.
- redo endpoint: LearningStore.clear_questions() instead of poking _questions_path.
- remove unused StreamEventType.USER_INPUT enum; document the WS message types.

Stability:
- LearningStore: question read-modify-write (save_question_answers/_meta),
  delete(), and clear_questions() now hold _cas_lock — consistent concurrency
  model; _atomic_write_text cleans up its temp file on failure.

Cleanliness/clarity:
- router: shared _validate_book_id() (9 endpoints) + _parse_modules()
  (init/replace); _classify_error drops unused expected_answer param.
- guided_learning: hoist logging/RAGService imports + module logger; move tuning
  constants to class top; ContextVar declared after imports.
- storage: hoist json import (7 inline copies removed).
- pocketbase_store: move _VALID_ID/_validate_id below the import block.
- rename misleading mastered_pct -> avg_mastery_pct (service + web consumers).

Frontend:
- learning [bookId] page uses lib fetchProgress (apiFetch -> auth redirect)
  instead of a raw credentials fetch; track/clear the retry + auto-advance
  timers on unmount; drop dead currentStage state + ModuleTree prop.
- learning-api: remove orphaned submitAnswer + AnswerRequest.
- CreateModuleDialog: use the static bookApi import; reset manualBookId to ''
  to match initial state; learning list page: stop shadowing the t() translator.

Conflict-resolution carryover: dropped the PR's incidental 300s factory timeout
(kept dev's stream runner).

Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>

… subsystem)

New self-contained deeptutor/learning/ subsystem (models, storage, service,
scheduler, grading) + 12-stage guided_learning capability, REST router, and
web learning pages, with 164 tests.

Conflict resolutions:
- services/llm/factory.py: kept dev's stream runner (allow_image_fallback
  multimodal path); dropped the PR's incidental 300s asyncio.wait_for wrapper
  and its now-orphaned TimeoutError handler / unused logger — the blanket
  timeout is unrelated to guided learning, dev already has consumer-side
  timeouts, and 300s would truncate long legitimate streams (book/research).
- web/components/sidebar/WorkspaceSidebar.tsx: kept dev's structure, added a
  useCallback handleNewChat that cancels any in-flight streaming turn before
  newSession() (mirrors handleDeleteSession) and wired it to onNewChat.

Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>

…#529/HKUDS#484

HKUDS#493 (sqlite): route _initialize() through the _connect() contextmanager
(the one remaining raw sqlite3.connect FD leak); document the auto-commit
contract so the redundant explicit commits are understood.

HKUDS#529 (book):
- _strip_thinking_preamble: guard `{ not in text` before rindex() so plain
  prose (refusals/errors) no longer raises ValueError -> ERROR block;
  hoist json import to module top.
- llm_json: honor caller max_tokens as max(max_tokens, 2600) instead of
  discarding it; bump default to 2600; fix stale 'minimal' docstring -> 'low'.
- engine.compile_page: rebuild OVERVIEW pages deterministically via
  _materialize_overview_page on force, instead of running the generic LLM
  compiler over hand-built intro/concept-graph/index blocks.
- kb_health.scan_log_health: key repeated-failure detection on the op, not
  the free-text message, removing false positives/negatives + dead block_error.
- services/__init__: drop orphaned notebook_manager lazy-import + __all__ entry.
- PageReader.tsx: restore t() i18n on regenerate buttons; add 'Regenerating…'.
- remove PATCHES.md (developer-local scratch notes).

HKUDS#484 (zulip): also match the disambiguated @**Name|user_id** mention form;
make the docstring truthful; add coverage.

HKUDS#500: remove stray PR_DESCRIPTION.md committed to repo root.

Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>

Security/correctness:
- Stop leaking diagnostic answers: persist a _sanitize_diagnostic() snapshot
  (drops top-level answers + inline answer keys) into progress.diagnostic,
  which is returned verbatim by the /progress endpoints. Grading is unaffected
  (authoritative answers live in LearningStore).
- _safe_json_parse + generate_from_notebook now use the shared fence-stripping
  parse_json_response instead of bare json.loads, so the common fenced/lightly
  -malformed LLM output is recovered instead of silently dropped / 500'd.

Decoupling:
- unified_ws change_module: move module lookup + PRETEST reset into
  LearningService.switch_module(); router keeps only the WS ordering
  (module_changed before cancel) and no longer imports learning.models.
- unified_ws check_active_turn: use new public TurnRuntimeManager
  .has_live_execution() instead of reaching into _lock/_executions.
- redo endpoint: LearningStore.clear_questions() instead of poking _questions_path.
- remove unused StreamEventType.USER_INPUT enum; document the WS message types.

Stability:
- LearningStore: question read-modify-write (save_question_answers/_meta),
  delete(), and clear_questions() now hold _cas_lock — consistent concurrency
  model; _atomic_write_text cleans up its temp file on failure.

Cleanliness/clarity:
- router: shared _validate_book_id() (9 endpoints) + _parse_modules()
  (init/replace); _classify_error drops unused expected_answer param.
- guided_learning: hoist logging/RAGService imports + module logger; move tuning
  constants to class top; ContextVar declared after imports.
- storage: hoist json import (7 inline copies removed).
- pocketbase_store: move _VALID_ID/_validate_id below the import block.
- rename misleading mastered_pct -> avg_mastery_pct (service + web consumers).

Frontend:
- learning [bookId] page uses lib fetchProgress (apiFetch -> auth redirect)
  instead of a raw credentials fetch; track/clear the retry + auto-advance
  timers on unmount; drop dead currentStage state + ModuleTree prop.
- learning-api: remove orphaned submitAnswer + AnswerRequest.
- CreateModuleDialog: use the static bookApi import; reset manualBookId to ''
  to match initial state; learning list page: stop shadowing the t() translator.

Conflict-resolution carryover: dropped the PR's incidental 300s factory timeout
(kept dev's stream runner).

Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>