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Phase 2 Backlog
Superseded by GitHub Issues #29–#42. Do not use this page to select work. Only an issue labeled
status:readymay be started.
Turn implemented shell into reliable daily Ph.D. paper-reading workflow. Core-loop breakages take precedence over backlog breadth. All UI cards require automated tests and live Electron verification. Format: Task-Template.
Scope Per-paper freeform notes, persisted to SQLite. Markdown editor in the right-panel Notes tab. Acceptance notes CRUD per paper · persists across restart · autosave · tests.
Scope Select text in reader and show contextual actions: Add to chat, Explain, and highlight colors. Add to chat inserts quoted selection with paper and page context. Explain starts a grounded Ask turn. Highlights appear in Annotations tab and jump back to anchored PDF text. Acceptance selection actions work in live reader · Add to chat preserves quote and source context · Explain produces grounded turn · highlight persists in SQLite · annotations list + jump · delete · restart verification · tests.
Scope Make [n] reference markers in the reader clickable → jump to the
reference / show a tooltip.
Acceptance citation markers detected · click scrolls to reference · tests.
Scope Author markers become clickable ORCID links where available. Acceptance badge renders when ORCID present · opens profile · graceful absence.
Scope Sidebar folder tree backed by collections / paper_collections.
Drag papers into collections; filter library by collection.
Acceptance create/rename/nest collections · assign papers · library filter · tests.
Scope The sidebar Files / Chats toggle → a browsable list of past chat sessions across papers. Acceptance lists sessions (title, paper, backend, date) · reopen restores thread.
Scope Generate clickable suggested questions per paper (agent), shown in the Ask panel; clicking runs one. Acceptance 3–5 relevant questions generated · click runs it · cached per paper.
Scope Soft-delete papers to a Trash view; restore or purge (removes files + rows). Acceptance soft delete hides from library · restore · purge removes files+rows · tests.
Scope Surface plan-credit / token usage for ACP calls where the adapters expose it (see ACP-Integration — plan credit is finite). Acceptance per-session or per-day usage shown · degrades if adapter lacks metrics.
Scope The top-left account/workspace switcher → multiple local libraries
(separate data/ roots or a workspace column).
Acceptance create/switch workspace · library scoped to active workspace.
Scope Slash-commands (skills) and @-mentions (add files/papers to context)
in the chat input.
Acceptance / opens a skill picker · @ adds a paper/file to the turn's
context files · both reach the ACP prompt.