# Changelog
## [Unreleased]

## [0.48.1] - 2026-05-21

### Changed

- Bump `haiku.skills>=0.17.1` and `pydantic-ai-slim>=1.100.0` (the last pre-2.0 release). Migrate off two APIs slated for removal in pydantic-ai 2.0: `Agent(tool_retries=, output_retries=)` → `Agent(retries={"tools": …, "output": …})` in the LLM-as-judge evaluator, and `Evaluator.evaluation_name` class attribute → overriding `get_default_evaluation_name()` on `CitationMRREvaluator` / `CitationMAPEvaluator`.
- Drop the `item.annotations` fallback in `_picture_description_text`. Docling's `PictureItem` runs a `@model_validator(mode="after")` on load that migrates the deprecated `annotations` field into `meta.description`, so reading `meta.description.text` covers both legacy and current blobs. Tests in `test_converters.py` switched to `meta.description.text` for the same reason.
- Chat TUI now generates a stable per-launch `thread_id` (rotated on "Clear chat") instead of hardcoding `"tui"`. AGUIAdapter forwards it as the `gen_ai.conversation.id` OTel attribute, so multi-turn TUI sessions group into one Logfire conversation instead of collapsing every launch into a single bucket.
- Documentation generator swapped from `mkdocs-material` to `zensical`. Drops `mkdocs` / `mkdocs-material` dev deps, replaces `mkdocs.yml` with `zensical.toml`, adds `overrides/main.html` (OG/Twitter share meta) and `docs/stylesheets/extra.css`. `build-docs` workflow now runs `uv run zensical build` and publishes via the GitHub Pages artifact actions instead of `mkdocs gh-deploy`.

### Fixed

- mxbai reranker crashing inside the chat TUI with `ValueError: bad value(s) in fds_to_keep`. tqdm constructs a `multiprocessing.RLock` on first use, whose `resource_tracker` spawn picks up `sys.stderr.fileno()`; Textual's redirected stderr returns `-1`, failing the `fork_exec` validation. The reranker now pins tqdm's class lock to a `threading.RLock`.
- `migrate` failing on DBs upgrading through v0.45.0 with `Field 'heading_level' not found in target schema`. The v0.45.0 picture-data backfill was building rows from the current `DocumentItemRecord` Pydantic model — which now carries `heading_level` / `tree_depth` added in v0.48.0 — and feeding them to `merge_insert` against a pre-v0.48.0 schema. Both v0.40.0 and v0.45.0 now build their PyArrow inputs from explicit per-migration column sets so future model additions can't retroactively break them.

## [0.48.0] - 2026-05-20

### Added

- `heading_level` and `tree_depth` on `DocumentItem`, populated by `extract_items` and persisted on `document_items`. 0.48.0 migration backfills existing rows from each doc's docling structure blob.
- `toc.json` in the analysis sandbox VFS at `/documents/{id}/toc.json`. Nested tree on HTML/markdown sources, flat sibling list on PDFs. Each node carries `{self_ref, level, title, page_numbers, item_range, chunk_ids, children}`. `chunk_ids` aggregates the citable chunks across the section's `item_range`, so the analysis skill can `cite()` a section from one VFS read instead of falling back to a corpus-wide `search()` that risks cross-document hits.
- `chunk_ids` on every `items.jsonl` row (the citable chunks that contain that item).
- `picture_refs` on sandbox `search()` result dicts and on `Citation` (subset of `doc_item_refs` starting with `#/pictures/`).
- `picture_captions: dict[str, str]` on `SearchResult`, populated alongside `image_data` and rendered as a labelled line in `format_for_agent` for picture-bearing chunks.
- Chat TUI renders picture citations inline via `textual_image.widget.Image` inside the existing `CitationWidget`.
- CLI citation panel renders `picture_refs` inline via `textual_image.renderable.Image` next to the text preview. `format_citations_rich` is async and takes an optional `HaikuRAG` client; without one, figures fall back to `[Figure: <ref>]` markers.
- BTree scalar indexes on `document_items.{document_id, position, self_ref}`. The 0.48.0 migration creates them on existing DBs. Per-doc lookups go from full-table scans (~100–300 ms) to point queries (~3–21 ms) on small/medium corpora.
- Per-doc lazy cache for `items.jsonl` and `toc.json` in the analysis sandbox. First read fetches; subsequent reads of either file in the same `execute_code` session hit a serialized cache. One DB fetch per doc per session.
- `cite` tool now accepts chunk_ids that resolve via the chunks table, not only chunk_ids from a prior `search()` result. Lets the model cite directly from `items.jsonl` / `toc.json` rows. The hallucination guard (`ModelRetry` on chunk_ids that don't exist in the DB) is preserved.
- `AppConfig.evaluations` (`EvaluationsConfig`) with an optional `judge: ModelConfig`. Lets the eval CLI pin the LLM-as-judge per-yaml — including a custom `base_url` for any OpenAI-compatible endpoint (vLLM, LM Studio) without env-var routing.

### Removed

- **Multi-agent research workflow.** Removes `agents/research/` (graph, state, deps, models, prompts), `client.research`, the CLI `research` command, the MCP `research_question` tool, `ResearchConfig`, `AppConfig.research`, `PromptsConfig.synthesis`, and the corresponding wiring in `chat/__init__.py` and `client/downloads.py`. The pydantic-graph workflow was a three-node loop whose differentiators vs the rag skill (planner step, structured `ResearchReport`, iteration bound) were either redundant with `qa.max_searches` or sat on pre-cite-tool legacy. Multi-step questions go through `client.ask` (rag skill).
- `llm()` from the analysis sandbox. Sandbox externals are now `search` and `list_documents` only.
- `list_documents` top-level tool from the analysis skill (still available as `await list_documents()` inside `execute_code`).
- `documents=` kwarg on `client.analyze` (and the `--document` flag on `haiku-rag analyze` / MCP `analyze` tool). The pre-loaded `documents` Python variable inside the sandbox is no longer populated. Use `filter=` (SQL WHERE clause) to scope analysis to specific documents.
- `AnalysisResult.program`. The per-execution programs are still tracked on `AnalysisState.executions` (the analysis skill's `execute_code` tool populates it); consumers that need the executed code should pull it from the skill state instead of the function return value.
- `--cite` flag on `haiku-rag ask`. Citations always render after the answer now.
- `system_prompt` kwarg on `client.ask`. No production caller used it; `config.prompts.domain_preamble` already covers the preamble use case.
- Standalone QA agent (`haiku.rag.agents.qa.*`) and analysis agent module (`haiku.rag.agents.analysis.agent`, `haiku.rag.agents.analysis.prompts`). Also drops `RawAnalysisResult`, `CodeExecution`, `AnalysisDeps`, and the dead `documents=` preload path in `Sandbox`.
- `prompts.qa` config field.
- `evaluations optimize` subcommand and GEPA prompt-optimization. Drops `gepa` dep.
- `--target qa` from `evaluations run`. Default is now `rag-skill`.
- `--judge-model` flag from `evaluations run`. Set the judge in `config.evaluations.judge` instead.
- `position` field on `toc.json` nodes (redundant with `item_range[0]`).
- `position` and `tree_depth` from `items.jsonl` row serialization. Both fields are still persisted on `DocumentItem`; they are no longer surfaced to the sandbox.

### Changed

- `haiku.rag.agents.analysis` moved to `haiku.rag.sandbox`. Public surface: `from haiku.rag.sandbox import Sandbox, SandboxResult, AnalysisContext, AnalysisResult`.
- `Citation` and `resolve_citations` moved to `haiku.rag.store.models.citation` (was `haiku.rag.agents.research.models`), peer to the other output domain models.
- `search.limit` default lowered from `10` to `5`.
- Search result formatter surfaces picture captions on a labelled line when a chunk's expanded refs include pictures.
- Picture bytes attached to `search()` results are bounded to the pre-expansion chunk's `doc_item_refs`. Section expansion that sweeps in adjacent picture-bearing items no longer pulls their bytes into the response. Observed ~16× reduction on tool-response payload sizes; eliminates a class of cross-figure contamination in the agent's view.
- rag-analysis SKILL.md steers structural lookups ("which section X", "list sections of Y", "summarize section Z") to read `/documents/{id}/toc.json` first and cite the matching node's `chunk_ids` directly, instead of calling `search()`. Empirically validated on the ORB multimodal and Wix corpora: locator and orientation questions now cite the correct document instead of falling back to cross-document search hits.
- CLI citation panel compacted: 300-char text preview (no full chunk dump), `[N] Title (URI) — pp. — §Section` header, dimmed `doc: <id>  chunk: <id>` footer. Green "Citations" label matches the green "Answer:" label.
- `AnalysisConfig.model` defaults to `None` (was `ollama:gpt-oss/no-thinking/temp=0`). Resolves via `config.analysis.model or config.qa.model`.
- `client.ask` and `client.analyze` route through the rag and rag-analysis skills internally.
- Bump `docling>=2.93.0` and `docling-core>=2.75.0`.
- Bump `pydantic-ai-slim>=1.96.0`. Migrate off deprecated APIs: AG-UI imports use `pydantic_ai.ui.ag_ui`, docs/CLI examples use the explicit `openai-chat:` model prefix, and `Agent(retries=)` is split into `tool_retries=` + `output_retries=`.
- Bump `pydantic-monty>=0.0.17`. Migrate off deprecated `pydantic_monty.run_repl_async(repl, ...)` to `repl.feed_run_async(...)`.
- Cap `transformers<5.0.0` in the `mxbai` extra: `mxbai-rerank>=0.1.6` calls `tokenizer.prepare_for_model` which transformers 5 removed.
- Refresh the rest of the lockfile to latest within current constraints (pydantic, pydantic-ai, rich, ruff, ty, pytest, torch, textual, textual-image, watchfiles, pre-commit, datasets, and transitives).

### Fixed

- Chat TUI's state-edit screen syntax-highlights JSON instead of falling back to plain text. Adds `tree-sitter` + `tree-sitter-json` to the `[tui]` extra.

### Documentation

- Rework documentation

## [0.47.0] - 2026-05-14

### Added

- **`cross-encoder` reranking provider.** Runs any HuggingFace cross-encoder reranker in-process via `sentence_transformers.CrossEncoder` — no separate server. Useful for BGE (`BAAI/bge-reranker-v2-m3`), Qwen3-Reranker, MS-MARCO MiniLM, and other CrossEncoder-compatible models when vLLM is not an option. New `[cross-encoder]` extra pulls `sentence-transformers`.

### Fixed

- **`rebuild --embed-only` no longer buffers the entire corpus in memory.** The previous implementation accumulated every chunk's id, content, content_fts, metadata, and new embedding vector in a single Python list before flushing. The rebuild now stream-copies non-vector columns into a `chunks_rebuild_staging` table (1000 rows / page), recreates the chunks table fresh to honour vector-dim changes, then streams from staging one document at a time, embedding in batches of `embeddings.batch_size` and flushing to the new chunks table every 50 documents.
- **`rebuild --embed-only` is now idempotent across crashes.** A second table, `chunks_rebuild_marker`, is written immediately after phase 1 (staging copy) finishes. Its presence flips the next rebuild into resume mode: phase 1 is skipped, the live chunks table is recreated, and phase 2 (re-embed) runs from the existing staging snapshot. Cleanup drops the marker before the staging table, so an interruption between the two drops leaves a markerless staging that the next run discards harmlessly. A staging table without a marker is treated as a partial phase 1 and dropped (the live chunks table is still authoritative). Running a non-embed-only mode (FULL / RECHUNK / DESCRIPTIONS / TITLE_ONLY) after a crashed embed-only correctly discards the staging recovery state. Phase 1's pagination was switched from `offset/limit` to `to_batches`, removing the latent offset-drift risk and the O(N²) cost at high offsets.

## [0.46.0] - 2026-05-13

### Added

- **`processing.conversion_options.fetch_remote_images`** (default `true`). Controls whether docling fetches images referenced by URL in HTML and Markdown inputs. docling-local only — docling-serve cannot fetch external images via its API regardless of this flag.
- **`s3://` is a first-class document source.** `create_document_from_source`, the CLI `haiku-rag add-src`, and the MCP `add_document_from_url` tool all dispatch on the `s3` URL scheme. Two-stage change detection keeps `metadata["md5"]` semantically uniform across all sources: HEAD ETag matching the stored `metadata["etag"]` short-circuits without GET; if ETag differs but bytes hash to the same MD5 (multipart re-upload, server-side `CopyObject`, SSE mode change), only the etag refreshes — no re-chunk or re-embed. Closes #357.
- **S3 / object-storage monitoring.** `monitor.s3: list[S3MonitorEntry]` adds a polling watcher per bucket prefix alongside the existing local-directory watcher. Each entry has its own `poll_interval`, `include_patterns`, `ignore_patterns`, `delete_orphans`, and `storage_options`. The same `serve --monitor` flag enables both. Orphan deletion is per-entry (scoped via `uri LIKE 's3://bucket/prefix/%'`); other buckets and prefixes are never touched.
- **`[s3]` optional extra** (`obstore>=0.9`). Required for `s3://` sources and the S3 watcher. Uses obstore — the Python binding to the same Rust `object_store` crate that LanceDB uses internally — so `monitor.s3[*].storage_options` accepts the same dict shape as `lancedb.storage_options`. Empty/missing options fall back to the AWS default credential chain.
- **`scripts/run-integration-tests.sh`** — wraps `docker compose up --wait`, `pytest -m integration`, and tear-down so the SeaweedFS-backed integration suite is a one-liner.
- **`ModelConfig.extra_body`**. Optional dict forwarded verbatim to `ModelSettings.extra_body`, the raw pass-through pydantic-ai exposes for openai/ollama/anthropic/groq. Lets configs reach provider-specific keys without haiku.rag modelling them — e.g. `extra_body: {chat_template_kwargs: {enable_thinking: false}}` to disable Qwen3 thinking on a vLLM endpoint, where the high-level `enable_thinking` flag is a no-op.
- **`embeddings.batch_size`** (default `512`). Number of text chunks per `/v1/embeddings` call during ingest. Lower it when your provider caps total tokens per request. Closes #365.

### Changed

- **Chat TUI streams markdown incrementally.** Assistant messages now use Textual's `MarkdownStream` (`Markdown.get_stream`) and write per-token deltas instead of re-parsing the entire accumulated message on every token. Removes the O(n²) re-parse that visibly stuttered long responses. Bumps `textual` floor to `>=8.2.4` so `Markdown.get_stream` is reachable via the public API.
- **Embedding compatibility check only raises on `vector_dim` mismatch.** `provider` and `name` drift (legitimate when the same model is served by a different stack, e.g. Ollama → vLLM-via-openai) now logs a one-time warning and updates the stored settings to match the current config. Subsequent opens are silent. Run `rebuild --embed-only` if you also want to re-embed under the new stack.
- **`processing.pictures` enum replaces `picture_description.enabled`.** Three modes: `none` (skip picture generation entirely — lower RAM, smaller DBs), `description` (generate images, run VLM, store bytes), `image` (default — generate images, store bytes, no VLM). Closes #366. Breaking change: rename `picture_description.enabled: true` → `pictures: description`, `picture_description.enabled: false` → `pictures: image`. The pre-April-30 `generate_picture_images` flag is also gone; use `pictures: none` for that opt-out.

### Fixed

- **Picture bytes attached to multimodal tool returns are PNG-verified via `PIL.Image.verify()`.** Bytes that fail verification are dropped.
- **Conversion options now apply to non-PDF formats.** `DoclingLocalConverter` previously wired its `PdfPipelineOptions` only to `InputFormat.PDF`, so user settings (OCR knobs, `picture_description.enabled`, `images_scale`, etc.) silently no-op'd for HTML, Markdown, DOCX, PPTX, and IMAGE inputs. The converter now shares a single `PdfPipelineOptions` instance across PDF, IMAGE, HTML, MD, DOCX, and PPTX `FormatOption`s. SimplePipeline-backed formats ignore the PDF-specific fields; `ConvertPipelineOptions`-level enrichments (picture description / classification / chart extraction) now run uniformly. HTML and Markdown additionally receive `HTMLBackendOptions` / `MarkdownBackendOptions` gated on `fetch_remote_images`.
- **HTML text ingest path picks up converter options.** `convert_text(format="html"/"md")` previously used a bare `DoclingDocConverter()` with zero format options — the wix corpus ingest path. It now uses the same shared `_build_format_options()` helper as the file path.
- **Relative `<img>` paths resolve during URL ingest.** `HaikuRAG.convert()` and the converter `convert_file` / `convert_text` methods now thread a `source_uri` through to `HTMLBackendOptions.source_uri` / `MarkdownBackendOptions.source_uri`. URL ingest uses the originating URL; file ingest uses `file://`; raw text accepts an optional override. docling-serve accepts the kwarg as a no-op (its API has no equivalent option).
- **CLI tracebacks no longer dump per-frame locals.** The Typer app now passes `pretty_exceptions_show_locals=False`, so exceptions involving a `DoclingDocument` (or any large object) print readable rich tracebacks instead of pages of inline base64 image URIs. Set `_TYPER_STANDARD_TRACEBACK=1` for plain Python tracebacks.
- **Batch ingest no longer hits HF Hub's 429 rate limit.** The chunking tokenizer is now loaded once per process via `@functools.cache` instead of once per chunker instance.

### Documentation

- New "External image fetching" subsection in `docs/configuration/processing.md` documenting `fetch_remote_images`, the SSRF / size / timeout guards inherited from docling, and a per-format table of which conversion options actually apply (PDF, IMAGE, HTML, MD, DOCX/PPTX, others).
- New "HTML Image Fetching" section in `docs/remote-processing.md` calling out that docling-serve cannot fetch external `<img>` URLs and recommending docling-local for HTML ingest when picture bytes matter.
- New "S3 / Object Storage Monitoring" section in `docs/server.md` and `docs/configuration/processing.md` covering the `[s3]` extra, polling cadence, ETag semantics, credentials, and CLI usage.
- New "Deployment Pattern: One Writer, Many Readers" subsection in `docs/configuration/storage.md` documenting the recommended IAM split (one ingestion process + N read-only consumers).

## [0.45.0] - 2026-05-08

### Added

- **Vision capabilities.** Picture-aware ingestion, vision QA, multimodal embeddings, and image-as-query search.
- **Picture bytes always stored** at ingest in a new `document_items.picture_data` column (`large_binary`), addressable by `(document_id, self_ref)`. Bulk read paths project metadata-only so bytes never leak into context expansion or analysis-sandbox builds. The 0.45.0 migration adds the column on existing DBs and backfills it from each doc's docling blob; URIs are then stripped from the blob so bytes live in one place.
- **VLM picture descriptions** at ingest via `processing.conversion_options.picture_description.enabled` (default `false`). When enabled, descriptions are woven into chunk text. The earlier `generate_picture_images` flag is dropped with a one-time warning. `haiku-rag rebuild --descriptions` runs the VLM over stored bytes after the fact, idempotently — skipping the docling parse entirely.
- **Multimodal embedder (`provider="vllm"`)** for cross-modal retrieval. Talks HTTP to a vLLM `/v1/embeddings` endpoint (`input` array for text, `messages` superset with `image_url` for images). Tested with `Qwen/Qwen3-VL-Embedding-8B` and `jinaai/jina-embeddings-v4`. No new Python ML dependencies. Under multimodal embedders, ingest emits one synthetic picture chunk per `PictureItem`, sharing the chunks table with text.
- **Image-as-query search.** `client.search()` accepts `str | bytes | PIL.Image.Image`. Image queries embed once and run vector-only against the chunks table. New CLI flag `haiku-rag search --image PATH` and new MCP tool `search_documents_by_image(image_base64, ...)` (registered only when the embedder supports images).
- **Vision QA via `qa.model.vision: bool` flag** on `ModelConfig` (default `false`). When `true`, the agent's `search` tool attaches picture bytes as `BinaryContent` parts on its `ToolReturn`. Default is `false` because providers behave inconsistently when an image is sent to a text-only model (Ollama silently accepts and confabulates; OpenAI returns 400). `SearchResult.image_data: dict[str, str] | None` carries base64 picture bytes keyed by `self_ref`; `client.search()` and MCP `search_documents` gain `include_images: bool = True`.
- **Silent-failure guard for picture descriptions.** When `picture_description.enabled=true` and a conversion returns at least one picture but zero descriptions, log a warning naming the source, picture count, VLM model, and base URL. Surfaces docling-serve's swallowed VLM errors (unreachable host, missing model) before they pollute a long ingest.
- **Inspector renders attached pictures** under `qa.model.vision=true` in the context modal (`c` key) so the inspector reflects what the LLM actually receives.

### Fixed

- **`rebuild --descriptions` no longer destroys `docling_pages`.** The previous implementation called `set_docling()` after a structure-only docling load, which writes `docling_pages=None` and clobbered page rasters for every doc with at least one undescribed picture (silently breaking `visualize_chunk` for the affected docs).
- **docling-serve picture-image extraction.** docling-serve only emits picture bytes under `image_export_mode="referenced"` (upstream [docling-project/docling-serve#576](https://github.com/docling-project/docling-serve/issues/576)). The converter switches to `referenced` + `target_type="zip"` when picture images are requested and rehydrates `artifacts/<filename>` URIs back into `data:` URIs.
- **`rebuild --rechunk` reuses the stored docling blob** instead of re-converting from the markdown export, which dropped every `PictureItem` on the floor. Documents without a stored docling blob now raise instead of silently falling back.

### Changed

- **Lazy document hydration during rebuild.** Each mode loop now fetches one full record at a time instead of eagerly loading all docs with their multi-MB blobs. Drops startup memory from ~15 GB to ~one document on a 1000-doc database.

## [0.44.0] - 2026-04-29

### Added

- **Skill-based QA evaluation via `evaluations run --target {qa,rag-skill,analysis-skill}`.** Benchmark the RAG and analysis skills end-to-end alongside the existing QA agent path, against the same datasets and judge. `--skill-model "provider:name"` overrides the skill model independently from the judge.
- **Citation retrieval as a second eval metric.** `CitationMRREvaluator` and `CitationMAPEvaluator` score the URIs the skill registered via the `cite` tool against each dataset's gold `expected_uris`, alongside the existing LLMJudge. Console output gains a "Citation Retrieval" summary (mean score, cite rate, mean citations per case). Zero extra skill runs — cited URIs are surfaced via `pydantic_evals.set_eval_attribute`.
- Bumps `haiku.skills` to `>=0.16.0` for the public `run_skill` API and `Skill.request_limit`.

### Changed

- **Pinned eval judge defaults to `ollama:qwen3.6`.** Previously `--judge-model` defaulted to `config.qa.model`, so changing the QA or skill model also changed the judge — destabilizing cross-run comparisons and re-introducing self-judging whenever the answerer matched. A 2×2 calibration vs Claude Opus 4.7 (gpt-oss / qwen3.6 as both answerer and judge) showed `qwen3.6` had κ ≥ 0.66 on both same- and cross-family answerers (vs 0.39–0.55 for `gpt-oss`) with no detectable self-preference bias. Pass `--judge-model provider:name` to override.
- **Tightened `cite` framing in the RAG skill's `SKILL.md`.** `cite` is now a precondition for the final answer: the model identifies supporting chunk IDs and calls `cite` *before* writing the response. The "MUST cite before answering" requirement carries an explicit refusal carve-out so the model does not cite irrelevant chunks when knowledge is missing. On the wix benchmark this lifted cite rate from 32% → 96%, mean `cited_map` from 0.15 → 0.48, and cut the "correct answer with no citation" pattern from 52% of cases to 1%, with QA accuracy holding at ~78%.
- **Removed dataset-specific eval system prompts.** `WIX_SUPPORT_PROMPT` and `ORB_SYSTEM_PROMPT` duplicated guidance already in the shipped `QA_SYSTEM_PROMPT` and `SKILL.md`, and ORB's referenced the obsolete `search_documents` tool name. The eval-side machinery for injecting them (`DatasetSpec.system_prompt`, `resolve_system_prompt()`) is removed. `config.prompts.qa` remains as the user-facing override knob.

## [0.43.1] - 2026-04-25

### Fixed

- **Relative `db_path` no longer trips the LanceDB cloud-URI sanitizer.** The 0.43 migration to `lancedb.connect_async` started routing the path through an async URI sanitizer that treats anything not clearly an absolute local path as a possible cloud URI, raising `ValueError: An api_key is required when connecting to LanceDb Cloud` on invocations like `haiku-rag info --db db/rag.lancedb`. The path is now made absolute before being handed to LanceDB.

## [0.43.0] - 2026-04-24

### Changed

- **Native async LanceDB**: all table I/O now uses LanceDB's async API (`connect_async`, `AsyncConnection`, `AsyncTable`). Previously, repository methods were declared `async def` but called blocking sync LanceDB under the hood, stalling the event loop on every read/write. No change to the documented `async with HaikuRAG(...) as client:` usage pattern.
- **BREAKING (internal): `HaikuRAG` must be used via `async with`.** Store initialization now happens in `__aenter__`; constructing `HaikuRAG(...)` and calling methods directly without entering the context manager no longer works.
- **BREAKING (internal): `download_models` is no longer a method on `HaikuRAG`.** It's now a module-level function: `from haiku.rag.client.downloads import download_models; async for progress in download_models(config): ...`. The CLI and in-repo consumers are updated.
- **Concurrency: background vacuum tracked as a task** on the client. `__aexit__` and `rebuild_database` now await it explicitly, preventing `CreateIndex transaction was preempted` commit conflicts when destructive operations follow a `create_document` that scheduled a background vacuum.

### Fixed

- **Chat TUI now renders citations again.** After the 0.42.1 flattening of skill state `citations` to `list[str]`, the TUI still indexed `citations[-1]` and iterated the resulting chunk-id string character-by-character, so no citations resolved through `citation_index` and the citation panel stayed empty. Fixed by iterating `state.citations` directly.
- **`search(..., filter=...)` no longer silently under-returns.** The filter path used to materialize LanceDB's top-N window, filter to matching `document_id`s in pandas, and `head(limit)`. When matching chunks lived outside that top-N window (selective filters, broad queries), the caller got fewer than `limit` results even though plenty of matching chunks existed in the index. The document filter is now pushed down into the chunk query as `document_id IN (...)` so `.limit(limit)` applies to matching chunks directly. Behavior change: searches that previously under-returned will start returning the requested count.

## [0.42.1] - 2026-04-22

### Changed

- **BREAKING: Skill state `citations` is now `list[str]` instead of `list[list[str]]`.** With per-invocation state scoping (0.42), the outer list no longer tracked turn boundaries — it only grouped chunk ids per `cite` call within a single invocation, which has no downstream meaning. The field is now a flat, deduplicated list of chunk ids cited during the current invocation. Clients resolve each id through `citation_index` as before. Applies to both `RAGState` and `AnalysisState`.

## [0.42.0] - 2026-04-22

### Fixed

- **`create_document`, `update_document`, and rebuild (`RECHUNK` / full fallback) no longer misread URL-prefixed text as a URL to fetch.** These paths passed known-text content through `HaikuRAG.convert()`, which dispatches on `urlparse(source).scheme`; text whose first line was `https://...` (common for clipped web pages and notes) got handed to `httpx.get` and crashed with `httpx.InvalidURL` on embedded whitespace. Fixed by calling `converter.convert_text(...)` directly at those sites; `convert()` itself is unchanged for `create_document_from_source`.

### Changed

- **Skills share a single `HaikuRAG` client per invocation** via the new `haiku.skills>=0.15.0` `lifespan` hook. The skill's sub-agent opens one read-only client on entry, all tool calls reuse it, and it closes on exit — replacing the old pattern of open/close around every `search` / `list_documents` / `get_document` call.
- **`max_searches` tracked on `RAGRunDeps.search_count`** instead of a module-level `ctx.run_id`-keyed dict. Eliminates a memory leak in long-running processes where old run ids were never evicted.
- **Analysis sandbox persists variables across `execute_code` calls within one invocation.** Re-enables the incremental-exploration workflow (search in one call, process results in the next). Each new skill invocation constructs a fresh `Sandbox` via the analysis lifespan, so there is no cross-invocation leak.
- **Skill state is scoped to the current invocation.** Lifespans now clear `citations`, `searches`, and (for analysis) `executions` at the start of each invocation, so state deltas sent to the AG-UI client reflect only the in-progress turn. `citation_index` is preserved across invocations so past-turn citation chunk ids remain resolvable, and `document_filter` is preserved as session-level config.

## [0.41.0] - 2026-04-20

### Added

- **Document virtual filesystem in analysis sandbox**: Documents mounted at `/documents/{id}/` with `metadata.json` (eager), `content.txt` (lazy), and `items.jsonl` (lazy). Standard Python `pathlib.Path` for browsing and reading document content and structure.
- **`execute_code` skill tool**: Direct code execution in the sandbox, surfaced as individual AG-UI events in the chat TUI. Items VFS uses a lazy bulk cache (~1s for 1000 documents vs 60s+ per-document queries).
- **`cite` skill tool**: Explicit citation registration with per-turn tracking via `citation_index` and `citations` fields in state
- **`--skill` flag for chat TUI**: `haiku-rag chat -s rag -s analysis` to enable specific skills
- **`--model` overrides all agents**: Chat, QA, research, and analysis agents all use the specified model
- **Collapsible program display in chat TUI**: Analysis code execution results shown as expandable code blocks

### Changed

- **BREAKING: Flatten skill architecture**: Skill sub-agents now call `search`, `execute_code`, `cite`, `list_documents`, `get_document` directly — every tool call surfaces as an AG-UI event. Removes the 3rd agent layer where `ask`/`analyze`/`research` spawned inner agents whose tool calls were invisible.
- **BREAKING: Rename RLM agent to analysis agent** throughout:
  - `agents/rlm/` → `agents/analysis/`, all classes renamed (`RLMResult` → `AnalysisResult`, etc.)
  - `client.rlm()` → `client.analyze()`
  - CLI: `haiku-rag rlm` → `haiku-rag analyze`
  - MCP: `rlm_question` → `analyze`
  - Config: `rlm:` → `analysis:` in YAML, `RLMConfig` → `AnalysisConfig`
  - Skill entrypoint: `rag-rlm` → `rag-analysis`
- **Analysis sandbox `search()` returns expanded results** with `doc_item_refs` and `labels` for cross-referencing with `items.jsonl`
- **`list_documents` skill tool** takes no parameters — returns all documents
- **Per-turn citation tracking**: `citation_index: dict[str, Citation]` (deduplicated) + `citations: list[list[str]]` (per-turn chunk IDs) replaces flat citation list
- **Search rate limiting**: Skill search tool enforces `config.qa.max_searches`
- **Context expansion respects section boundaries**: Sections within the char budget are returned whole regardless of item count. Too-large sections expand bounded by section edges. Adjacent sections no longer merge — only overlapping ranges do.
- **Visualization shows full expanded section**: `visualize_chunk` expands context before resolving bounding boxes, so all pages the section spans get highlighted.

### Removed

- **`ask` skill tool**: Replaced by direct `search` + `cite` — the skill sub-agent searches and answers directly
- **`analyze` skill tool**: Replaced by direct `execute_code` + `search` + `cite`
- **`research` skill tool**: Removed from skill layer (still available via CLI `haiku-rag research` and MCP)
- **`get_document()`, `get_docling_document()`**: Removed from analysis sandbox — replaced by VFS
- **`get_chunk()`**: Removed from analysis sandbox — search results include expanded context
- **`create_analysis_toolset()`**: Removed unused `tools/analysis.py` module
- **`qa_history`, `reports` from skill state**: Conversational context handled by the outer chat agent
- **`combine_filters`, `build_document_filter`**: Removed from public API
- **`max_context_items`**: Removed from `SearchConfig` — `max_context_chars` is the sole expansion constraint
- **`QAHistoryEntry`, `tools/qa.py`**: Removed unused QA history model and relevance threshold

## [0.40.1] - 2026-04-17

### Fixed

- **`haiku-rag info` on pre-migration databases**: `info` no longer fails with a misleading `Cannot create tables in read-only mode` error when a required table added by a later version (e.g. `document_items` in 0.40.0) is absent. It now reports stats for the tables that do exist, marks the missing ones as `absent`, and shows a dedicated section listing any pending migrations with the `haiku-rag migrate` hint ([#346](https://github.com/ggozad/haiku.rag/issues/346))

## [0.39.0] - 2026-04-16

### Added

- **Document items table**: Pre-extracted document items stored as individual rows with scalar indexes, enabling context expansion via indexed range queries (~2.5ms) instead of full DoclingDocument deserialization (~8.7s for large documents)
- **Section-bounded context expansion**: Expansion is now automatic and structure-aware — stays within section boundaries for structured documents, grows outward for unstructured ones. Noise labels (footnotes, page headers/footers) are filtered. Results without `doc_item_refs` pass through unexpanded.

### Changed

- **Database migration required**: Run `haiku-rag migrate` to populate `document_items` table for existing documents
- **Pin docling-core**: Upper bound added (`<2.72`) to prevent uncontrolled schema changes
- **`max_searches` default**: Raised from 3 to 5 — faster expansion makes additional searches inexpensive
- **Improved QA prompt**: Stronger instruction to refuse answering from tangentially related content
- **Improved judge prompt**: Asymmetric evaluation — generated answers that are more comprehensive than expected are not penalized

### Removed

- **`context_radius` config**: Replaced by automatic section-bounded expansion. Context expansion no longer requires configuration.
- **DoclingDocument LRU cache**: No longer needed — the document_items table replaces in-memory caching for context expansion
- **`cachetools` dependency**: No longer used

## [0.39.0] - 2026-04-09

### Added

- **S3/Object storage support**: Connect to LanceDB on S3, GCS, Azure Blob, or HDFS via `lancedb.uri` and `storage_options` config. Supports S3-compatible stores with custom endpoints.
- **Remote skill generation**: `create-skill` now supports remote databases — omit `--db` and provide `--config-file` to generate skills that connect to object storage at runtime instead of bundling the database.

### Fixed

- **Skill `list_documents` ignores `document_filter`**: `list_documents` tool now respects `state.document_filter`, consistent with `search`, `ask`, and `research`
- **Skill `analyze` ignores `document_filter`**: `analyze` tool now uses `state.document_filter` (combined with any explicit `filter` parameter). Added `document_filter` field to `RLMState`

## [0.38.0] - 2026-04-07

### Added

- **Separate page storage**: Page images stored in dedicated `docling_pages` column — search/expand never loads page data
- **zstd compression**: Switch from gzip to zstd for docling document storage (Python 3.14 stdlib, zstandard package for older versions)
- **`Document.set_docling()`**: Helper method that handles split compression and version assignment, replacing 11 manual call sites
- **`Document.get_page_images()`**: Load page images without the document structure, for visualize_chunk
- **`DocumentRepository.get_pages_data()`**: Load only page data column for a document

### Changed

- **Database migration required**: Run `haiku-rag migrate` to split existing docling blobs into structure + pages and re-compress with zstd

### Fixed

- **Generated skill `domain_preamble`**: Apply `config.prompts.domain_preamble` to instructions in generated skill packages

## [0.37.0] - 2026-04-07

### Changed

- **Dependency updates**: lancedb 0.30.2, pydantic-ai-slim ≥1.77.0, docling ≥2.84.0, docling-core ≥2.71.0, haiku.skills ≥0.13.0, cachetools ≥7.0.5, pydantic-monty ≥0.0.9, cohere ≥5.21.1, textual ≥8.2.1, ty ≥0.0.28, ruff ≥0.15.9
- **Search result model**: `SearchResult` now includes `order` field propagated from chunk order

### Fixed

- **Type checking**: Fix 37 new ty 0.0.28 diagnostics with proper None guards, assertions, and specific ignore codes
- **Search performance**: Avoid loading full document blobs (docling_document, content) during search — use column projection to fetch only needed metadata (id, uri, title, metadata)
- **Context expansion performance**: Load only docling columns during expand_context (skip content blob), and only when doc_item_refs exist
- **Chunk expansion performance**: Fetch only chunks in the needed order range during context expansion instead of all chunks for a document
- **Embedding batching**: Batch embedding calls in groups of 512 to avoid request size limits and timeouts with large documents
- **DoclingDocument validation**: Strip page images before validation on the read path — pages are only needed for visualize_chunk and account for ~99% of the JSON size

## [0.36.3] - 2026-04-01

### Fixed

- **Citation formatting**: Replace raw UUIDs (`[doc_id:chunk_id]`) with human-readable identifiers (`[index] title`) in `format_citations()` output, preventing LLMs from hallucinating opaque ID markers in answers
- **domain_preamble propagation**: `domain_preamble` now flows to skill subagents and the main agent preamble, not just internal agents (QA, research). Fixes ambiguous queries failing when domain context was needed.

### Changed

- **domain_preamble docs**: Clarified that `domain_preamble` is for domain context (subject matter, terminology), not behavioral instructions (tone, response style).

## [0.36.2] - 2026-03-28

### Fixed

- **Skill extras**: Include `db_path` and `config` in skill extras for both RAG and RLM skills, enabling post-creation reconfiguration

## [0.36.1] - 2026-03-27

## [0.36.0] - 2026-03-26

### Added

- **Chunk visualization for generated skills**: `visualize_chunk(chunk_id)` function exposed in generated skill packages, enabling callers to render visual grounding from chunk IDs in skill state
- **Configurable generated skills**: Generated skill `create_skill()` now accepts optional `db_path` and `config` parameters, enabling post-discovery reconfiguration via `skill.reconfigure()` (requires haiku.skills >= 0.11.0)

### Fixed

- **Generated skill packages**: Include SKILL.md and assets in wheel distributions. Add README to generated packages.
- **Docling-serve chunker**: Detect per-document failure status that was silently returning 0 chunks when the task-level status was "success" but individual documents failed
- **Docling local chunker**: Re-enable `repeat_table_header` for self-contained table chunks, improving retrieval quality and matching docling-serve behavior

## [0.35.1] - 2026-03-24

### Added

- **`create-skill` CLI command**: Generate standalone skill packages with embedded LanceDB databases. Generated packages register as `haiku.skills` entry points.

## [0.35.0] - 2026-03-24

### Added

- **Configurable judge and reflect models**: `evaluations run` and `evaluations optimize` accept `--judge-model provider:name`; `optimize` also accepts `--reflect-model provider:name`. Both fall back to `config.qa.model` when not specified.
- **`parse_model_option`**: Utility in `haiku.rag.utils` for parsing `provider:name` strings into `ModelConfig`
- **New format extensions**: `.tex`, `.latex`, `.qmd` (Quarto), `.rmd` (R Markdown) supported in both local and serve converters

### Changed

- **LLMJudge**: Custom evaluator now accepts `ModelConfig` instead of a model name string
- **Docling upgrade**: docling-core ≥2.70.2 (schema 1.10.0), docling ≥2.81.0. Adds field data model support for structured form/KV content, wide table chunking fixes, and rich table cell hang fix
- **pydantic-ai ≥1.70.0**: Bumped minimum version. Removed `structured_output_type` helper — all supported providers now handle native structured output, so agents pass result types directly

## [0.34.1] - 2026-03-16

### Added

- **PlantUML support**: `.puml`, `.plantuml`, and `.pu` files are now indexed as `plantuml` code blocks

## [0.34.0] - 2026-03-13

### Added

- **Activity events**: TUI and web frontend now display skill sub-agent tool calls via `ActivitySnapshotEvent`

### Changed

- **RLM sandbox**: Bumped pydantic-monty to 0.0.8. Removed `regex_*` external functions — the sandbox now has native `re` and `math` modules via `import`. Also adds `filter()` and `getattr()` builtins.
- **Frontend deps**: Upgraded CopilotKit to 1.54.0 and @ag-ui/client to 0.0.47

## [0.33.3] - 2026-03-12

### Added

- **GEPA prompt optimization**: `evaluations optimize` command for automated QA system prompt improvement using evolutionary optimization with LLM-judged scoring. Cases are split 50/50 into train/val sets; GEPA budget is auto-computed from `--num-candidates` and dataset size.
- **Tuning docs**: Added step 7 (Optimize QA Prompts) to the tuning workflow in `docs/tuning.md`
- **Evaluations test coverage**: Tests for evaluators (MAP, MRR), config, benchmark helpers, dataset mappers/builders, and optimization

### Fixed

- **Read-only mode table creation**: `--read-only` no longer creates lance tables when pointed at an empty directory. `Store._init_tables()` now raises `ReadOnlyError` when tables are missing in read-only mode.

## [0.33.2] - 2026-03-11

### Changed

- **QA search cap**: Replace dead `max_iterations`/`max_concurrency` config with `max_searches` (default: 3). The QA agent now enforces a per-run search limit, reducing average response time from ~30s to ~15s while maintaining accuracy. The limit resets per agent run so toolsets can be safely reused.
- **Default search limit**: Increased from 5 to 10 results per search query for better coverage.

### Fixed

- **QA citations**: Strengthened prompt to clarify chunk ID format (complete IDs without brackets). `resolve_citations` now strips `[]` from IDs, handling models that copy brackets from search result formatting.

## [0.33.1] - 2026-03-06

### Changed

- **Default model temperatures**: Set task-appropriate temperature defaults — 0.3 for QA, research, and title generation; 0.0 for RLM and picture description. Previously unset (provider defaults, typically 0.7–1.0).
- **QA thinking enabled by default**: `enable_thinking` now defaults to `True` for QA agent, improving answer quality with reasoning models.
- **Default title max_tokens**: Set `max_tokens=100` for title generation model to keep titles concise
- **Evaluation judge**: Set `temperature=0.0` and `enable_thinking=True` for deterministic, higher-quality judging. Removed unused judge config from retrieval benchmarks.
- **Test suite cleanup**: Removed stale VCR cassettes, dead fixtures, orphaned directories, and redundant tests. Strengthened weak assertions across search, context enhancement, and converter tests. Relocated misplaced `SearchResult._get_primary_label` test to `test_search.py`
- **Parallel test execution**: Added `pytest-xdist` and enabled parallel test runs by default (`-n auto`), reducing test suite time from ~3.5 min to ~2 min

## [0.33.0] - 2026-03-04

### Added

- **Module-level skill introspection API**: `STATE_TYPE`, `STATE_NAMESPACE`, `skill_metadata()`, `instructions()`, and `state_metadata()` on `haiku.rag.skills.rag` and `haiku.rag.skills.rlm` — allows introspecting skill configuration without calling `create_skill()`
- **Automatic structured output detection**: Native JSON schema output is used automatically when the model supports it, with tool-call fallback otherwise. No configuration needed.

### Changed

- **`haiku.skills` dependency**: Bumped to `>=0.7.0` for `StateMetadata` dataclass

## [0.32.3] - 2026-03-03

### Changed

- **AG-UI skill streaming**: Tool calls within skills are now streamed as real-time AG-UI events to the frontend. Requires `haiku.skills>=0.6.0`

### Fixed

- **Search tool regression**: Removed LLM-facing `filter` parameter from search and list_documents tools. The SQL WHERE clause description confused LLMs, degrading QA accuracy. Document filtering is now handled programmatically via `base_filter` and `state.document_filter`

## [0.32.2] - 2026-02-28

### Fixed

- **Compatibility with haiku.skills 0.5.1**: Replaced removed `SkillToolset.system_prompt` with `build_system_prompt(toolset.skill_catalog)` across chat TUI, backend app, and examples
- **Minimum dependency**: Bumped `haiku.skills` requirement to `>=0.5.1`
- **Chat model default**: Chat TUI and backend app now use the configured QA model instead of hardcoded `openai:gpt-4o`

## [0.32.1] - 2026-02-26

### Added

- **Automatic title generation**: Documents can now have titles auto-generated during ingestion via `processing.auto_title: true`. Uses two-tier extraction: structural metadata from DoclingDocument (HTML `<title>`, h1, section headers) first, with LLM fallback via configurable `processing.title_model`
- **`generate_title()`**: Public method on `HaikuRAG` to generate a title for an existing document on demand
- **`rebuild --title-only`**: New rebuild mode that generates titles only for untitled documents without re-chunking or re-embedding
- **`add --title`**: CLI option to set a title when adding text documents

## [0.32.0] - 2026-02-24

### Changed

- **RLM sandbox**: Replaced Docker-based code execution with [pydantic-monty](https://github.com/pydantic/monty), a minimal secure Python interpreter written in Rust. Eliminates Docker as a runtime dependency for RLM with sub-millisecond sandbox startup
- **RLM sandbox functions**: Added `get_chunk(chunk_id)` for retrieving chunk content and metadata from search results. `get_docling_document(document_id)` now returns the full document structure as a JSON dict. All sandbox functions now require `await`
- **`RLMConfig`**: Removed `docker_image` and `docker_memory_limit` fields

### Added

- **RLM sandbox regex functions**: `regex_findall`, `regex_sub`, `regex_search`, `regex_split` for pattern matching without LLM calls
- **`HaikuRAG.get_chunk_by_id()`**: Public method for chunk lookup by ID

### Removed

- **`docker_sandbox.py`**, **`runner.py`**: Docker container plumbing replaced by `sandbox.py`

## [0.31.1] - 2026-02-20

### Fixed

- **`info` and `history` commands**: Open database in read-only mode to prevent write failures on read-only filesystems

## [0.31.0] - 2026-02-20

### Added

- **RAG skill** (`haiku.rag.skills.rag`): haiku.skills integration with search, list_documents, get_document, ask, and research tools plus managed `RAGState`
- **RLM skill** (`haiku.rag.skills.rlm`): haiku.skills integration with analyze tool for computational analysis via code execution
- **`HaikuRAG.research()`**: Client method for multi-agent research
- **haiku.skills entry points**: `rag = "haiku.rag.skills.rag:create_skill"`, `rag-rlm = "haiku.rag.skills.rlm:create_skill"`

### Changed

- **Chat TUI**: Rebuilt on RAG skill + haiku.skills `SkillToolset`
- **Web app backend**: Rebuilt on RAG skill + `AGUIAdapter`
- **Toolsets simplified**: Removed `ToolContext`, `SessionState`, `AgentDeps`, `Toolkit`; kept core `FunctionToolset` factories
- **Research graph**: Removed `session_context` and conversational output mode

### Removed

- **`agents/chat/`**: Entire chat agent module (replaced by RAG skill)
- **`--deep` flag**: Removed from `ask` CLI (use `research` command instead)
- **`--context`/`--context-file`**: Removed from `ask` CLI
- **`tools/` state machinery**: `ToolContext`, `ToolContextCache`, `SessionState`, `AgentDeps`, `Toolkit`, etc.

## [0.30.2] - 2026-02-19

### Fixed

- Added `cachetools` as an explicit dependency (was only available transitively, causing `ModuleNotFoundError` for some installations)
- **download-models**: Show actionable error message when Ollama is not running instead of cryptic "All connection attempts failed" (#277)

## [0.30.1] - 2026-02-17

### Changed

- **AG-UI state sync**: `ask` tool now emits `StateDeltaEvent` (JSON Patch) instead of `StateSnapshotEvent`, consistent with the `search` tool

## [0.30.0] - 2026-02-16

### Added

- **Composable toolsets**: New `haiku.rag.tools` module with reusable `FunctionToolset` factories that can be mixed into any pydantic-ai agent
  - `create_search_toolset()` — hybrid search with context expansion and citation tracking
  - `create_document_toolset()` — document listing, retrieval, and summarization
  - `create_qa_toolset()` — question answering via research graph with prior answer recall
  - `create_analysis_toolset()` — computational analysis via RLM agent (Docker sandbox)
- **`Toolkit` and `build_toolkit()`**: High-level factory that bundles toolsets, prompt, and context creation for a given feature set. Reduces agent composition from ~15 lines to ~5. `build_chat_toolkit()` adds chat-specific defaults (background summarization callback)
- **`ToolContext`**: Namespace-based state container shared across toolsets. Toolsets register Pydantic models under string namespaces, enabling state accumulation (search results, citations, QA history) across invocations
- **`ToolContextCache`**: In-memory TTL-based cache for `ToolContext` instances, keyed by external session/thread ID. Replaces module-level caches for embeddings and summaries
- **`run_qa_core()`**: Extracted core QA function for direct programmatic use without an agent
- **Feature-based chat agent**: `create_chat_agent()` accepts a `features` list to select which toolsets are enabled (`search`, `documents`, `qa`, `analysis`). System prompt is composed to match
- **New documentation**: `docs/tools.md` covers all toolsets, `ToolContext`, state management, filter helpers, and composing custom agents

### Changed

- **Toolset factories decoupled from runtime dependencies**: `create_search_toolset()`, `create_qa_toolset()`, `create_document_toolset()`, `create_analysis_toolset()`, and `create_chat_agent()` no longer take `client` or `context` parameters. Instead, tool functions receive these via pydantic-ai's `RunContext.deps`. This enables toolset and agent creation at configuration time (cacheable, created once), with only lightweight deps created per-request. Deps must satisfy the `RAGDeps` protocol (`client: HaikuRAG`, `tool_context: ToolContext | None`)
- **Toolset factory return types narrowed to `FunctionToolset[RAGDeps]`**: All four toolset factories now declare their return type as `FunctionToolset[RAGDeps]` instead of bare `FunctionToolset`
- **`create_chat_agent()` accepts optional `toolkit` parameter**: Pass a pre-built `Toolkit` to share toolsets between agent and context creation, avoiding duplicate construction
- **`ChatDeps` now includes `client`**: `ChatDeps(config=..., client=..., tool_context=...)` — the `client` field was added since it's no longer captured by the agent factory
- **`prepare_chat_context()` helper**: Extracted from `create_chat_agent()` for idempotent namespace registration, since the agent factory no longer has access to the context
- **Chat agent architecture**: Rebuilt on composable toolsets instead of monolithic tool definitions. Chat agent is now a thin wrapper around `create_search_toolset`, `create_document_toolset`, `create_qa_toolset`, and `create_analysis_toolset`
- **State management simplified**: Removed `session_id`, `incoming_session_id`, and `incoming_session_context` from the state layer. `ToolContextCache` preserves all state (embeddings, summaries, QA history) on cached `ToolContext` instances, eliminating the need for module-level caches
- **AG-UI state sync**: `ask` tool now emits `StateSnapshotEvent` instead of `StateDeltaEvent`, ensuring background summarization results are reliably delivered to clients
- **TUI simplified**: Chat TUI reads directly from `ToolContext` namespace states instead of maintaining a separate `ChatSessionState` and manually syncing via AG-UI state events
- **AG-UI web app**: Uses `ToolContextCache` to maintain per-thread state across requests
- **Frontend session management**: Persistent chat sessions with localStorage, wired to backend `ToolContextCache` via CopilotKit `threadId`
  - Session manager dropdown: create, switch, delete, and export sessions to markdown
  - Messages, chat state, and citations restored on session switch
  - Session title derived from first user message
  - Inline citation blocks injected after assistant responses via `qa_history` correlation

### Removed

- **`SearchAgent`**: Replaced by `create_search_toolset()`
- **Module-level session caches**: `_session_cache`, `cache_session_context`, `get_cached_session_context`, `cache_question_embedding`, `get_cached_embedding` — all replaced by cached `ToolContext`
- **`ChatSessionState` from TUI**: TUI no longer maintains its own copy of session state

## [0.29.1] - 2026-02-10

### Fixed

- **Document listing memory usage**: `list_documents` no longer loads full document content and docling blobs by default, preventing out-of-memory errors on large databases. Use `include_content=True` when content is needed.
- **Chat session_id not persisting across AG-UI requests**: `ChatSessionState.session_id` now defaults to `""` instead of auto-generating a UUID. This ensures the session_id assignment is detected as a state change and included in the `StateDeltaEvent` delta, allowing clients to persist it across requests.

## [0.29.0] - 2026-02-06

### Added

- **docling-serve Chunker OCR Options**: The docling-serve chunker now respects OCR settings from `conversion_options`
  - Passes `do_ocr`, `force_ocr`, `ocr_engine`, and `ocr_lang` to the chunking API
  - Allows disabling OCR via config when running docling-serve in read-only containers
- **RLM Agent (Recursive Language Model)**: New agent for complex analytical tasks via sandboxed Python code execution
  - Solves problems traditional RAG can't handle: aggregation, computation, multi-document analysis
  - Docker-based sandbox with full Python environment (no import restrictions)
  - Container reuse within a single `rlm()` call for reduced latency
  - Available functions: `search()`, `list_documents()`, `get_document()`, `get_docling_document()`, `llm()`
  - Pre-loaded documents support via `documents` variable
  - Context filter for scoping searches without LLM control
  - New `client.rlm(question)` method on HaikuRAG client
  - New `haiku-rag rlm` CLI command
  - New `rlm_question` MCP tool
  - New config options: `docker_image`, `docker_memory_limit`
- **CI**: Docker sandbox integration tests run in GitHub Actions

### Fixed

- **CI**: Cache HuggingFace tokenizer to prevent flaky test failures when HuggingFace has transient outages

## [0.28.0] - 2026-01-31

### Changed

- **Iterative Research Planning**: Research graph now uses an iterative feedback loop instead of batch question processing
  - Planner proposes ONE question at a time, sees the answer, then decides whether to continue
  - Removes `gather_context` tool — planner proposes questions directly
  - Simpler flow: `plan_next` → `search_one` → loop back until complete → `synthesize`
  - Consolidated `build_conversational_graph()` into `build_research_graph(output_mode="conversational")`

### Removed

- **Dead config options**: Removed vestigial fields from iterative planning refactor
  - `confidence_threshold` from `ResearchConfig` and `ResearchState` (LLM decides completion via `is_complete`)
  - `max_sub_questions` from `QAConfig` (iterative flow uses one question at a time)
  - `sub_questions` field from `ResearchContext` (no longer populated)

## [0.27.2] - 2026-01-29

### Added

- **Deep Ask Evaluations**: QA benchmarks can now use the research graph for multi-step reasoning
  - New `--deep` flag on `evaluations run` enables deep ask mode
  - Uses research graph with `max_iterations=2` and `confidence_threshold=0.0`
  - Evaluation name automatically suffixed with `_deep` when enabled
  - Experiment metadata includes `deep_ask` field for tracking
- **Chat Agent Document Awareness Tools**: Two new tools for browsing and understanding the knowledge base
  - `list_documents` — Returns `DocumentListResponse` with paginated documents (50 per page), page number, total pages, and total count; respects session document filter
  - `summarize_document` — Generate LLM-powered summaries of specific documents
- **Document Count API**: New `count_documents(filter)` method on `HaikuRAG` client for efficient document counting
- **Read-Only Initial Context**: Initial context is now locked after the first message, providing consistent session context
  - Chat TUI: `--initial-context` CLI option sets background context for the session
  - Context can be edited via command palette before the first message is sent
  - After first message, context becomes read-only (view only)
  - Clearing chat resets context to CLI value and unlocks editing
  - Web app: Memory panel now serves dual purpose - edit initial context before first message, view session context after
  - Agent uses `initial_context` as fallback when `session_context` is empty

### Changed

- **AG-UI State Delta Updates**: Web application now sends `StateDeltaEvent` (JSON Patch RFC 6902) instead of full `StateSnapshotEvent` for state updates
  - Reduces bandwidth when state grows large (e.g., 50 Q&As with citations)
  - First request still sends full snapshot; subsequent requests send only changes
  - Backend logging shows incoming/outgoing state events for debugging

### Fixed

- **Chat TUI Session State Sync**: TUI now syncs full session state from AG-UI events

## [0.27.1] - 2026-01-27

### Added

- **Initial Context for Chat Sessions**: New `initial_context` field on `ChatSessionState` allows external clients to seed sessions with background context
  - Static context set once at session creation, used as fallback when no cached session context exists
  - Incorporated into first summarization, after which evolved `session_context` takes precedence
  - Eliminates need for clients to import and call internal cache functions (`cache_session_context`, `get_cached_session_context`)
  - `session_id` now auto-generates a UUID if not provided (previously defaulted to empty string)

### Fixed

- **AG-UI StateSnapshotEvent JSON Serialization**: Chat agent tools now use `model_dump(mode="json")` when creating `StateSnapshotEvent`
  - Fixes `TypeError: Object of type datetime is not JSON serializable` when external clients persist AG-UI state to database JSON columns

## [0.27.0] - 2026-01-26

### Added

- **Evaluation Database Hosting**: Pre-built evaluation databases available on HuggingFace
  - `evaluations download <dataset>` downloads pre-built databases from `ggozad/haiku-rag-eval-dbs`
  - `evaluations upload <dataset>` uploads databases to HuggingFace (maintainer only)
  - Supports `all` argument to download/upload all datasets at once
  - Use `--force` flag to overwrite existing databases
  - Avoids lengthy database rebuild times for users running benchmarks
- **Stable Citation Registry**: Citation indices now persist across tool calls within a session
  - Same `chunk_id` always returns the same citation index (first-occurrence-wins)
  - New `citation_registry: dict[str, int]` field on `ChatSessionState`
  - New `get_or_assign_index(chunk_id)` method for stable index assignment
  - Registry serialized/restored via AG-UI state protocol
- **Prior Answer Recall**: The `ask` tool automatically checks conversation history before research
  - Finds semantically similar prior answers using embedding similarity (0.7 cosine threshold)
  - Relevant prior answers are passed to the research planner as context
  - Planner can return empty sub_questions when context is sufficient, avoiding redundant searches
- **Dynamic Session Context**: Compressed conversation history for multi-turn chat
  - New `SessionContext` model stores summarized conversation state instead of raw Q&A history
  - Background LLM-based summarization runs after each `ask` tool call (non-blocking)
  - Previous summarization tasks are cancelled when new ones start
  - Research graph receives compact context (~1,000-2,000 tokens) instead of raw qa_history (potentially thousands of tokens)
  - New `session_context` field on `ChatSessionState` synced via AG-UI state protocol
  - Chat TUI: New context modal (`Ctrl+O`) to view current session context
- **Session Document Filter**: Restrict all search/ask operations to selected documents
  - New `document_filter` field on `ChatSessionState` stores list of document titles/URIs
  - Session filter combines with per-tool `document_name` filter using AND logic
  - Multi-document selection uses OR logic within the session filter
  - Filter persists across tool calls and chat clears via AG-UI state protocol
  - Chat TUI: Access via command palette ("Filter documents" command)
  - Web Application: Filter button in header shows count of selected documents

### Changed

- **Dependencies**: Updated core dependencies
  - `pydantic-ai-slim`: 1.44.0 → 1.46.0
  - `lancedb`: 0.26.1 → 0.27.0
  - `docling`: 2.68.0 → 2.69.1
  - `docling-core`: 2.59.0 → 2.60.1
- **VoyageAI Embeddings**: Now uses pydantic-ai-slim's native VoyageAI support instead of custom implementation
  - Removed `haiku.rag.embeddings.voyageai` module
  - The `voyageai` extra now delegates to `pydantic-ai-slim[voyageai]`

### Removed

- **Q&A History Functions**: Removed standalone conversation history utilities
  - `rank_qa_history_by_similarity()` - similarity matching now integrated into `ask` tool
  - `format_conversation_context()` - replaced by `SessionContext` summarization
  - Associated embedding cache and helper functions also removed

## [0.26.9] - 2026-01-22

### Fixed

- **v0.25.0 Migration Failure**: Fixed "Table 'documents' already exists" error during migration caused by held table references preventing `drop_table()` from succeeding. Added recovery logic to restore documents from staging table if a previous migration attempt failed mid-way.

## [0.26.8] - 2026-01-22

### Added

- **Jina Reranker v3**: Added support for Jina reranking with API mode (`provider: jina`) and local inference (`provider: jina-local`, requires `[jina]` extra)
- **Model Downloads**: `download-models` now pre-downloads HuggingFace models for `sentence-transformers`, `mxbai`, and `jina-local`
- **Reranker Factory**: Removed unreliable `id(config)`-based caching from `get_reranker()`; factory now always instantiates fresh

### Changed

- **Agent Search Result Display**: Search results now show rank position instead of raw scores
  - `SearchResult.format_for_agent()` accepts optional `rank` and `total` parameters
  - Output changes from `(score: 0.02)` to `[rank 1 of 5]` when rank is provided
  - Prevents LLMs from misinterpreting low RRF hybrid search scores as "2% relevant"
  - QA and Research agents updated to pass rank/total to formatted results
  - Agent prompts updated to reference rank-based ordering instead of scores

### Fixed

- **Test Cassette Organization**: Consolidated all VCR cassettes to `tests/cassettes/`
- **Environment Loading**: Fixed `.env` file loading to search from current working directory instead of source file directory ([#250](https://github.com/ggozad/haiku.rag/pull/250)) - thanks @tianyicui

## [0.26.7] - 2026-01-20

### Added

- **OCR Engine Selection**: New `ocr_engine` option in `conversion_options` to explicitly select OCR backend ([#246](https://github.com/ggozad/haiku.rag/issues/246))
  - Supported engines: `auto` (default), `easyocr`, `rapidocr`, `tesseract`, `tesserocr`, `ocrmac`
  - Works with both `docling-local` and `docling-serve` converters
  - Fixes inconsistent OCR engine selection between docling-serve startup and conversion requests

### Removed

- **A2A Example**: Removed `examples/a2a-server/` A2A protocol server example
- **Stale Example References**: Cleaned up references to removed `ag-ui-research` example from documentation

### Changed

- **MCP Error Handling**: MCP tools now let exceptions propagate naturally; FastMCP converts them to proper MCP error responses
- **Chunk Contextualization**: Consolidated duplicate `contextualize` logic into `Chunk.contextualize_content()` method
- **Type Checker**: Replaced pyright with [ty](https://github.com/astral-sh/ty), Astral's extremely fast Python type checker
  - Added explicit `Agent[Deps, Output]` type annotations to all pydantic-ai agents for better type inference
  - Removed ~24 unnecessary `# type: ignore` comments that ty correctly infers
- **Dependencies**: Updated to latest versions
  - `pydantic-ai-slim`: 1.39.0 → 1.44.0
  - `docling`: 2.67.0 → 2.68.0
  - `pathspec`: 0.12.1 → 1.0.3
  - `textual`: 7.0.0 → 7.3.0
  - `datasets`: 4.4.2 → 4.5.0
  - `ruff`: 0.14.11 → 0.14.13
  - `opencv-python-headless`: 4.12.0.88 → 4.13.0.90

### Fixed

- **Chat TUI**: Fixed crash when logfire is installed but user is not authenticated ([#247](https://github.com/ggozad/haiku.rag/issues/247))

## [0.26.6] - 2026-01-19

### Changed

- **Explicit Database Migrations**: Database migrations are no longer applied automatically on open
  - Opening a database with pending migrations now raises `MigrationRequiredError` with a clear message
  - New `haiku-rag migrate` command to explicitly apply pending migrations
  - Version-only updates (no schema changes) are applied silently in writable mode
  - New `skip_migration_check` parameter on `Store` for tools that need to bypass the check
  - `Store.migrate()` method returns list of applied migration descriptions

## [0.26.5] - 2026-01-16

### Added

- **Background Context Support**: Pass background context to agents via CLI or Python API
  - `haiku-rag ask --context "..." --context-file path` for Q&A with background context
  - `haiku-rag research --context "..." --context-file path` for research with background context
  - `haiku-rag chat --context "..." --context-file path` for chat sessions with persistent context
  - `ResearchContext(background_context="...")` for Python API usage
  - `ChatSessionState(background_context="...")` for chat agent sessions
  - Context is included in agent system prompts and research graph planning
- **Frontend Background Context**: Settings panel in the chat app to configure persistent background context
  - Context is stored in localStorage and sent with each conversation
- **Frontend Linting**: Added Biome for linting and formatting the frontend codebase

## [0.26.4] - 2026-01-15

### Added

- **AGUI_STATE_KEY Constant**: Exported `AGUI_STATE_KEY` (`"haiku.rag.chat"`) from `haiku.rag.agents.chat` for namespaced AG-UI state emission
  - Enables integrators to use a consistent key when combining haiku.rag with other agents
  - Backend, TUI, and frontend now use this key for state emission and extraction

## [0.26.3] - 2026-01-15

### Added

- **Enhanced Database Info**: `haiku-rag info` now displays `pydantic-ai` version and `docling-document schema` version
- **Keyed State Emission for Chat Agent**: New `state_key` parameter in `ChatDeps` for namespaced AG-UI state snapshots
  - When set, tools emit `{state_key: snapshot}` instead of bare state, enabling state merging when multiple agents share state
  - Default `None` preserves backwards compatibility (bare state emission)
- **Page Image Generation Control**: New `generate_page_images` option in `ConversionOptions` to control PDF page image extraction

### Changed

- **CLI Error Handling**: Commands (`rebuild`, `vacuum`, `create-index`, `ask`, `research`) now propagate errors with proper exit codes instead of swallowing exceptions

### Fixed

- **Embed-only rebuild with changed vector dimensions**: Fixed `haiku-rag rebuild --embed-only` failing when the configured embedding model has different dimensions than the database
  - Store now reads stored vector dimension when opening existing databases, allowing chunks to be read regardless of current config
  - `_rebuild_embed_only` recreates the chunks table to handle dimension changes
  - `generate_page_images: bool = True` - Enable/disable rendered page images (used by `visualize_chunk()`)
  - Works with both `docling-local` and `docling-serve` converters
  - For `docling-serve`, maps to `image_export_mode` API parameter (`embedded`/`placeholder`)
  - Note: `generate_picture_images` (embedded figures/diagrams) works with local converter but has limited support in docling-serve

## [0.26.2] - 2026-01-13

### Changed

- **Dependencies**: Updated docling dependencies for latest docling-serve compatibility ([#229](https://github.com/ggozad/haiku.rag/issues/229))
  - `docling-core`: 2.57.0 → 2.59.0 (supports schema 1.9.0)
  - `docling`: 2.65.0 → 2.67.0

## [0.26.1] - 2026-01-13

### Fixed

- **Docling Schema Version Mismatch**: Fixed incompatibility between `docling` and `docling-core` causing `ValidationError: Doc version 1.9.0 incompatible with SDK schema version 1.8.0` when adding documents ([#229](https://github.com/ggozad/haiku.rag/issues/229))
  - Root cause: `docling-core` was reverted to 2.57.0 (schema 1.8.0) for docling-serve compatibility, but `docling` remained at 2.67.0 (schema 1.9.0)
  - Fix: Reverted `docling` from 2.67.0 to 2.65.0 to match `docling-core` schema version

## [0.26.0] - 2026-01-13

### Added

- **Conversational RAG Application**: Full-stack application (`app/`) with CopilotKit frontend and pydantic-ai AG-UI backend
  - Next.js frontend with chat interface, citation display, and visual grounding
  - Starlette backend using pydantic-ai's native `AGUIAdapter` for streaming
  - Docker Compose setup for development (`docker-compose.dev.yml`) and production
  - Logfire integration for debugging LLM calls
  - SSE heartbeat to prevent connection timeouts
- **Chat Agent** (`haiku.rag.agents.chat`): New conversational RAG agent optimized for multi-turn chat
  - `create_chat_agent()` factory function for creating chat agents with AG-UI support
  - `SearchAgent` for internal query expansion with deduplication
  - `ChatDeps` and `ChatSessionState` for session management
  - `CitationInfo` and `QAResponse` models for structured responses
  - Natural language document filtering via `build_document_filter()`
  - Configurable search limit per agent
- **Chat TUI** (`haiku-rag chat`): Terminal-based chat interface using Textual
  - Single chat window with inline tool calls and expandable citations
  - Visual grounding (`v` key) reuses inspector's `VisualGroundingModal`
  - Database info (`i` key) shows document/chunk counts and storage info
  - Keybindings: `q` quit, `Ctrl+L` clear chat, `Escape` focus input
- **Q/A History Management**: Intelligent conversation history with semantic ranking
  - FIFO queue with 50 max entries
  - Embedding cache to avoid re-embedding Q/A pairs
  - `rank_qa_history_by_similarity()` returns top-K most relevant history entries
  - Confidence filtering to exclude low-confidence answers from context
- **Conversational Research Graph**: Simplified single-iteration research graph for chat
  - `build_conversational_graph()` optimized for conversational Q&A
  - Context-aware planning (generates fewer sub-questions when history exists)
  - `ConversationalAnswer` output type with direct answer and citations

### Changed

- **BREAKING: Module Reorganization**: Consolidated all agent code under `haiku.rag.agents`
  - Moved `haiku.rag.qa` → `haiku.rag.agents.qa`
  - Moved `haiku.rag.graph.research` → `haiku.rag.agents.research`
  - Added `haiku.rag.agents.chat` module with conversational RAG agent
  - Deleted `haiku.rag.graph` module (research graph now at `haiku.rag.agents.research.graph`)

### Removed

- **BREAKING: Custom AG-UI Infrastructure**: Removed custom AG-UI event handling in favor of pydantic-ai's native AG-UI support
  - Deleted `haiku.rag.graph.agui` module (`AGUIEmitter`, `AGUIConsoleRenderer`, `stream_graph()`, `create_agui_server()`)
  - Removed `--agui` flag from `serve` command
  - Removed `--verbose` flags from `ask` and `research` commands
  - Removed `--interactive` flag from `research` command
  - Removed `AGUIConfig` from configuration
  - Deleted `cli_chat.py` interactive chat module
  - Research graph now uses `graph.run()` directly instead of `stream_graph()`
  - For AG-UI streaming, use pydantic-ai's native `AGUIAdapter` with `ToolReturn` and `StateSnapshotEvent` (see `app/backend/` for example)
- **AG-UI Research Example**: Removed `examples/ag-ui-research/` (replaced by `app/`)

## [0.25.0] - 2026-01-12

### Fixed

- **Large Document Storage Overflow**: Fixed "byte array offset overflow" panic when vacuuming/rebuilding databases with many large PDF documents ([#225](https://github.com/ggozad/haiku.rag/issues/225))
  - Root cause: Arrow's 32-bit string column offsets limited to ~2GB per fragment
  - Changed `docling_document_json` (string) to `docling_document` (bytes) with `large_binary` Arrow type (64-bit offsets)
  - Added gzip compression for DoclingDocument JSON (~1.4x compression ratio)
  - Migration automatically compresses existing documents in batches to avoid memory issues
  - **Breaking**: Migration is destructive - all table version history is lost after upgrade

### Changed

- **Dependencies**: Updated lancedb 0.26.0 → 0.26.1, docling 2.65.0 → 2.67.0

### Removed

- **Legacy Migrations**: Removed obsolete database migration files (`v0_9_3.py`, `v0_10_1.py`, `v0_19_6.py`). These migrations were for versions prior to 0.20.0 and are no longer needed since the current release requires a database rebuild anyway.

## [0.24.2] - 2026-01-08

### Fixed

- **Base64 Images in Expanded Context**: Fixed base64 image data leaking into expanded search results when `expand_context()` processed `PictureItem` objects. The issue was `PictureItem.export_to_markdown()` defaulting to `EMBEDDED` mode. Now explicitly uses `PLACEHOLDER` mode to prevent base64 data while still including VLM descriptions and captions.

## [0.24.1] - 2026-01-08

### Fixed

- **OpenAI Non-Reasoning Models**: Fixed `reasoning_effort` parameter being sent to non-reasoning OpenAI models (gpt-4o, gpt-4o-mini), causing 400 errors. Now correctly detects reasoning models (o1, o3 series) using pydantic-ai's model profile.
- **Bedrock Non-Reasoning Models**: Fixed same issue for OpenAI models on Bedrock.

## [0.24.0] - 2026-01-07

### Added

- **VLM Picture Description**: Describe embedded images using Vision Language Models during document conversion
  - Images are sent to a VLM for automatic description via OpenAI-compatible API
  - Descriptions become searchable text, improving RAG retrieval for visual content
  - Configure via `processing.conversion_options.picture_description` with `enabled`, `model`, `timeout`, `max_tokens`
  - Default prompt customizable via `prompts.picture_description`
  - Requires OpenAI-compatible `/v1/chat/completions` endpoint (Ollama, OpenAI, vLLM, LM Studio)

## [0.23.2] - 2026-01-05

### Fixed

- **AG-UI Concurrent Step Tracking**: Emitter now correctly tracks multiple concurrent steps ([#216](https://github.com/ggozad/haiku.rag/issues/216))

### Changed

- **Dependencies**: Updated core and development dependencies

## [0.23.1] - 2025-12-29

### Added

- **Contextualized FTS Search**: Full-text search now includes section headings
  - New `content_fts` column stores contextualized content (headings + body text)
  - FTS index now searches `content_fts` for better keyword matching on section context
  - Original `content` column preserved for display and context expansion
  - Migration automatically populates `content_fts` for existing databases
- **GitHub Actions CI**: Test workflow runs pytest, pyright, and ruff on push/PR to main
- **VCR Cassette Recording**: Integration tests use recorded HTTP responses for deterministic CI runs
  - LLM tests (QA, embeddings, research graph) replay from cassettes without real API calls
  - docling-serve tests run without Docker container in CI
  - Uses pytest-recording with custom JSON body serializer

## [0.23.0] - 2025-12-26

### Added

- **Prompt Customization**: Configure agent prompts via `prompts` config section
  - `domain_preamble`: Prepended to all agent prompts for domain context
  - `qa`: Full replacement for QA agent prompt
  - `synthesis`: Full replacement for research synthesis prompt

### Changed

- **Embeddings**: Migrated to pydantic-ai's embeddings module
  - Uses pydantic-ai v1.39.0+ embeddings with instrumentation and token counting support
  - Explicit `embed_query()` and `embed_documents()` API for query/document distinction
  - New providers available: Cohere (`cohere:`), SentenceTransformers (`sentence-transformers:`)
  - VoyageAI refactored to extend pydantic-ai's `EmbeddingModel` base class
- **Configuration**: Added `base_url` to `ModelConfig` and `EmbeddingModelConfig`
  - Enables custom endpoints for OpenAI-compatible providers (vLLM, LM Studio, etc.)
  - Model-level `base_url` takes precedence over provider config

### Deprecated

- **vLLM and LM Studio providers**: Use `openai` provider with `base_url` instead
  - `provider: vllm` → `provider: openai` with `base_url: http://localhost:8000/v1`
  - `provider: lm_studio` → `provider: openai` with `base_url: http://localhost:1234/v1`

### Removed

- Deleted obsolete embedder implementations: `ollama.py`, `openai.py`, `vllm.py`, `lm_studio.py`, `base.py`
- Removed `VLLMConfig` and `LMStudioConfig` from configuration (use `base_url` in model config instead)

## [0.22.0] - 2025-12-19

### Added

- **Read-Only Mode**: Global `--read-only` CLI flag for safe database access without modifications
  - Blocks all write operations at the Store layer
  - Skips database upgrades and settings saves on open
  - Excludes write tools (`add_document_*`, `delete_document`) from MCP server
  - Disables file monitor with warning when `--read-only` is used with `serve --monitor`
- **Time Travel**: Query the database as it existed at a previous point in time
  - Global `--before` CLI flag accepts datetime strings (ISO 8601 or date-only)
  - Automatically enables read-only mode when time-traveling
  - New `history` command shows version history for database tables
  - Useful for debugging and auditing
  - Supported throughout: CLI, Client, App, Inspector

### Fixed

- **File Monitor Path Validation**: Monitor now validates directories exist before watching ([#204](https://github.com/ggozad/haiku.rag/issues/204))
  - Provides clear error message pointing to `haiku.rag.yaml` configuration
  - Prevents cryptic `FileNotFoundError: No path was found` from watchfiles
- **Docker Documentation**: Improved Docker setup instructions
  - Added volume mount examples for config file and documents directory
  - Clarified that `monitor.directories` must use container paths, not host paths

### Changed

- **Dependencies**: Updated core dependencies
  - `pydantic-ai-slim`: 1.27.0 → 1.36.0 (FileSearchTool, web chat UI, GPT-5.2 support, prompt caching)
  - `lancedb`: 0.25.3 → 0.26.0
  - `docling`: 2.64.0 → 2.65.0
  - `docling-core`: 2.54.0 → 2.57.0

## [0.21.0] - 2025-12-18

### Added

- **Interactive Research Mode**: Human-in-the-loop research using graph-based decision nodes
  - `haiku-rag research --interactive` starts conversational CLI chat
  - Natural language interpretation for user commands (search, modify questions, synthesize)
  - Chat with assistant before starting research, and during decision points
  - Review collected answers and pending questions at each decision point
  - Add, remove, or modify sub-questions through natural conversation
  - New `human_decide` graph node emits AG-UI tool calls (`TOOL_CALL_START/ARGS/END`) for frontend integration
  - New `emit_tool_call_start()`, `emit_tool_call_args()`, `emit_tool_call_end()` AG-UI event helpers
  - New `AGUIEmitter.emit()` method for direct event emission
- **AG-UI Research Example**: Human-in-the-loop research with client-side tool calling
  - Frontend handles `human_decision` tool calls via AG-UI `TOOL_CALL_*` events
  - Tool results sent directly to backend `/v1/research/stream` endpoint
  - Backend queues decisions and continues the research graph
- **HotpotQA Evaluation**: Added HotpotQA dataset adapter for multi-hop QA benchmarks
  - Extracts unique documents from validation set context paragraphs
  - Uses MAP for retrieval evaluation (multiple supporting documents per question)
  - Run with `evaluations hotpotqa`
- **Plain Text Format**: Added `format="plain"` for text conversion
  - Use when content is plain text without markdown/HTML structure
  - Falls back gracefully when docling cannot detect markdown format in content
  - Supported in `create_document()`, `convert()`, and all converter classes

### Changed

- **AG-UI Events**: Replaced custom event classes with `ag_ui.core` types
  - Removed `haiku.rag.graph.agui.events` module
  - Event factory functions (`emit_*`) now wrap official `ag_ui.core` event classes
- **Chunker Sets Order**: Chunkers now set `chunk.order` directly
- **Unified Research Graph**: Simplified and unified research and deep QA into a single configurable graph
  - Removed `analyze_insights` node - graph now flows directly from `collect_answers` to `decide`
  - Simplified `EvaluationResult` to: `is_sufficient`, `confidence_score`, `reasoning`, `new_questions`
  - Simplified `ResearchContext` - removed insight/gap tracking methods
  - `ask --deep` now uses research graph with `max_iterations=2`, `confidence_threshold=0.0`
  - `ask --deep` output now shows executive summary, key findings, and sources
  - Added `include_plan` parameter to `build_research_graph()` for plan-less execution
  - Added `max_iterations` and `confidence_threshold` overrides to `ResearchState.from_config()`
- **Improved Synthesis Prompt**: Updated synthesis agent prompt to produce direct answers
  - Executive summary now directly answers the question instead of describing the report
  - Added explicit examples of good vs bad output style
- **Evaluations Vacuum Strategy**: `populate_db` now uses periodic vacuum to prevent disk exhaustion with large datasets
  - Disables auto_vacuum during population, vacuums every N documents with retention=0
  - New `--vacuum-interval` CLI option (default: 100) to control vacuum frequency
  - Prevents disk space issues when building databases with thousands of documents (e.g., HotpotQA)
- **Benchmarks Documentation**: Restructured benchmarks.md for clarity
  - Added dedicated Methodology section explaining MRR, MAP, and QA Accuracy metrics
  - Organized results by dataset with retrieval and QA subsections

### Removed

- **Deep QA Graph**: Removed `haiku.rag.graph.deep_qa` module entirely
  - Use `build_research_graph()` with appropriate parameters instead
  - `ask --deep` CLI command now uses research graph internally
- **Insight/Gap Tracking**: Removed over-engineered insight and gap tracking from research graph
  - Removed `InsightRecord`, `GapRecord`, `InsightAnalysis`, `InsightStatus`, `GapSeverity` models
  - Removed `format_analysis_for_prompt()` helper
  - Removed `INSIGHT_AGENT_PROMPT` from prompts

## [0.20.2] - 2025-12-12

### Fixed

- **LLM Schema Compliance**: Improved prompts to prevent LLMs from returning objects instead of plain strings for `list[str]` fields
  - All graph prompts now explicitly state that list fields must contain plain strings only
  - Added missing `query` and `confidence` fields to search agent output format documentation
  - Fixes validation errors with less capable models that ignore JSON schema constraints
- **AG-UI Frontend Types**: Fixed TypeScript interfaces in ag-ui-research example to match backend Python models
  - `EvaluationResult`: `confidence` → `confidence_score`, `should_continue` → `is_sufficient`, `gaps_identified` → `gaps`, `follow_up_questions` → `new_questions`, added `key_insights`
  - `ResearchReport`: `question` → `title`, `summary` → `executive_summary`, `findings` → `main_findings`, removed `insights_used`/`methodology`, added `limitations`/`recommendations`/`sources_summary`
  - Updated Final Report UI to display new fields (Recommendations, Limitations, Sources)
- **Citation Formatting**: Citations in CLI now render properly with Rich panels
  - Content is rendered as markdown with proper code block formatting
  - No longer truncates or flattens newlines in citation content

## [0.20.1] - 2025-12-11

### Added

- **Search Filter for Graphs**: Research and Deep QA graphs now support `search_filter` parameter to restrict searches to specific documents
  - Set `state.search_filter` to a SQL WHERE clause (e.g., `"id IN ('doc1', 'doc2')"`) before running the graph
  - Enables document-scoped research workflows
  - CLI: `haiku-rag research "question" --filter "uri LIKE '%paper%'"`
  - CLI: `haiku-rag ask "question" --filter "title = 'My Doc'"`
  - Python: `client.ask(question, filter="...")` and `agent.answer(question, filter="...")`
- **AG-UI Research Example**: Added bidirectional state demonstration with document filter
  - New `/api/documents` endpoint to list available documents
  - Frontend document selector component with search and multi-select
  - Demonstrates client-to-server state flow via AG-UI protocol
- **Inspector Info Modal**: New `i` keyboard shortcut opens a modal displaying database information

### Changed

- **Inspector Lazy Loading**: Chunks panel now loads chunks in batches of 50 with infinite scroll
  - Fixes unresponsive UI when viewing documents with large numbers of chunks
  - New `ChunkRepository.get_by_document_id()` pagination with `limit` and `offset` parameters
  - New `ChunkRepository.count_by_document_id()` method

## [0.20.0] - 2025-12-10

### Added

- **DoclingDocument Storage**: Full DoclingDocument JSON is now stored with each document, enabling rich context and visual grounding
  - Documents store the complete DoclingDocument structure (JSON) and schema version
  - Chunks store metadata with JSON pointer references (`doc_item_refs`), semantic labels, section headings, and page numbers
  - New `ChunkMetadata` model for structured chunk provenance: `doc_item_refs`, `headings`, `labels`, `page_numbers`
  - `Document.get_docling_document()` method to parse stored DoclingDocument
  - `ChunkMetadata.resolve_doc_items()` to resolve JSON pointer refs to actual DocItem objects
  - `ChunkMetadata.resolve_bounding_boxes()` for visual grounding with page coordinates
  - LRU cache (100 documents) for parsed DoclingDocument objects to avoid repeated JSON parsing
- **Enhanced Search Results**: `search()` and `expand_context()` now return full provenance information
  - `SearchResult` includes `page_numbers`, `headings`, `labels`, and `doc_item_refs`
  - QA and research agents use provenance for better citations (page numbers, section headings)
- **Type-Aware Context Expansion**: `expand_context()` now uses document structure for intelligent expansion
  - Structural content (tables, code blocks, lists) expands to complete structures regardless of chunking
  - Text content uses radius-based expansion via `text_context_radius` setting
  - `max_context_items` and `max_context_chars` settings control expansion limits
  - `SearchResult.format_for_agent()` method formats expanded results with metadata for LLM consumption
- **Visual Grounding**: View page images with highlighted bounding boxes for chunks
  - Inspector modal with keyboard navigation between pages
  - CLI command: `haiku-rag visualize <chunk_id>`
  - Requires `textual-image` dependency and terminal with image support
- **Processing Primitives**: New methods for custom document processing pipelines
  - `convert()` - Convert files, URLs, or text to DoclingDocument
  - `chunk()` - Chunk a DoclingDocument into Chunk objects
  - `contextualize()` - Prepend section headings to chunk content for embedding
  - `embed_chunks()` - Generate embeddings for chunks
- **New `import_document()` Method**: Import pre-processed documents with custom chunks
  - Accepts `DoclingDocument` directly for rich metadata (visual grounding, page numbers)
  - Use when document conversion, chunking, or embedding were done externally
  - Chunks without embeddings are automatically embedded
- **Automatic Chunk Embedding**: `import_document()` and `update_document()` automatically embed chunks that don't have embeddings
  - Pass chunks with or without embeddings - missing embeddings are generated
  - Chunks with pre-computed embeddings are stored as-is
- **Format Parameter for Text Conversion**: New `format` parameter for `convert()` and `create_document()` to specify content type
  - Supports `"md"` (default) for markdown and `"html"` for HTML content
  - HTML format preserves document structure (headings, lists, sections) in DoclingDocument
  - Enables proper parsing of HTML content that was previously treated as plain text
- **Inspector Context Modal**: Press `c` in the inspector to view expanded context for the selected chunk
- **Auto-Vacuum Configuration**: New `storage.auto_vacuum` setting to control automatic vacuuming behavior
  - When `true` (default), vacuum runs automatically after document create/update operations and rebuilds
  - When `false`, vacuum only runs via explicit `haiku-rag vacuum` command
  - Disabling can help avoid potential crashes in high-concurrency scenarios due to LanceDB race conditions

### Changed

- **BREAKING: `create_document()` API**: Removed `chunks` parameter
  - `create_document()` now always processes content (converts, chunks, embeds)
  - Use `import_document()` for pre-processed documents with custom chunks
- **BREAKING: `update_document()` API**: Unified with `update_document_fields()`
  - Old: `update_document(document)` - pass modified Document object
  - New: `update_document(document_id, content=, metadata=, chunks=, title=, docling_document=)`
  - `content` and `docling_document` are mutually exclusive
- **BREAKING: Chunker Interface**: `DocumentChunker.chunk()` now returns `list[Chunk]` instead of `list[str]`
  - Chunks include structured metadata (doc_item_refs, labels, headings, page_numbers)
- **Search Config**: New settings in `search` section for search behavior and context expansion
  - `search.limit` - Default number of search results (default: 5). Used by CLI, MCP server, and API when no limit specified
  - `search.context_radius` - DocItems before/after to include for text content expansion (default: 0)
  - `search.max_context_items` - Maximum items in expanded context (default: 10)
  - `search.max_context_chars` - Maximum characters in expanded context (default: 10000)
- **Rebuild Performance**: Batched database writes during `rebuild` command reduce LanceDB versions by ~98%
  - All rebuild modes (FULL, RECHUNK, EMBED_ONLY) now batch writes across documents
  - Eliminates redundant per-document chunk deletions and vacuum calls
  - Significantly reduces storage overhead and improves rebuild speed for large databases
- **Embedding Architecture**: Moved embedding generation from `ChunkRepository` to client layer
  - Repository is now a pure persistence layer
  - Client handles embedding via `_ensure_chunks_embedded()`
- **Chunk Text Storage**: Chunks store raw text; headings prepended only at embedding time
  - Stored chunk content stays clean without duplicate heading prefixes
  - Local and serve chunkers now produce identical output
- **Citation Models**: Introduced `RawSearchAnswer` for LLM output, `SearchAnswer` with resolved citations
- **Page Image Generation**: Always enabled for local docling converter (required for visual grounding)
- **Download Models Progress**: `haiku-rag download-models` now shows real-time progress with Rich progress bars for Ollama model downloads

### Removed

- **BREAKING: `markdown_preprocessor` Config Option**: Use processing primitives (`convert()`, `chunk()`, `embed_chunks()`) for custom pipelines
- **`update_document_fields()`**: Merged into `update_document()`

### Migration

This release requires a database rebuild to populate the new DoclingDocument fields:

```bash
haiku-rag rebuild
```

Existing documents without DoclingDocument data will work but won't have provenance information.

## [0.19.6] - 2025-12-03

### Changed

- **BREAKING: Explicit Database Creation**: Databases must now be explicitly created before use
  - New `haiku-rag init` command creates a new empty database
  - Python API: `HaikuRAG(path, create=True)` to create database programmatically
  - Operations on non-existent databases raise `FileNotFoundError`
- **BREAKING: Embeddings Configuration**: Restructured to nested `EmbeddingModelConfig`
  - Config path changed from `embeddings.{provider, model, vector_dim}` to `embeddings.model.{provider, name, vector_dim}`
  - Automatic migration upgrades existing databases to new format
- **Database Migrations**: Always run when opening an existing database

## [0.19.5] - 2025-12-01

### Changed

- **Rebuild Performance**: Optimized `rebuild --embed-only` to use batch updates via LanceDB's `merge_insert` instead of individual chunk updates, and skip chunks with unchanged embeddings

## [0.19.4] - 2025-11-28

### Added

- **Rebuild Modes**: New options for `rebuild` command to control what gets rebuilt
  - `--embed-only`: Only regenerate embeddings, keeping existing chunks (fastest option when changing embedding model)
  - `--rechunk`: Re-chunk from existing document content without accessing source files
  - Default (no flag): Full rebuild with source file re-conversion
  - Python API: `rebuild_database(mode=RebuildMode.EMBED_ONLY | RECHUNK | FULL)`

## [0.19.3] - 2025-11-27

### Changed

- **Async Chunker**: `DoclingServeChunker` now uses `httpx.AsyncClient` instead of sync `requests`

### Fixed

- **OCR Options**: Fixed `DoclingLocalConverter` using base `OcrOptions` class which docling's OCR factory doesn't recognize. Now uses `OcrAutoOptions` for automatic OCR engine selection.
- **Dependencies**: Added `opencv-python-headless` to the `docling` optional dependency for table structure detection.

## [0.19.2] - 2025-11-27

### Changed

- **Async Converters**: Made document converters fully async
  - `BaseConverter.convert_file()` and `convert_text()` are now async methods
  - `DoclingLocalConverter` wraps blocking Docling operations with `asyncio.to_thread()`
  - `DoclingServeConverter` now uses `httpx.AsyncClient` instead of sync `requests`
- **Async Model Prefetch**: `prefetch_models()` is now async
  - Uses `httpx.AsyncClient` for Ollama model pulls
  - Wraps blocking Docling and HuggingFace downloads with `asyncio.to_thread()`

## [0.19.1] - 2025-11-26

### Added

- **LM Studio Provider**: Added support for LM Studio as a provider for embeddings and QA/research models
  - Configure with `provider: lm_studio` in embeddings, QA, or research model settings
  - Supports thinking control for reasoning models (gpt-oss, etc.)
  - Default base URL: `http://localhost:1234`

### Fixed

- **Configuration**: Fixed `init-config` command generating invalid configuration files (#165)
  - Refactored `generate_default_config()` to use Pydantic model serialization instead of manual dict construction
  - Updated `qa`, `research`, and `reranking` sections to use new `ModelConfig` structure

## [0.19.0] - 2025-11-25

### Added

- **Model Customization**: Added support for per-model configuration settings
  - New `enable_thinking` parameter to control reasoning behavior (true/false/None)
  - Support for `temperature` and `max_tokens` settings on QA and research models
  - All settings apply to any provider that supports them
- **Database Inspector**: New `inspect` CLI command launches interactive TUI for browsing documents and chunks & searching
- **Evaluations**: Added `evaluations` CLI script for running benchmarks (replaces `python -m evaluations.benchmark`)
- **Evaluations**: Added `--db` option to override evaluation database path
  - Default database location moved to haiku.rag data directory:
    - macOS: `~/Library/Application Support/haiku.rag/evaluations/dbs/`
    - Linux: `~/.local/share/haiku.rag/evaluations/dbs/`
    - Windows: `C:/Users/<USER>/AppData/Roaming/haiku.rag/evaluations/dbs/`
  - Previously stored in `evaluations/data/` within the repository
- **Evaluations**: Added comprehensive experiment metadata tracking for better reproducibility
  - Records dataset name, test case count, and all model configurations
  - Tracks embedder settings: provider, model, and vector dimensions
  - Tracks QA model: provider and model name
  - Tracks judge model: provider and model name for LLM evaluation
  - Tracks processing parameters: `chunk_size` and `context_chunk_radius`
  - Tracks retrieval configuration: `retrieval_limit` for number of chunks retrieved
  - Tracks reranking configuration: `rerank_provider` and `rerank_model`
  - Enables comparison of evaluation runs with different configurations in Logfire
- **Evaluations**: Refactored retrieval evaluation to use pydantic-ai experiment framework
  - New `evaluators` module with `MRREvaluator` (Mean Reciprocal Rank) and `MAPEvaluator` (Mean Average Precision)
  - Retrieval benchmarks now use `Dataset.evaluate()` with full Logfire experiment tracking
  - Dataset specifications now declare their retrieval evaluator (MRR for RepliQA, MAP for Wix)
  - Replaced Recall@K and Success@K with industry-standard MRR and MAP metrics
  - Unified evaluation framework for both retrieval and QA benchmarks
- **AG-UI Events**: Enhanced ActivitySnapshot events with richer structured data
  - Added `stepName` field to identify which graph node emitted each activity
  - Added structured fields to activity content while preserving backward-compatible `message` field:
    - **Planning**: `sub_questions` - list of sub-question strings
    - **Searching**: `query` - the search query, `confidence` - answer confidence (on success), `error` - error message (on failure)
    - **Analyzing** (research): `insights` - list of insight objects, `gaps` - list of gap objects, `resolved_gaps` - list of resolved gap strings
    - **Evaluating** (research): `confidence` - confidence score, `is_sufficient` - sufficiency flag
    - **Evaluating** (deep QA): `is_sufficient` - sufficiency flag, `iterations` - iteration count

### Changed

- **Evaluations**: Renamed `--qa-limit` CLI parameter to `--limit`, now applies to both retrieval and QA benchmarks
- **Evaluations**: Retrieval evaluator selection moved from runtime logic to dataset configuration

## [0.18.0] - 2025-11-21

### Added

- **Manual Vector Indexing**: New `create-index` CLI command for explicit vector index creation
  - Creates IVF_PQ indexes
  - Requires minimum 256 chunks (LanceDB training data requirement)
  - New `search.vector_index_metric` config option: `cosine` (default), `l2`, or `dot`
  - New `search.vector_refine_factor` config option (default: 30) for accuracy/speed tradeoff
  - Indexes not created automatically during ingestion to avoid performance degradation
  - Manual rebuilding required after adding significant new data
- **Enhanced Info Command**: `haiku-rag info` now shows storage sizes and vector index statistics
  - Displays storage size for documents and chunks tables in human-readable format
  - Shows vector index status (exists/not created)
  - Shows indexed and unindexed chunk counts for monitoring index staleness

### Changed

- **BREAKING: Default Embedding Model**: Changed default embedding model from `qwen3-embedding` to `qwen3-embedding:4b` with vector dimension 2560 (previously 4096)
  - New installations will use the smaller, more efficient 4B parameter model by default
  - **Action required**: Existing databases created with the old default will be incompatible. Users must either:
    - Explicitly set `embeddings.model: "qwen3-embedding"` and `embeddings.vector_dim: 4096` in their config to maintain compatibility with existing databases
    - Or run `haiku-rag rebuild` to re-embed all documents with the new default
  - This change provides better performance for most use cases while reducing resource requirements
- **Evaluations**: Improved evaluation dataset naming and simplified evaluator configuration
  - `EvalDataset` now accepts dataset name for better organization in Logfire
  - Added `--name` CLI parameter to override evaluation run names
  - Removed `IsInstance` evaluator, using only `LLMJudge` for QA evaluation
- **Search Accuracy**: Applied `refine_factor` to vector and hybrid searches for improved accuracy
  - Retrieves `refine_factor * limit` candidates and re-ranks in memory
  - Higher values increase accuracy but slow down queries

### Fixed

- **AG-UI Activity Events**: Activity events now correctly use structured dict content instead of strings
- **Graph Configuration**: Graph builder functions now properly accept and use non-global config (#149)
  - `build_research_graph()` and `build_deep_qa_graph()` now pass config to all agents and model creation
  - `get_model()` utility function accepts `config` parameter (defaults to global Config)
  - Allows creating multiple graphs with different configurations in the same application


## [0.17.2] - 2025-11-19

### Added

- **Document Update API**: New `update_document_fields()` method for partial document updates
  - Update individual fields (content, metadata, title, chunks) without fetching full document
  - Support for custom chunks or auto-generation from content

### Changed

- **Chunk Creation**: `ChunkRepository.create()` now accepts both single chunks and lists for batch insertion
  - Batch insertion reduces LanceDB version creation when adding multiple chunks with custom chunks
  - Batch embedding generation for improved performance with multiple chunks
- Updated core dependencies

## [0.17.1] - 2025-11-18

### Added

- **Conversion Options**: Fine-grained control over document conversion for both local and remote converters
  - New `conversion_options` config section in `ProcessingConfig`
  - OCR settings: `do_ocr`, `force_ocr`, `ocr_lang` for controlling OCR behavior
  - Table extraction: `do_table_structure`, `table_mode` (fast/accurate), `table_cell_matching`
  - Image settings: `images_scale` to control image resolution
  - Options work identically with both `docling-local` and `docling-serve` converters

### Changed

- Increase reranking candidate retrieval multiplier from 3x to 10x for improved result quality
- **Docker Images**: Main `haiku.rag` image no longer automatically built and published
- **Conversion Options**: Removed the legacy `pdf_backend` setting; docling now chooses the optimal backend automatically

## [0.17.0] - 2025-11-17

### Added

- **Remote Processing**: Support for docling-serve as remote document processing and chunking service
  - New `converter` config option: `docling-local` (default) or `docling-serve`
  - New `chunker` config option: `docling-local` (default) or `docling-serve`
  - New `providers.docling_serve` config section with `base_url`, `api_key`, and `timeout`
  - Comprehensive error handling for connection, timeout, and authentication issues
- **Chunking Strategies**: Support for both hybrid and hierarchical chunking
  - New `chunker_type` config option: `hybrid` (default) or `hierarchical`
  - Hybrid chunking: Structure-aware splitting that respects document boundaries
  - Hierarchical chunking: Preserves document hierarchy for nested documents
- **Table Serialization Control**: Configurable table representation in chunks
  - New `chunking_use_markdown_tables` config option (default: `false`)
  - `false`: Tables serialized as narrative text ("Value A, Column 2 = Value B")
  - `true`: Tables preserved as markdown format with structure
- **Chunking Configuration**: Additional chunking control options
  - New `chunking_merge_peers` config option (default: `true`) to merge undersized successive chunks
- **Docker Images**: Two Docker images for different deployment scenarios
  - `haiku.rag`: Full image with all dependencies for self-contained deployments
  - `haiku.rag-slim`: Minimal image designed for use with external docling-serve
  - Multi-platform support (linux/amd64, linux/arm64)
  - Docker Compose examples with docling-serve integration
  - Automated CI/CD workflows for both images
  - Build script (`scripts/build-docker-images.sh`) for local multi-platform builds

### Changed

- **BREAKING: Chunking Tokenizer**: Switched from tiktoken to HuggingFace tokenizers for consistency with docling-serve
  - Default tokenizer changed from tiktoken "gpt-4o" to "Qwen/Qwen3-Embedding-0.6B"
  - New `chunking_tokenizer` config option in `ProcessingConfig` for customization
  - `download-models` CLI command now also downloads the configured HuggingFace tokenizer
- **Docker Examples**: Updated examples to demonstrate remote processing
  - `examples/docker` now uses slim image with docling-serve
  - `examples/ag-ui-research` backend uses slim image with docling-serve
  - Configuration examples include remote processing setup

## [0.16.1] - 2025-11-14

### Changed

- **Evaluations**: Refactored QA benchmark to run entire dataset as single evaluation for better Logfire experiment tracking
- **Evaluations**: Added `.env` file loading support via `python-dotenv` dependency

## [0.16.0] - 2025-11-13

### Added

- **AG-UI Protocol Support**: Full AG-UI (Agent-UI) protocol implementation for graph execution with event streaming
  - New `AGUIEmitter` class for emitting AG-UI events from graphs
  - Support for all AG-UI event types: lifecycle events (`RUN_STARTED`, `RUN_FINISHED`, `RUN_ERROR`), step events (`STEP_STARTED`, `STEP_FINISHED`), state updates (`STATE_SNAPSHOT`, `STATE_DELTA`), activity narration (`ACTIVITY_SNAPSHOT`), and text messages (`TEXT_MESSAGE_CHUNK`)
  - `AGUIConsoleRenderer` for rendering AG-UI event streams to terminal with Rich formatting
  - `stream_graph()` utility function for executing graphs with AG-UI event emission
  - State diff computation for efficient state synchronization
  - **Delta State Updates**: AG-UI emitter now supports incremental state updates via JSON Patch operations (`STATE_DELTA` events) to reduce bandwidth, configurable via `use_deltas` parameter (enabled by default)
- **AG-UI Server**: Starlette-based HTTP server for serving graphs via AG-UI protocol
  - Server-Sent Events (SSE) streaming endpoint at `/v1/agent/stream`
  - Health check endpoint at `/health`
  - Full CORS support configurable via `agui` config section
  - `create_agui_server()` function for programmatic server creation
- **Deep QA AG-UI Support**: Deep QA graph now fully supports AG-UI event streaming
  - Integration with `AGUIEmitter` for progress tracking
  - Step-by-step execution visibility via AG-UI events
- **CLI AG-UI Flag**: New `--agui` flag for `serve` command to start AG-UI server
- **Graph Module**: New unified `haiku.rag.graph` module containing all graph-related functionality
- **Common Graph Nodes**: New factory functions (`create_plan_node`, `create_search_node`) in `haiku.rag.graph.common.nodes` for reusable graph components
- **AG-UI Research Example**: New full-stack example (`examples/ag-ui-research`) demonstrating agent+graph architecture with CopilotKit frontend
  - Pydantic AI agent with research tool that invokes the research graph
  - Custom AG-UI streaming endpoint with anyio memory streams
  - React/Next.js frontend with split-pane UI showing live research state
  - Real-time progress tracking of questions, answers, insights, and gaps
  - Docker Compose setup for easy local development

### Changed

- **Vacuum Retention**: Default `vacuum_retention_seconds` increased from 60 seconds to 86400 seconds (1 day) for better version retention in typical workflows
- **BREAKING**: Major refactoring of graph-related code into unified `haiku.rag.graph` module structure:
  - `haiku.rag.research` → `haiku.rag.graph.research`
  - `haiku.rag.qa.deep` → `haiku.rag.graph.deep_qa`
  - `haiku.rag.agui` → `haiku.rag.graph.agui`
  - `haiku.rag.graph_common` → `haiku.rag.graph.common`
- **BREAKING**: Research and Deep QA graphs now use AG-UI event protocol instead of direct console logging
  - Removed `console` and `stream` parameters from graph dependencies
  - All progress updates now emit through `AGUIEmitter`
- **BREAKING**: `ResearchState` converted from dataclass to Pydantic `BaseModel` for JSON serialization and AG-UI compatibility
- Research and Deep QA graphs now emit detailed execution events for better observability
- CLI research command now uses AG-UI event rendering for `--verbose` output
- Improved graph execution visibility with step-by-step progress tracking
- Updated all documentation to reflect new import paths and AG-UI usage
- Updated examples (ag-ui-research, a2a-server) to use new import paths

### Fixed

- **Document Creation**: Optimized `create_document` to skip unnecessary DoclingDocument conversion when chunks are pre-provided
- **FileReader**: Error messages now include both original exception details and file path for easier debugging
- **Database Auto-creation**: Read operations (search, list, get, ask, research) no longer auto-create empty databases. Write operations (add, add-src, delete, rebuild) still create the database as needed. This prevents the confusing scenario where a search query creates an empty database. Fixes issue #137.

### Removed

- **BREAKING**: Removed `disable_autocreate` config option - the behavior is now automatic based on operation type
- **BREAKING**: Removed legacy `ResearchStream` and `ResearchStreamEvent` classes (replaced by AG-UI event protocol)

## [0.15.0] - 2025-11-07

### Added

- **File Monitor**: Orphan deletion feature - automatically removes documents from database when source files are deleted (enabled via `monitor.delete_orphans` config option, default: false)

### Changed

- **Configuration**: All CLI commands now properly support `--config` parameter for specifying custom configuration files
- Configuration loading consolidated across CLI, app, and client with consistent resolution order
- `HaikuRAGApp` and MCP server now accept `config` parameter for programmatic configuration
- Updated CLI documentation to clarify global vs per-command options
- **BREAKING**: Standardized configuration filename to `haiku.rag.yaml` in user directories (was incorrectly using `config.yaml`). Users with existing `config.yaml` in their user directory will need to rename it to `haiku.rag.yaml`

### Fixed

- **File Monitor**: Fixed incorrect "Updated document" logging for unchanged files - monitor now properly skips files when MD5 hash hasn't changed

### Removed

- **BREAKING**: A2A (Agent-to-Agent) protocol support has been moved to a separate self-contained package in `examples/a2a-server/`. The A2A server is no longer part of the main haiku.rag package. Users who need A2A functionality can install and run it from the examples directory with `cd examples/a2a-server && uv sync`.
- **BREAKING**: Removed deprecated `.env`-based configuration system. The `haiku-rag init-config --from-env` command and `load_config_from_env()` function have been removed. All configuration must now be done via YAML files. Environment variables for API keys (e.g., `OPENAI_API_KEY`, `ANTHROPIC_API_KEY`) and service URLs (e.g., `OLLAMA_BASE_URL`) are still supported and can be set via `.env` files.

## [0.14.1] - 2025-11-06

### Added

- Migrated research and deep QA agents to use Pydantic Graph beta API for better graph execution
- Automatic semaphore-based concurrency control for parallel sub-question processing
- `max_concurrency` parameter for controlling parallel execution in research and deep QA (default: 1)

### Changed

- **BREAKING**: Research and Deep QA graphs now use `pydantic_graph.beta` instead of the class-based graph implementation
- Refactored graph common patterns into `graph_common` module
- Sub-questions now process using `.map()` for true parallel execution
- Improved graph structure with cleaner node definitions and flow control
- Pinned critical dependencies: `docling-core`, `lancedb`, `docling`

## [0.14.0] - 2024-11-05

### Added

- New `haiku.rag-slim` package with minimal dependencies for users who want to install only what they need
- Evaluations package (`haiku.rag-evals`) for internal benchmarking and testing
- Improved search filtering performance by using pandas DataFrames for joins instead of SQL WHERE IN clauses

### Changed

- **BREAKING**: Restructured project into UV workspace with three packages:
  - `haiku.rag-slim` - Core package with minimal dependencies
  - `haiku.rag` - Full package with all extras (recommended for most users)
  - `haiku.rag-evals` - Internal benchmarking and evaluation tools
- Migrated from `pydantic-ai` to `pydantic-ai-slim` with extras system
- Docling is now an optional dependency (install with `haiku.rag-slim[docling]`)
- Package metadata checks now use `haiku.rag-slim` (always present) instead of `haiku.rag`
- Docker image optimized: removed evaluations package, reducing installed packages from 307 to 259
- Improved vector search performance through optimized score normalization

### Fixed

- ImportError now properly raised when optional docling dependency is missing

## [0.13.3] - 2024-11-04

### Added

- Support for Zero Entropy reranker
- Filter parameter to `search()` for filtering documents before search
- Filter parameter to CLI `search` command
- Filter parameter to CLI `list` command for filtering document listings
- Config option to pass custom configuration files to evaluation commands
- Document filtering now respects configured include/exclude patterns when using `add-src` with directories
- Max retries to insight_agent when producing structured output

### Fixed

- CLI now loads `.env` files at startup
- Info command no longer attempts to use deprecated `.env` settings
- Documentation typos

## [0.13.2] - 2024-11-04

### Added

- Gitignore-style pattern filtering for file monitoring using pathspec
- Include/exclude pattern documentation for FileMonitor

### Changed

- Moved monitor configuration to its own section in config
- Improved configuration documentation
- Updated dependencies

## [0.13.1] - 2024-11-03

### Added

- Initial version tracking

[Unreleased]: https://github.com/ggozad/haiku.rag/compare/0.48.1...HEAD
[0.48.1]: https://github.com/ggozad/haiku.rag/compare/0.48.0...0.48.1
[0.48.0]: https://github.com/ggozad/haiku.rag/compare/0.47.0...0.48.0
[0.47.0]: https://github.com/ggozad/haiku.rag/compare/0.46.0...0.47.0
[0.46.0]: https://github.com/ggozad/haiku.rag/compare/0.45.0...0.46.0
[0.45.0]: https://github.com/ggozad/haiku.rag/compare/0.44.0...0.45.0
[0.44.0]: https://github.com/ggozad/haiku.rag/compare/0.43.1...0.44.0
[0.43.1]: https://github.com/ggozad/haiku.rag/compare/0.43.0...0.43.1
[0.43.0]: https://github.com/ggozad/haiku.rag/compare/0.42.1...0.43.0
[0.42.1]: https://github.com/ggozad/haiku.rag/compare/0.42.0...0.42.1
[0.42.0]: https://github.com/ggozad/haiku.rag/compare/0.41.0...0.42.0
[0.41.0]: https://github.com/ggozad/haiku.rag/compare/0.40.1...0.41.0
[0.40.1]: https://github.com/ggozad/haiku.rag/compare/0.39.0...0.40.1
[0.39.0]: https://github.com/ggozad/haiku.rag/compare/0.38.0...0.39.0
[0.38.0]: https://github.com/ggozad/haiku.rag/compare/0.37.0...0.38.0
[0.37.0]: https://github.com/ggozad/haiku.rag/compare/0.36.3...0.37.0
[0.36.3]: https://github.com/ggozad/haiku.rag/compare/0.36.2...0.36.3
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