v0.4.0

PDF extraction overhaul, envelope routing for the rest of the --json surface,
typed exit codes wired up across all command error paths, and a CI repair pass.
schema_version bumps to 1.1.0.

Added

• MinerU PDF extractor alongside the existing pymupdf-based extractor, with
  a new BasePdfExtractor abstract class and automatic fallback when MinerU
  fails (zot pdf KEY --extractor mineru). Configure via [pdf] extractor,
  [pdf] mineru_token, or MINERU_TOKEN / ZOT_PDF_EXTRACTOR env vars.
• zot pdf --outline — list every heading in the document as a numbered
  outline so agents can navigate without dumping the full text.
• zot pdf --section N — extract just the content under the N-th heading
  from --outline. Useful for "show me the methods section" workflows.
• zot workspace index --extractor — choose the PDF extractor used during
  RAG indexing.
• Embedding provider router with first-class support for Aliyun
  (DashScope, OpenAI-compatible) and Jina endpoints. Routes via the new
  [embedding] provider, [embedding] aliyun_api_key config keys plus
  ZOT_EMBEDDING_PROVIDER / ZOT_EMBEDDING_ALIYUN_KEY env vars.
• Attachment resolver that handles storage: paths, file:// URLs,
  Zotero's attachments: paths, Windows drive letters, and base-attachment
  prefs. PDFs in non-default storage directories now resolve correctly.
• progress_callback plumbing through the PDF extraction path so MinerU
  batch operations and per-PDF extraction surface progress to the caller.

Changed

• Envelope routing extended to the remaining --json commands:
  zot pdf (incl. --outline / --section), zot workspace list,
  zot workspace query, and zot config cache list now emit the standard
  {ok, data, meta} envelope. workspace query data becomes
  {mode, results} rather than the bare results list.
• schema_version 1.0.0 → 1.1.0 to reflect the envelope-coverage extension
  and the typed-exit-code parity. docs/agent-interface.md updated.
• Typed exit codes wired across all command error paths. Previously many
  error paths called print_error(...); return, printing the error message
  but silently exiting 0. They now use emit_error(...) with the appropriate
  typed code:
  • not_found (4): item / PDF / workspace / collection / profile / index /
    section missing — affects cite, export, summarize, open, pdf,
    workspace delete/add/remove/show/export/import/search/index/query,
    config profile_set.
  • validation_error (3): bad page range in pdf, missing required source
    flag in workspace import, invalid workspace name.
  • auth_missing (2): all tag / trash restore / collection
    write commands when API credentials aren't configured.
  • conflict (6): workspace new when the workspace already exists,
    and zot duplicates now exits 6 when duplicates are found so
    agents can branch on if zot duplicates …; then …; else act_on_dups; fi.
  • runtime_error (1): caught PdfExtractionError in pdf and
    ZoteroWriteError in collection move/delete/rename.
• zot relate KEY with no related items is now a normal exit-0 outcome
  (matching zot search on no matches) rather than an error message.
• config cache list robustness: graceful fallback when the cache DB is
  unreachable; closes the connection in a finally block.

Fixed

• 20 pre-existing test failures on main repaired (some were envelope-shape
  drift between tests and production; the rest were genuine exit-code
  regressions covered by the migration above). The ci.yml pytest run goes
  green again.
• tests/test_extracts_text no longer breaks on hosts without
  ~/.config/zot/config.toml. The previous over-broad Path.exists mock
  also patched load_pdf_config's file-existence check; tightened to a
  targeted load_pdf_config mock.

Breaking

• Tools / agents parsing --json output from zot pdf, zot workspace list, zot workspace query, or zot config cache list need to unwrap
  the standard envelope (result["data"]). Other commands were already
  enveloped; this brings the rest of the surface into line.
• Error paths that previously exited 0 with a printed message now exit
  with their typed code (1, 2, 3, 4, or 6). Scripts that ran
  zot cite NONEXIST && echo ok and similar will now correctly fail.
• zot duplicates exits 6 (CONFLICT) when duplicates are detected.
  Scripts that ignored the exit code or used if zot duplicates; then
  will need to invert the branch.