PaperQuay: vanhemmat versiot ja versiohistoria

- Per-paper AI conversations now survive app restarts. The active session and preset are restored, and tab switches or app shutdown flush pending history without replacing it with an empty session.
- Full-document translations now persist reliably across restarts, including when a custom MinerU cache directory is used. Cache writes are serialized and atomic, and storage failures are shown instead of being silently ignored.
- WebDAV backup is substantially more reliable: Nutstore-friendly request pacing, Retry-After handling, transient-error retries, streamed uploads, adaptive timeouts, detailed failed-object reporting, progress updates, and cleanup of temporary snapshots.
- Review Word export now supports editable OMML equations, localized Chinese/English headings, correct first-line indentation, richer references, missing-image fallbacks, and figures placed alongside relevant model-generated content.
- Review generation now keeps completed sections when another writing task fails, reports failed tasks individually, and processes the full queued workload before offering resume.

- Review Word export now supports editable OMML formulas, missing-figure fallbacks, localized section titles, 480-twip paragraph indentation, richer references, and inline figure placement from model output.
- Review writing is more resilient: failed writing tasks no longer stop the whole queue, and more retrieved papers can contribute detailed RAG context.
- Knowledge graph workflows now support synced Crossref reference data, citation edges for papers already in the library, co-author relations, clearer edge legends, graph export, searchable relation targets, and direct node interactions.
- MinerU parsing can use a configurable API base URL, so local MinerU deployments can be used while the official endpoint remains the default.
- Library storage folder changes now migrate the existing storage structure and attachment paths into the new location.
- Reader and notes workflows now include selection-translation highlighting, a resizable library navigation sidebar, paper-list sorting, and safer note external-update detection after local saves.

- Optimized macOS titlebar behavior: the app now uses the native traffic-light controls and removes duplicate custom window buttons on macOS.
- Improved PDF.js lifecycle cleanup to reduce stale worker/render-task errors when opening, switching, or closing PDFs.
- Improved Agent RAG answers with clickable citation tags that jump back to the referenced paper block or page.
- Added and clarified the RAG Top-K setting for controlling how many nearest context blocks are sent to the model.
- Refined selection and paragraph translation popovers, including independent Settings switches and safer positioning around selected text.
- Improved side-panel chat input behavior, multi-session QA handling, and Agent interaction polish.

- Added PDF block click context, including click position and rendered block bounds, so paragraph translation popovers can be placed accurately.
- Reused selected-excerpt translation state for cached paragraph translations without triggering unnecessary automatic selected-text translation requests.
- Added nearest-block hit detection to make PDF paragraph clicks more forgiving near paragraph edges.
- Added selection rectangle capture for PDF text selection, structured-block selection, and PDF annotation workspace selection.
- Rendered selection quick actions through a body-level portal with a higher layer so the panel is not clipped by reader panes or sidebars.
- Made PDF note-anchor overlays non-interactive except for their small numbered jump button.
- Updated the thumbnail sidebar preference key and default collapsed state for the new reading experience.
- Updated English and Chinese README introductions for the current feature set and architecture.

- Added manual WebDAV remote backup and additive restore, with local SQLite online backup staging, atomic remote object upload, latest-backup inspection, and settings UI integration.
- Improved restore behavior so missing PDFs and derived parse/translation/summary caches can be pulled back from the latest backup without deleting extra local content.
- Fixed the reader workspace switch behavior so an opened PDF no longer turns blank after switching from Library to Agent and back.
- Reworked the detached document chat window so it opens as a true chat workspace instead of a nested sidebar shell, with corrected docking behavior and cleaner window UI.
- Tightened document chat semantics so the detach action only applies to the chat panel and docking returns users to the chat panel consistently.

- Added local RAG indexing and retrieval with persistent sqlite-vec storage, configurable embedding settings, and backend-only embedding requests.
- Improved document Q&A citation handling so inline references such as [1] can jump back to the referenced MinerU block.
- Added Agent composer controls for file upload, image upload, screenshots, RAG mode, and per-chat model switching.
- Improved Agent tool-call robustness, including malformed JSON argument repair and safer rename handling for read-status prefixes.
- Improved translation reliability so completed block translations are saved incrementally and failed batches can be retried without discarding finished work.
- Refactored large reader, translation, library, settings, and RAG modules into smaller files while preserving existing behavior.