Add ability to import and bidirectionally sync Zotero reference collections

[petebachant]

Resolves #146

[Copilot]

Pull request overview

Adds Zotero-backed reference management to Calkit projects, including importing Zotero collections, syncing (pull) updates, and editing/viewing reference items and notes in the UI, with corresponding backend APIs and generated client updates.

Changes:

• Implement Zotero import/sync endpoints plus reference item + note CRUD (with optional Zotero note/PDF integration).
• Revamp the References page UI to support collection selection, search, item details modal (PDF + notes), and collection/item creation/editing flows.
• Add BibTeX/LaTeX display-cleanup helpers (with tests) and introduce a project-wide Cmd/Ctrl+K command palette.

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
frontend/src/routes/_layout/$accountName/$projectName/_layout/references.tsx	New references UI with collection selection, search, modals, and Zotero import entry points
frontend/src/routes/_layout/$accountName/$projectName/_layout.tsx	Mount project command palette in the main project layout
frontend/src/lib/bibtex.ts	Add helpers to clean/display BibTeX/LaTeX field values
frontend/src/lib/bibtex.test.ts	Test coverage for BibTeX display helpers
frontend/src/components/References/ReferencesInfoPanel.tsx	Add info/comments panel for a selected references collection + Zotero sync button
frontend/src/components/References/ReferenceItemModal.tsx	Full-screen reference item modal with PDF viewer + anchored notes editing
frontend/src/components/References/NewReferencesCollection.tsx	Modal to create a new empty .bib references collection
frontend/src/components/References/ImportFromZoteroModal.tsx	Modal flow to import from Zotero (whole collection or selected items)
frontend/src/components/References/FileViewModal.tsx	Minor import/style adjustment for reference file viewing
frontend/src/components/References/EditReferenceItemModal.tsx	Modal to add/edit a BibTeX entry in a collection
frontend/src/components/Common/SidebarItems.tsx	Export project nav items for reuse by the command palette
frontend/src/components/Common/ProjectCommandPalette.tsx	New Cmd/Ctrl+K project section jump palette
frontend/src/client/types.gen.ts	Generated client types for new references/Zotero/note APIs
frontend/src/client/sdk.gen.ts	Generated SDK methods for new references/Zotero/note endpoints
frontend/src/client/schemas.gen.ts	Generated schemas for new references/Zotero/note models
backend/app/zotero.py	Zotero Web API integration + BibTeX formatting + note (de)serialization helpers
backend/app/users.py	Add helper to fetch Zotero API key plus Zotero user id
backend/app/tests/api/routes/projects/test_core.py	Add extensive API tests for Zotero import/sync, PDF, reference items, and notes
backend/app/api/routes/projects/core.py	Add/extend project routes for references collections, items, Zotero import/sync, and notes
AGENTS.md	Add troubleshooting guidance for stale frontend client vs backend behavior

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[Copilot]

Pull request overview

Copilot reviewed 22 out of 22 changed files in this pull request and generated 4 comments.

Comments suppressed due to low confidence (1)

frontend/src/routes/_layout/$accountName/$projectName/_layout/references.tsx:244

• These reference-item rows are clickable (onClick) but aren’t keyboard-focusable and don’t respond to Enter/Space, which is an accessibility issue for keyboard-only users.

                        <Text
                          key={item.key}
                          fontSize="xs"
                          noOfLines={1}
                          py={0.5}
                          cursor="pointer"
                          fontWeight={isActive ? "semibold" : "normal"}
                          color={isActive ? "blue.500" : undefined}
                          _hover={{ color: "blue.500" }}
                          onClick={() => onSelectItem(item.key)}
                        >