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"nodes": [ { "id": 1, "change_id": "9fd43626-34a5-4eab-92b9-0ab335433356", "node_type": "goal", "title": "Build a personal research library pipeline: arXiv papers → structured metadata → AI synthesis → Obsidian vault notes", "description": "Core vision: ingest academic papers (arXiv IDs, local PDFs) and automatically produce formatted Obsidian markdown notes with citations and synthesis.\\n\\nSources:\\n- f91011d: 'add claude mvp v01'\\n- 2c4b078: 'Initial commit'", "status": "pending", "created_at": "2026-03-24T10:49:42.463199-07:00", "updated_at": "2026-03-24T10:49:42.463199-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":100}" }, { "id": 2, "change_id": "1ced1d54-1171-41bf-89aa-8ba4c900a0bc", "node_type": "action", "title": "Implement arXiv fetcher + GROBID processor + synthesis generator + markdown writer (MVP)", "description": "Initial MVP: fetch arXiv metadata and PDF, send to GROBID for TEI XML parsing, call Claude Haiku for synthesis with XML-tagged structured output, write Obsidian markdown with YAML frontmatter.\\n\\nSources:\\n- f91011d: 'add claude mvp v01'\\n- 4dd5b7d: 'test #1 complete\\!\\!\\!'\\n- fc37da1: 'grobid is a very hungry caterpillar'", "status": "pending", "created_at": "2026-03-24T10:49:48.095062-07:00", "updated_at": "2026-03-24T10:49:48.095062-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 3, "change_id": "78f29186-a631-4187-b813-ffba944ef401", "node_type": "outcome", "title": "Working single-paper pipeline: arXiv → GROBID → Haiku synthesis → Obsidian note", "description": "First successful end-to-end test with 'Attention Is All You Need' (1706.03762). Pipeline established foundational flow.\\n\\nSources:\\n- 4dd5b7d: 'test #1 complete\\!\\!\\!'", "status": "pending", "created_at": "2026-03-24T10:49:57.878086-07:00", "updated_at": "2026-03-24T10:49:57.878086-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 4, "change_id": "f3241c9a-62b1-4386-b8b2-b1ca80a1f12c", "node_type": "goal", "title": "Design data models that capture full bibliographic richness without losing citation data", "description": "After MVP, recognized that citations extracted by GROBID were being discarded or inadequately represented. The shared base model approach would enable future citation graph features.\\n\\nSources:\\n- 8edd301: 'stop wasting citation data\\!\\!\\!\\!'\\n- 0706560: 'implement new models\\!'", "status": "pending", "created_at": "2026-03-24T10:50:08.932861-07:00", "updated_at": "2026-03-24T10:50:08.932861-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 5, "change_id": "3498b93d-02fd-4c6f-ab80-fd52ed0ba488", "node_type": "option", "title": "Flat ad-hoc dicts for citations (simple, no structure)", "description": "Keep citations as informal dictionaries without a formal model.", "status": "rejected", "created_at": "2026-03-24T10:50:08.950717-07:00", "updated_at": "2026-03-24T10:50:23.806802-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":80}" }, { "id": 6, "change_id": "6172575a-b4ff-40b5-bff3-cb95e12b59a8", "node_type": "option", "title": "BibliographicEntry base + Citation/PaperMetadata subclasses (shared base, promotes future citation graph)", "description": "Define BibliographicEntry as shared base enabling both citations and papers to be treated uniformly. Citations get a contexts field for text snippets; enables future promotion of citations to full papers.\\n\\nSources:\\n- 0706560: 'implement new models\\!'\\n- 8edd301: 'stop wasting citation data\\!\\!\\!\\!' ", "status": "pending", "created_at": "2026-03-24T10:50:08.968637-07:00", "updated_at": "2026-03-24T10:50:08.968637-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 7, "change_id": "1a359146-57c9-4789-9639-8021bdfc734b", "node_type": "decision", "title": "Use Pydantic BibliographicEntry shared base model", "description": "Chose rich shared-base Pydantic models. BibliographicEntry is the common ancestor for both Citation (extracted references) and PaperMetadata (the paper being processed). This shared base enables future promotion of citations to full papers in a citation graph.\\n\\nSources:\\n- 0706560: 'implement new models\\!'\\n- 8edd301: 'stop wasting citation data\\!\\!\\!\\!'", "status": "pending", "created_at": "2026-03-24T10:50:17.440409-07:00", "updated_at": "2026-03-24T10:50:17.440409-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 8, "change_id": "13d9f434-9f08-4662-ac33-552e63ca335c", "node_type": "action", "title": "Implement Pydantic models: BibliographicEntry, Citation, PaperMetadata, Synthesis, ProcessingState", "description": "Created models.py with shared base BibliographicEntry. Citation has contexts list for future extraction. Synthesis model captures summary/why_cared/key_concepts/quote/cost.\\n\\nSources:\\n- 0706560: 'implement new models\\!'\\n- 6c3ad75: 'oops fix models'", "status": "pending", "created_at": "2026-03-24T10:50:28.602258-07:00", "updated_at": "2026-03-24T10:50:28.602258-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 9, "change_id": "1405f4da-9545-43eb-af06-986a3c3dc4cc", "node_type": "goal", "title": "Filter low-quality citations from GROBID output", "description": "GROBID sometimes extracts garbage citations (garbled text, broken references) that pollute the output notes. Need a heuristic to detect and drop them.\\n\\nSources:\\n- 298a3d2: 'Filter garbage citations from GROBID'\\n- d4515ec: 'work on garbage citation detection'\\n- 01d006d: 'better filtering for garbage citations'", "status": "pending", "created_at": "2026-03-24T10:50:36.181157-07:00", "updated_at": "2026-03-24T10:50:36.181157-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 10, "change_id": "9c90073d-af04-48fa-9745-d0ceb1ab7659", "node_type": "action", "title": "Implement heuristic garbage-score filter in grobid_processor.py (threshold >60)", "description": "Built a scoring system that assigns penalty points to citations with garbled text, missing fields, implausible dates, etc. Citations scoring above 60 are dropped. Required multiple iterations to tune.\\n\\nSources:\\n- 298a3d2: 'Filter garbage citations from GROBID'\\n- d4515ec: 'work on garbage citation detection'\\n- 01d006d: 'better filtering for garbage citations'\\n- 1322ac3: 'Document citation jank'", "status": "pending", "created_at": "2026-03-24T10:50:44.178389-07:00", "updated_at": "2026-03-24T10:50:44.178389-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":88}" }, { "id": 11, "change_id": "f93d4f50-8d20-44f3-a830-c760f19880f0", "node_type": "outcome", "title": "GROBID citation output cleaned of garbage entries", "description": "Heuristic filter with threshold >60 removes garbled citations while preserving legitimate ones.\\n\\nSources:\\n- 01d006d: 'better filtering for garbage citations'", "status": "pending", "created_at": "2026-03-24T10:50:47.796905-07:00", "updated_at": "2026-03-24T10:50:47.796905-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85}" }, { "id": 12, "change_id": "7d2294a4-24e9-4080-8814-f9038a29611b", "node_type": "goal", "title": "Support batch processing of multiple papers from a file list", "description": "Single-paper workflow sufficient for testing but research use requires processing many papers at once.\\n\\nSources:\\n- 5144306: 'prepare to test batch processing'\\n- 39deb6a: 'Test batch processing\\!'\\n- 7c732e3: 'Allow --force flag in batch'", "status": "pending", "created_at": "2026-03-24T10:50:54.541812-07:00", "updated_at": "2026-03-24T10:50:54.541812-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 13, "change_id": "e465bc86-d828-49b1-9618-730558b12fa7", "node_type": "action", "title": "Implement batch_process.py with deduplication via StateManager and --force flag", "description": "Created batch_process.py wrapping PaperProcessor for file-list ingestion. StateManager tracks processed arXiv IDs/DOIs/URLs to avoid reprocessing. --force flag bypasses deduplication.\\n\\nSources:\\n- 39deb6a: 'Test batch processing\\!'\\n- 7c732e3: 'Allow --force flag in batch'\\n- 75d5e04: 'be honest about deduplication, claude'\\n- e8e55f4: 'Redo batch tests'", "status": "pending", "created_at": "2026-03-24T10:51:02.186420-07:00", "updated_at": "2026-03-24T10:51:02.186420-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":88}" }, { "id": 14, "change_id": "7fb17e59-24c2-4b55-9808-64ab8b01d156", "node_type": "outcome", "title": "39-paper batch processing working cleanly", "description": "Batch pipeline processes lists of arXiv IDs, skips duplicates via state tracking, supports --force for reprocessing.\\n\\nSources:\\n- 7306bb0: 'wrap up v0.2.0' (39-paper batch clean noted)", "status": "pending", "created_at": "2026-03-24T10:51:06.825292-07:00", "updated_at": "2026-03-24T10:51:06.825292-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":88}" }, { "id": 15, "change_id": "045be92a-702d-40fa-8787-992990e837cc", "node_type": "goal", "title": "Migrate synthesis from inline prompts to native Anthropic Skills API for modular writing style control", "description": "The inline prompt approach was monolithic. The Skills API allows composable skill documents and a 3-axis register system for writing style (jargon/structure/depth).\\n\\nSources:\\n- e1eacba: 'think about transition to skill architecture'\\n- e5c13bf: 'Integrate native Agent Skills API for synthesis'", "status": "pending", "created_at": "2026-03-24T10:51:12.426594-07:00", "updated_at": "2026-03-24T10:51:12.426594-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 16, "change_id": "d56dfd33-4e34-46df-97bf-db90ce227f16", "node_type": "option", "title": "Keep inline prompts with parameterized style flags", "description": "Simpler approach: pass style parameters directly to prompt template. No external API for skill management.", "status": "rejected", "created_at": "2026-03-24T10:51:20.649547-07:00", "updated_at": "2026-03-24T10:51:27.696521-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":70}" }, { "id": 17, "change_id": "856af3cb-8c9a-42ed-833a-2b5dd734a877", "node_type": "option", "title": "Use native Anthropic Skills API with SKILL.md documents and register-controller", "description": "Upload skills as documents via Anthropic Skills API. Compose 7 skills per request. Register system controls 3 independent axes: jargon (none/selective/heavy), structure (conversational/mixed/formal), depth (hand-holding/balanced/assume-knowledge).\\n\\nSources:\\n- e5c13bf: 'Integrate native Agent Skills API for synthesis'", "status": "pending", "created_at": "2026-03-24T10:51:20.667560-07:00", "updated_at": "2026-03-24T10:51:20.667560-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 18, "change_id": "21f4442d-f1d9-47a0-8734-f16a0406d250", "node_type": "decision", "title": "Use Anthropic Skills API with 7 SKILL.md files and 3-axis register system", "description": "Chose native Skills API over inline prompts to get modular, composable skill documents and clean 3-axis register control. IDs cached in skills/skill_ids.json to avoid re-upload.\\n\\nSources:\\n- e5c13bf: 'Integrate native Agent Skills API for synthesis'", "status": "pending", "created_at": "2026-03-24T10:51:24.874725-07:00", "updated_at": "2026-03-24T10:51:24.874725-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 19, "change_id": "ddea15ac-f44f-4b4d-a965-ca86d8c8fce8", "node_type": "action", "title": "Create 7 SKILL.md files, SkillsManager with ID caching, synthesis_generator.py using beta.messages with container.skills", "description": "Created skills/ directory with 7 skills: understand-academic-text, extract-arguments, identify-terminology, register-controller (with 9 axis reference files), quick-summary, detailed-summary, glossary-extraction. SkillsManager uploads via client.beta.skills.create and caches IDs in skills/skill_ids.json.\\n\\nSources:\\n- e5c13bf: 'Integrate native Agent Skills API for synthesis'\\n- 6bd8ae0: 'Fix skills API integration: code execution required, last text block for output'", "status": "pending", "created_at": "2026-03-24T10:51:33.997732-07:00", "updated_at": "2026-03-24T10:51:33.997732-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 20, "change_id": "d72a5601-26be-4990-8025-2b89b2bd1501", "node_type": "observation", "title": "Skills API requires code-execution beta enabled and output is in the LAST text block, not the first", "description": "Discovered that the skills container requires code-execution-2025-08-25 beta even when skills don't use scripts. Response parsing must use the last text block; the model reads skill files in multi-step tool calls first.\\n\\nSources:\\n- 6bd8ae0: 'Fix skills API integration: code execution required, last text block for output'", "status": "pending", "created_at": "2026-03-24T10:51:41.174866-07:00", "updated_at": "2026-03-24T10:51:41.174866-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 21, "change_id": "8cac51ed-f15c-41fd-8fe7-013c3edbf735", "node_type": "outcome", "title": "Skills API synthesis working with 7 skills and 3-axis register system", "description": "Synthesis calls use up to 8 skills per request. Register system allows jargon/structure/depth configuration. Quick-summary, detailed-summary, and glossary-extraction skills available.\\n\\nSources:\\n- 6bd8ae0: 'Fix skills API integration: code execution required, last text block for output'", "status": "pending", "created_at": "2026-03-24T10:51:44.959084-07:00", "updated_at": "2026-03-24T10:51:44.959084-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 22, "change_id": "dea0ef58-8683-4feb-845f-e847140daa5c", "node_type": "goal", "title": "Establish CI/CD: pytest suite, CLI, pre-commit hooks, devcontainer", "description": "Pipeline was tested via ad-hoc scripts. Need proper test infrastructure, a real CLI, and reproducible dev environment.\\n\\nSources:\\n- 326510b: 'integrate ci-cd: pytest suite, CLI, pre-commit, devcontainer'", "status": "pending", "created_at": "2026-03-24T10:51:51.631400-07:00", "updated_at": "2026-03-24T10:51:51.631400-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 23, "change_id": "e4660913-7a32-4851-bbfe-699ddfe61a38", "node_type": "action", "title": "Add pytest suite (unit/integration split), CLI (alcanzai commands), pre-commit, devcontainer", "description": "Created pytest suite with conftest.py, integration marker, ~130 tests across 4 files. CLI via paper_library/cli.py: alcanzai ingest/batch/stats/validate. pre-commit with black/ruff. .devcontainer/ for VS Code. Legacy script tests moved to tests/legacy/ and excluded.\\n\\nSources:\\n- 326510b: 'integrate ci-cd: pytest suite, CLI, pre-commit, devcontainer'", "status": "pending", "created_at": "2026-03-24T10:51:59.054149-07:00", "updated_at": "2026-03-24T10:51:59.054149-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 24, "change_id": "365b242e-23d1-4cf4-aa40-6fd05c8dae27", "node_type": "outcome", "title": "130 unit tests, proper CLI, reproducible dev environment in place", "description": "pytest -m 'not integration' runs fast unit tests. Full suite requires GROBID + API key. alcanzai CLI is the official entry point.\\n\\nSources:\\n- 326510b: 'integrate ci-cd: pytest suite, CLI, pre-commit, devcontainer'", "status": "pending", "created_at": "2026-03-24T10:52:04.535491-07:00", "updated_at": "2026-03-24T10:52:04.535491-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 25, "change_id": "88a39bf7-ebb2-453f-9f51-3f364c058d2f", "node_type": "goal", "title": "Expand input sources beyond arXiv: web articles, DOIs, local PDFs, PDF URLs", "description": "Pipeline only handles arXiv IDs. Research reading includes blog posts, journal papers by DOI, and local PDFs. Need unified ingestion.\\n\\nSources:\\n- 0f36b58: 'create web_fetcher.py'\\n- 01510d1: 'Add DOI fetcher: Crossref metadata + Unpaywall/S2 OA PDF discovery'\\n- 0abc91b: 'Step 4: web-fetcher integrated into orchestrator'", "status": "pending", "created_at": "2026-03-24T10:52:10.942679-07:00", "updated_at": "2026-03-24T10:52:10.942679-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 26, "change_id": "a7b03a22-c526-4e52-b69a-5142f124cabe", "node_type": "action", "title": "Implement WebFetcher: HTML article extraction, OG tags, Distill site support, PDF-URL routing", "description": "web_fetcher.py handles HTML articles via markdownify and OG tag extraction; detects Distill-framework sites (d-article); routes PDF URLs through _handle_pdf_from_url() to GROBID pipeline. UnsupportedSourceError blocks Twitter/Reddit/YouTube.\\n\\nSources:\\n- 0f36b58: 'create web_fetcher.py'\\n- 0abc91b: 'Step 4: web-fetcher integrated into orchestrator'\\n- c44251a: 'route PDF-from-URL inputs through GROBID pipeline'\\n- 5c25761: 'Fix web article processing for ArticleMetadata and Distill sites'", "status": "pending", "created_at": "2026-03-24T10:52:20.326276-07:00", "updated_at": "2026-03-24T10:52:20.326276-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 27, "change_id": "8a1e88af-08fa-4ce2-873a-a85ab7882b48", "node_type": "action", "title": "Implement DOI fetcher: Crossref metadata + Unpaywall/Semantic Scholar OA PDF discovery", "description": "doi_fetcher.py handles bare DOIs, doi.org URLs. Crossref REST API for metadata (strips JATS XML). Unpaywall → Semantic Scholar fallback for OA PDF. doi_only path for papers with no OA PDF.\\n\\nSources:\\n- 01510d1: 'Add DOI fetcher: Crossref metadata + Unpaywall/S2 OA PDF discovery'", "status": "pending", "created_at": "2026-03-24T10:52:25.180860-07:00", "updated_at": "2026-03-24T10:52:25.180860-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 28, "change_id": "916288ec-3903-48d1-9747-c55817888333", "node_type": "action", "title": "Add PDF landing page link finder to WebFetcher", "description": "Abstract/repository pages (PhilArchive, SSRN, ACL Anthology) link to PDFs but have minimal text content. When content extraction fails threshold, scan <a> tags scored by URL pattern and link text to find the PDF.\\n\\nSources:\\n- f1e39e1: 'Add PDF landing page link finder to WebFetcher'", "status": "pending", "created_at": "2026-03-24T10:52:32.316982-07:00", "updated_at": "2026-03-24T10:52:32.316982-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":88}" }, { "id": 29, "change_id": "2d2a6a50-aad2-4e35-92b8-60a1e0abeae0", "node_type": "observation", "title": "Distill-framework sites embed figures as base64 PNGs; author metadata scattered across multiple HTML patterns", "description": "transformer-circuits.pub and distill.pub use d-article/d-body elements and embed figures as inline base64 data URIs, producing thousands of garbage characters. Author extraction required checking OG tags, JSON-LD, d-byline, and CSS class patterns.\\n\\nSources:\\n- 73aed53: 'Fix citation context extraction and web fetcher content quality'", "status": "pending", "created_at": "2026-03-24T10:52:37.999695-07:00", "updated_at": "2026-03-24T10:52:37.999695-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 30, "change_id": "822ef5ed-7edc-4d82-8370-ed3e62708cae", "node_type": "outcome", "title": "Pipeline handles arXiv, DOI, web articles, PDF URLs, and local PDFs", "description": "Orchestrator branches on input type: arXiv ID, DOI, http/https URLs (articles or PDFs), local paths. Four processing paths: paper (full GROBID), article (lightweight), doi_only (abstract only), pdf_from_web.\\n\\nSources:\\n- 0abc91b: 'Step 4: web-fetcher integrated into orchestrator'\\n- 01510d1: 'Add DOI fetcher'\\n- 7306bb0: 'wrap up v0.2.0'", "status": "pending", "created_at": "2026-03-24T10:52:44.045279-07:00", "updated_at": "2026-03-24T10:52:44.045279-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":93}" }, { "id": 31, "change_id": "4d45cce9-6dc5-4c9f-ac3b-fe89c7e9231f", "node_type": "goal", "title": "Extract citation contexts: find where each reference is mentioned in the paper body", "description": "GROBID extracts bibliography but not where citations appear in the text. Knowing the narrative context of each citation would ground the synthesis 'why_you_cared' output.\\n\\nSources:\\n- 670ae22: 'Step 3: citation context extraction integrated'", "status": "pending", "created_at": "2026-03-24T10:52:48.647387-07:00", "updated_at": "2026-03-24T10:52:48.647387-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":93}" }, { "id": 32, "change_id": "33255866-d89c-459e-af6d-0d1e33b02bbf", "node_type": "option", "title": "Sentence-splitting approach: split text on '. ' then search", "description": "Split body text on '. ' to get sentences, then search for citation patterns within each sentence.", "status": "rejected", "created_at": "2026-03-24T10:52:56.639316-07:00", "updated_at": "2026-03-24T10:53:07.564359-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":70}" }, { "id": 33, "change_id": "bf571fcc-c307-4f09-a3c0-72161f0d2f3d", "node_type": "option", "title": "Regex full-text search with character-based context window extraction", "description": "Run re.finditer() on body text directly; extract sentence window via backwards/forwards character scan from match position. Avoids splitting on abbreviations like 'al.'\\n\\nSources:\\n- 73aed53: 'Fix citation context extraction and web fetcher content quality'", "status": "pending", "created_at": "2026-03-24T10:52:56.656779-07:00", "updated_at": "2026-03-24T10:52:56.656779-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 34, "change_id": "ae408f75-b024-4b26-8127-b4196c219a5f", "node_type": "observation", "title": "Sentence-splitting on '. ' broke 'Vaswani et al. (2017)' patterns at the 'al.' boundary, causing 0 matches on virtually every paper", "description": "The MVP sentence-splitter split 'Vaswani et al. (2017)' into two fragments, making the citation pattern unmatchable. Required redesign to character-based context extraction.\\n\\nSources:\\n- 73aed53: 'Replace sentence-splitting approach with full-text regex search + character-based context extraction. The old approach split on . which broke Vaswani et al. (2017) patterns right at al. causing 0 matches on virtually every paper.'", "status": "pending", "created_at": "2026-03-24T10:53:04.760056-07:00", "updated_at": "2026-03-24T10:53:04.760056-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":97}" }, { "id": 35, "change_id": "5831095c-dd73-4099-a338-ad2ef1ccf9e0", "node_type": "decision", "title": "Use regex full-text search with character-based context window", "description": "Sentence-splitting failed due to abbreviation dots. Full-text regex with character scan correctly handles 'et al.' and captures surrounding context.\\n\\nSources:\\n- 73aed53: 'Fix citation context extraction and web fetcher content quality'", "status": "pending", "created_at": "2026-03-24T10:53:11.433255-07:00", "updated_at": "2026-03-24T10:53:11.433255-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 36, "change_id": "c7893e7b-9bd9-4086-8e29-c42531d1d114", "node_type": "action", "title": "Implement CitationContextExtractor with author-year and numeric [N] pattern matching; attach contexts to Citation.contexts[]", "description": "citation_context.py: regex matches narrative (Smith et al. 2017) and parenthetical ((Smith et al., 2017)) author-year patterns; plus numeric [N] bracket patterns (dominant in CS/ML arXiv). Bibliography stripped before matching. Contexts injected into synthesis prompt and rendered as blockquotes in Cites section.\\n\\nSources:\\n- 670ae22: 'Step 3: citation context extraction integrated'\\n- f4a0c58: 'Add numeric [N] citation support'", "status": "pending", "created_at": "2026-03-24T10:53:20.531267-07:00", "updated_at": "2026-03-24T10:53:20.531267-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 37, "change_id": "e672b887-07c5-4918-b66a-62d09a5d345f", "node_type": "outcome", "title": "Citation contexts extracted and surfaced: blockquotes in notes, grounding synthesis", "description": "Each citation in vault notes shows 1-3 sentences from the paper body where it was cited. Synthesis receives formatted citation contexts to ground why_you_cared.\\n\\nSources:\\n- 670ae22: 'Step 3: citation context extraction integrated'\\n- f4a0c58: 'Add numeric [N] citation support'", "status": "pending", "created_at": "2026-03-24T10:53:25.015292-07:00", "updated_at": "2026-03-24T10:53:25.015292-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 38, "change_id": "9e9554c1-427a-4204-a387-150f2b5e945c", "node_type": "goal", "title": "Extract clean readable body text from PDFs for citation context matching and synthesis", "description": "Citation context matching requires clean text. The choice of extraction method affects text quality significantly for multi-column PDFs.\\n\\nSources:\\n- b0b45d0: 'Use GROBID body text instead of pdfplumber for synthesis and citation context'", "status": "pending", "created_at": "2026-03-24T10:53:30.682246-07:00", "updated_at": "2026-03-24T10:53:30.682246-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":93}" }, { "id": 39, "change_id": "8d65a288-48af-4379-84c4-8d34c8c1292b", "node_type": "option", "title": "Use pdfplumber for body text extraction", "description": "pdfplumber reads character positions from the PDF and reconstructs text. Simple dependency, widely used.", "status": "rejected", "created_at": "2026-03-24T10:53:54.790607-07:00", "updated_at": "2026-03-24T10:54:06.433422-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":70}" }, { "id": 40, "change_id": "1649cc33-62c6-465b-95e2-93271851bc80", "node_type": "option", "title": "Use GROBID TEI XML body text (itertext on <body>/<div>/<p>)", "description": "GROBID's TEI XML output correctly reconstructs reading order from 2-column layout. Bracket citation markers preserved inside <ref> elements.\\n\\nSources:\\n- b0b45d0: 'Use GROBID body text instead of pdfplumber for synthesis and citation context'", "status": "pending", "created_at": "2026-03-24T10:53:54.834933-07:00", "updated_at": "2026-03-24T10:53:54.834933-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 41, "change_id": "fb833dff-b1f9-4113-98ee-6c45e0185088", "node_type": "observation", "title": "pdfplumber reads 2-column PDFs across full page width, merging both columns and stripping inter-word spaces: produces 'Recurrentneuralnetworks,longshort-termmemory[13]'", "description": "Confirmed failure mode: pdfplumber ignores column boundaries in multi-column academic PDFs, producing garbled concatenated text. Also reverses arXiv header strings.\\n\\nSources:\\n- b0b45d0: 'pdfplumber reads 2-column PDFs across the full page width, merging both columns and stripping inter-word spaces — producing garbled text like Recurrentneuralnetworks,longshort-termmemory[13] and reversed arXiv header strings'", "status": "pending", "created_at": "2026-03-24T10:54:03.727267-07:00", "updated_at": "2026-03-24T10:54:03.727267-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":98}" }, { "id": 42, "change_id": "18b1276e-37b9-4616-bfb8-d6364d024019", "node_type": "decision", "title": "Use GROBID body text; remove pdfplumber dependency entirely", "description": "GROBID correctly reconstructs reading order from TEI XML. pdfplumber removed as dependency in v0.2.5 — short GROBID body text now just logs a warning (for scanned PDFs) rather than falling back.\\n\\nSources:\\n- b0b45d0: 'Use GROBID body text instead of pdfplumber'\\n- 4315aa3: 'Remove pdfplumber: dependency dropped, _extract_text removed, short GROBID body text now logs a warning instead of falling back'", "status": "pending", "created_at": "2026-03-24T10:54:11.452074-07:00", "updated_at": "2026-03-24T10:54:11.452074-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":97}" }, { "id": 43, "change_id": "cf2dd950-18ca-451e-a558-a35ba32c4564", "node_type": "action", "title": "Add body_text field to PaperMetadata; extract from GROBID TEI XML <body>; remove pdfplumber", "description": "models.py: add body_text: Optional[str] to PaperMetadata. grobid_processor.py: _extract_body_text() walks <body>/<div>/<p> with itertext(). orchestrator.py: prefer grobid_metadata.body_text. v0.2.5: pdfplumber removed entirely.\\n\\nSources:\\n- b0b45d0: 'Use GROBID body text instead of pdfplumber for synthesis and citation context'\\n- 4315aa3: 'Remove pdfplumber: dependency dropped, _extract_text removed'", "status": "pending", "created_at": "2026-03-24T10:54:18.800015-07:00", "updated_at": "2026-03-24T10:54:18.800015-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 44, "change_id": "64fd64ab-ab9a-4d24-9ee0-62be617d2ac4", "node_type": "outcome", "title": "Clean body text from GROBID; pdfplumber removed; citation matching works correctly on multi-column PDFs", "description": "Numeric citation markers like [1], [3, 5] preserved in GROBID itertext() output. Multi-column layout correctly reconstructed.\\n\\nSources:\\n- b0b45d0: 'Use GROBID body text instead of pdfplumber'\\n- 4315aa3: 'Remove pdfplumber'", "status": "pending", "created_at": "2026-03-24T10:54:23.395323-07:00", "updated_at": "2026-03-24T10:54:23.395323-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 45, "change_id": "9b29828b-add9-49c6-8862-dcd148c2df35", "node_type": "goal", "title": "Handle raw extracted content without bloating the main paper notes", "description": "Paper notes were embedding full pdfplumber text extracts inline, making notes enormous. Need to separate source material from the curated note.\\n\\nSources:\\n- 9d6dcfd: 'Split raw content into linked source notes in vault/Sources/'\\n- 87e8c7f: 'Fix token limit overflow and redundant PDF source notes'", "status": "pending", "created_at": "2026-03-24T10:54:29.336445-07:00", "updated_at": "2026-03-24T10:54:29.336445-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 46, "change_id": "f4aa0bda-6d33-4695-a2bc-47ff2fb86e87", "node_type": "action", "title": "Split raw content into vault/Sources/ linked notes; keep source notes only for web articles (PDFs already in vault/PDFs/)", "description": "Initially created vault/Sources/ for both papers and articles. Then recognized PDF papers already have source of truth in vault/PDFs/. Revised: source notes only for web articles (where the markdown conversion is the only backup). Token overflow fix: citation contexts capped at 10,000 chars.\\n\\nSources:\\n- 9d6dcfd: 'Split raw content into linked source notes in vault/Sources/'\\n- 87e8c7f: 'Fix token limit overflow and redundant PDF source notes'", "status": "pending", "created_at": "2026-03-24T10:54:37.045989-07:00", "updated_at": "2026-03-24T10:54:37.045989-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":88}" }, { "id": 47, "change_id": "621ab157-f673-4210-9163-5e27a9913071", "node_type": "outcome", "title": "Web articles have vault/Sources/ notes; PDF papers link to vault/PDFs/ directly", "description": "vault/Sources/ holds web article converted markdown. PDF pipeline skips source notes since the PDF file is the source of truth.\\n\\nSources:\\n- 87e8c7f: 'Fix token limit overflow and redundant PDF source notes'", "status": "pending", "created_at": "2026-03-24T10:54:40.928104-07:00", "updated_at": "2026-03-24T10:54:40.928104-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":88}" }, { "id": 48, "change_id": "2807254a-2fa9-4343-8a03-0253c67b00da", "node_type": "goal", "title": "Add observability: OTel tracing, structured logging, token-aware truncation for production use", "description": "v0.3.0 scope item. Pipeline runs in homelab K3s context needing traces for debugging. print() calls need to be replaced with structured logging. Token limits need smart handling.\\n\\nSources:\\n- 4315aa3: 'Add OTel instrumentation, structured logging, and token-aware truncation (v0.2.5)'", "status": "pending", "created_at": "2026-03-24T10:54:45.990816-07:00", "updated_at": "2026-03-24T10:54:45.990816-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":92}" }, { "id": 49, "change_id": "61454de2-497b-49c2-8454-fd2cc1eca141", "node_type": "action", "title": "Implement telemetry.py (OTel+structlog), token_utils.py (tiktoken), add spans across full pipeline, replace all print() calls", "description": "New paper_library/telemetry.py: OTel tracing + metrics with graceful no-op fallback when OTEL_EXPORTER_OTLP_ENDPOINT unset. structlog with console/JSON renderer. New paper_library/token_utils.py: tiktoken-based estimation and paragraph-boundary truncation. Spans on: process_paper, fetch_arxiv, fetch_doi, fetch_web, grobid_parse, claude_synthesize, skill_upload, extract_citation_contexts, write_markdown.\\n\\nSources:\\n- 4315aa3: 'Add OTel instrumentation, structured logging, and token-aware truncation (v0.2.5)'", "status": "pending", "created_at": "2026-03-24T10:54:56.643588-07:00", "updated_at": "2026-03-24T10:54:56.643588-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":93}" }, { "id": 50, "change_id": "a5eb556d-8805-493a-9596-aee9c6e64252", "node_type": "outcome", "title": "v0.2.5: Full pipeline traced with OTel spans, structured logs, tiktoken-based truncation; 157 tests passing", "description": "Pipeline fully instrumented. SYNTHESIS_TOKEN_BUDGET env var controls truncation (default 150k tokens). --diagnostics CLI flag enables DEBUG log level for per-call token detail.\\n\\nSources:\\n- 4315aa3: 'Add OTel instrumentation, structured logging, and token-aware truncation (v0.2.5)'", "status": "pending", "created_at": "2026-03-24T10:55:01.737830-07:00", "updated_at": "2026-03-24T10:55:01.737830-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":93}" }, { "id": 51, "change_id": "252ea644-c079-4ad4-a5d0-733b3428a4d2", "node_type": "observation", "title": "Hard Mode cluster deliberately deferred: OCR, humanities papers, annotation ingestion, acquisition stack, versioning — all interrelated, needs design session", "description": "These features were recognized as a cluster requiring joint design before any implementation begins. Premature implementation of one would constrain the others.\\n\\nSources:\\n- 39bd1ad: 'Add v0.2.0 milestone doc and update project log'\\n- MEMORY.md: 'Hard Mode batch cluster (OCR / humanities papers / annotation ingestion / acquisition stack / versioning) — intentionally deferred'", "status": "pending", "created_at": "2026-03-24T10:55:08.037862-07:00", "updated_at": "2026-03-24T10:55:08.037862-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 52, "change_id": "08467d5d-4d9c-4e98-8714-88f870200264", "node_type": "outcome", "title": "v0.2.0 milestone: full pipeline complete with all input sources, citation context, Skills API, 148 unit tests, 39-paper batch clean", "description": "Full pipeline achieved. All input sources (arXiv/DOI/web/local PDF), GROBID body text, Skills API synthesis with register control, citation contexts, source notes architecture, CI/CD.\\n\\nSources:\\n- 7306bb0: 'wrap up v0.2.0'\\n- 39bd1ad: 'Add v0.2.0 milestone doc and update project log'", "status": "pending", "created_at": "2026-03-24T10:55:15.850707-07:00", "updated_at": "2026-03-24T10:55:15.850707-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":98}" }, { "id": 53, "change_id": "2ed90754-7c09-4210-a977-9e56ca9ce5d0", "node_type": "observation", "title": "YAML frontmatter requires careful escaping: colons inside unquoted description values and special characters from non-ASCII author names break parsing", "description": "Multiple iterations needed to handle Unicode characters in author names, ALL_CAPS titles, copyright notices in extracted text, and YAML colon-space in description fields.\\n\\nSources:\\n- 348f084: 'improve special character handling'\\n- 6bf0db4: 'Fix character encoding'\\n- 384e7e5: 'Fix character encoding more'\\n- 40250e7: 'handle file truncation and escape quotes in yaml'", "status": "pending", "created_at": "2026-03-24T10:55:28.022724-07:00", "updated_at": "2026-03-24T10:55:28.022724-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":88}" }, { "id": 54, "change_id": "edbf68dd-992c-4cf9-b76a-3a0ba5fc0a87", "node_type": "observation", "title": "User's Victorianist background (humanities citation patterns) drove soft year boundaries in garbage scoring", "description": "User background: Victorianist (19th century lit) — citations routinely go back 50-100+ years, classics and medieval scholarship even older. Hard year-boundary rules (e.g., 'reject anything before 1900') would silently drop legitimate citations.\n\nThis directly informed the decision to use soft suspicion modifiers for year ranges rather than hard exclusions, and to raise score caps only when multiple garbage signals fire together (not on year alone).\n\nSources:\n- project.json context: 'User background: Victorianist (19th century lit) - citations routinely go back 50-100+ years, classics/medieval even older. System must handle humanities citation patterns, not just recent CS/AI papers'\n- project.json decided: 'Garbage detection should use soft suspicion modifiers for years, not hard boundaries - avoid breaking humanities citations or future cutting-edge work (2028+ thesis prep)'", "status": "pending", "created_at": "2026-03-24T11:02:30.648392-07:00", "updated_at": "2026-03-24T11:02:30.648392-07:00", "metadata_json": "{\"branch\":\"claude\"}" }, { "id": 55, "change_id": "ba7bf08c-e790-4de3-9cb4-bcda5829cfd7", "node_type": "option", "title": "Build file-based skill_loader.py reading SKILL.md files from disk, composed via register_config.py TOML presets", "description": "Designed and built before native Anthropic Skills API was available. skill_loader.py (~260 lines) read markdown skill files, resolved dependencies, and composed them into complete prompt text for Claude API calls. register_config.py (~240 lines) handled TOML-based preset system (learning/partner/litreview/scan/default).\n\nThis was a complete working implementation — 9 register files written, skill loader validated, presets defined — but was rendered unnecessary when the native Skills API (beta) became the chosen approach.\n\nSources:\n- claude-api-state.json built: 'Skill loader complete (skill_loader.py ~260 lines): loads and composes markdown skills with register configuration, file caching, validation. Plus register_config.py (~240 lines): TOML config management, preset system'\n- claude-api-state.json built: 'All 9 register skills complete - ready for skill loader implementation and integration testing'\n- unintegrated_code/skills/ contains the original monolithic SKILL.md files (pt 1) and 3-axis register system (pt 2) built for this loader", "status": "rejected", "created_at": "2026-03-24T11:02:43.809287-07:00", "updated_at": "2026-03-24T11:02:47.300802-07:00", "metadata_json": "{\"branch\":\"claude\"}" }, { "id": 56, "change_id": "7cd0f6f9-83e9-48ab-a58f-67f84e59493c", "node_type": "goal", "title": "Re-engage with alcanzai: v0.3.0 planning, notes-shape refactor, telemetry validation, issues-based workflow", "description": null, "status": "pending", "created_at": "2026-04-21T21:00:18.069360-07:00", "updated_at": "2026-04-21T21:00:18.069360-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85,\"prompt\":\"I'm returning to this project after some time away. I want to refamiliarize myself with it and figure out where to tune back in for development. This seemed like a good excuse to introduce you to the codebase, document the process, and maybe figure out a proper issues-based workflow for agentic development. How do you want to approach exploring it?\\n\\n[Follow-ups clarified:]\\n- Deciduous install from previous session should be committed\\n- Point of session: re-engage + roadmap Hard Mode cluster (everything on the table)\\n- \\\"Refactor notes that get produced\\\" on agenda early — prior undocumented conversation\\n was about moving sections of output notes around, adding a methodology section,\\n and other structured-recall stuff; pedagogical best-practices research was done\\n but no full redesign finalized\\n- Memory architecture: pbjson = \\\"why\\\" (architecture/design), deciduous = \\\"what\\\"\\n (coding sessions), GitHub issues = \\\"how/when\\\" (execution)\\n- Exomonad compatibility must be preserved (orchestrator that lets Claude delegate\\n to Gemini subagents; not currently in an exomonad session)\\n- Telemetry infra built in v0.2.5 but never set up/tested — user has forgotten\\n how it works; \\\"reacquaint with telemetry + get it running live\\\" is HIGH PRIORITY\\n- Brainstorming conversations viable in this session since logging tools available\"}" }, { "id": 57, "change_id": "fe04a5f9-ef0d-4e81-8256-d4de957f3fd7", "node_type": "action", "title": "Commit deciduous harness install (CLAUDE.md block, .gitignore update, .claude/ agent config, .github/workflows, docs/ viewer)", "description": null, "status": "pending", "created_at": "2026-04-21T21:00:22.452358-07:00", "updated_at": "2026-04-21T21:00:22.452358-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95,\"files\":[\"CLAUDE.md\",\".gitignore\",\".claude/agents.toml\",\".claude/settings.json\",\".github/workflows/deploy-pages.yml\",\".github/workflows/cleanup-decision-graphs.yml\",\"docs/.nojekyll\",\"docs/graph-data.json\",\"docs/index.html\"]}" }, { "id": 58, "change_id": "4bd4ae5a-d5c8-4782-8307-718cf046398c", "node_type": "observation", "title": "Memory architecture consensus: pbjson = 'why' (architecture conversations, design decisions, web-syncable), deciduous = 'what' (coding session flow, graph), GitHub issues = 'how/when' (execution queue). pbjson/project.json currently stale at v0.2.0 — needs catch-up pass to stay useful under this model.", "description": null, "status": "pending", "created_at": "2026-04-21T21:00:27.712447-07:00", "updated_at": "2026-04-21T21:00:27.712447-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":80}" }, { "id": 59, "change_id": "b620d249-326c-47f9-90f7-c6d6eaa4e787", "node_type": "observation", "title": "Telemetry infrastructure (OTel + structlog + token_utils, shipped v0.2.5 commit 4315aa3) was built but never validated end-to-end with real collector/backend. User has forgotten the wiring. Treat as high-priority reacquaint-and-verify task BEFORE adding new v0.3.0 features that would benefit from tracing.", "description": null, "status": "pending", "created_at": "2026-04-21T21:00:30.891415-07:00", "updated_at": "2026-04-21T21:00:30.891415-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85}" }, { "id": 60, "change_id": "83258054-a36c-4d94-948a-f5d32a8b29da", "node_type": "observation", "title": "Exomonad compatibility is a cross-cutting constraint: it's an orchestrator hooked into Claude Code via settings.local.json that lets Claude delegate to Gemini instances as subagents. Hooks on every lifecycle event (SessionStart/End, PreToolUse, PostToolUse, UserPromptSubmit, SubagentStart/Stop, Notification, PermissionRequest, PreCompact, Stop). Any workflow/tooling changes must preserve this integration.", "description": null, "status": "pending", "created_at": "2026-04-21T21:00:34.077658-07:00", "updated_at": "2026-04-21T21:00:34.077658-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90}" }, { "id": 61, "change_id": "cc261249-a446-4931-af1e-5d59a6e2572b", "node_type": "outcome", "title": "Clean working tree: deciduous harness committed as 1c75b7d, .DS_Store tracking killed, settings.local.json protected via .gitignore. 23 files / 3899 lines, zero project-code changes.", "description": null, "status": "pending", "created_at": "2026-04-21T21:01:42.877293-07:00", "updated_at": "2026-04-21T21:01:42.877293-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"1c75b7d\",\"confidence\":95}" }, { "id": 62, "change_id": "4b9caf71-1f1c-4fe2-bead-82d02bb97df8", "node_type": "action", "title": "Read telemetry/token_utils/orchestrator OTel instrumentation; produce reacquaint briefing; scaffold GitHub issues + epic for 'working telemetry'", "description": null, "status": "pending", "created_at": "2026-04-21T21:12:33.959330-07:00", "updated_at": "2026-04-21T21:12:33.959330-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85,\"files\":[\"paper_library/telemetry.py\",\"paper_library/token_utils.py\",\"paper_library/orchestrator.py\",\"paper_library/synthesis_generator.py\"]}" }, { "id": 63, "change_id": "fedffb15-1907-46df-8ae3-b099db584846", "node_type": "observation", "title": "Latent bug: paper_library/telemetry.py registers MeterProvider.shutdown() at atexit but NOT TracerProvider.shutdown(). BatchSpanProcessor is async-buffered; short-lived CLI processes may lose last-batch spans. Fix as part of Issue 4 (instrumentation hardening).", "description": null, "status": "pending", "created_at": "2026-04-21T22:07:02.044571-07:00", "updated_at": "2026-04-21T22:07:02.044571-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90,\"files\":[\"paper_library/telemetry.py\"]}" }, { "id": 64, "change_id": "c116f2e3-2ab1-4dc3-a1af-7bd873aa853c", "node_type": "observation", "title": "Test-suite audit wanted (user flagged): no systematic review of whether existing tests are well-formed. Should be an Opus-driven audit session, delegated via exomonad to Gemini for rewrite/triage to preserve budget. Filing as low-priority issue for tracker visibility.", "description": null, "status": "pending", "created_at": "2026-04-21T22:07:04.367516-07:00", "updated_at": "2026-04-21T22:07:04.367516-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85}" }, { "id": 65, "change_id": "85ef4295-1b48-47f7-bf3e-a92485743dd4", "node_type": "outcome", "title": "7 issues filed on GitHub: epic #2, #3 local validation, #4 design-question (Tailscale routing), #5 cluster deploy, #6 dashboards, #7 hardening; #8 standalone test audit. All under milestone v0.2.6 (except #8). Cross-refs initially off-by-one due to PR #1 occupying issue-number space; fixed via sed swap + gh issue edit.", "description": null, "status": "pending", "created_at": "2026-04-22T00:01:54.619124-07:00", "updated_at": "2026-04-22T00:01:54.619124-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 66, "change_id": "a2f4d62d-ee22-4f97-ac4c-e98ca29e5b41", "node_type": "outcome", "title": "Issue templates committed as 7329175 on claude branch: epic / feature / bug / design-question + config.yml. Scaffolding done; issue workflow ready for use.", "description": null, "status": "pending", "created_at": "2026-04-22T00:02:30.726171-07:00", "updated_at": "2026-04-22T00:02:30.726171-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"7329175\",\"confidence\":95}" }, { "id": 67, "change_id": "c1e1e570-29a8-4d70-97a8-32de7a078f67", "node_type": "action", "title": "Autonomous test-suite audit (issue #8): read every tests/*.py + corresponding module, categorize every test as keep-as-is / improve / rewrite / delete with rationale, produce structured findings doc (docs/test-audit-2026-04.md) for downstream Gemini-delegated fix session.", "description": null, "status": "pending", "created_at": "2026-04-22T00:08:10.634674-07:00", "updated_at": "2026-04-22T00:08:10.634674-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85,\"files\":[\"tests/test_arxiv_fetcher.py\",\"tests/test_doi_fetcher.py\",\"tests/test_web_fetcher.py\",\"tests/test_markdown_writer.py\",\"tests/test_citation_context.py\",\"tests/test_grobid_processor.py\",\"tests/test_telemetry.py\",\"tests/test_token_utils.py\",\"tests/test_synthesis_generator.py\",\"tests/conftest.py\",\"tests/test_pipeline.py\"]}" }, { "id": 68, "change_id": "b1613142-4dcf-4f58-bcda-814f82664049", "node_type": "outcome", "title": "Test-suite audit complete: docs/test-audit-2026-04.md written, issue #8 updated with summary. 11 active test files + 4 legacy reviewed; ~170 tests categorized. 3 files need major rework (test_pipeline, test_telemetry, test_synthesis_generator), 4 legacy files to delete, 5 modules have zero direct coverage (models, state, skills_manager, config, cli). Ready-to-delegate action queue (A1-A4 H-priority, B1-B8 M-priority, C1-C3 L-priority) with commit-message-ready prescriptions for each item.", "description": null, "status": "pending", "created_at": "2026-04-22T00:16:34.078547-07:00", "updated_at": "2026-04-22T00:16:34.078547-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95,\"files\":[\"docs/test-audit-2026-04.md\"]}" }, { "id": 69, "change_id": "56182fb3-89f3-4842-8f7c-b86e73ef3b74", "node_type": "action", "title": "Adversarial code review of paper_library/ + config surface: produce docs/code-review-2026-04.md (structured like test audit) + file H/M findings as small issues under a new review-followups epic. Axes: correctness, error-handling, design, operational, interface contracts, security, dead code, perf. Threshold for filing: 'almost-certainly-wrong' (~90% confident) or definite bug; softer nits stay in the doc only.", "description": null, "status": "pending", "created_at": "2026-04-22T19:04:33.386534-07:00", "updated_at": "2026-04-22T19:04:33.386534-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85}" }, { "id": 70, "change_id": "3775ae29-02f2-480b-bf13-fc6795388b37", "node_type": "outcome", "title": "Adversarial code review complete: docs/code-review-2026-04.md (740 lines) written + epic #9 filed with 18 sub-issues (#10-#27). Findings: 1 H (mojibake bullet in article byline), 16 M (data-loss pair in state persistence, silent fallbacks to wrong values for year/date/source, PDF verification gaps, HEAD+GET redundancy, acronym destruction, version drift, corrupt cache crash, fake Unpaywall email, HTTP arXiv), 1 cleanup bundle (ruff + dead code). 15 L items doc-only.", "description": null, "status": "pending", "created_at": "2026-04-22T19:20:02.436469-07:00", "updated_at": "2026-04-22T19:20:02.436469-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95,\"files\":[\"docs/code-review-2026-04.md\"]}" }, { "id": 71, "change_id": "dc7c8f66-196d-44e7-b716-28b3e4e2bd67", "node_type": "action", "title": "Fix issue #10 (mojibake) + #27 (R18 cleanup): one-line fix + regression test for #10, then ruff auto-fixes + E402 restructure + dead code removal + batch_process.py deletion for #27. Separate commits per logical unit.", "description": null, "status": "pending", "created_at": "2026-04-22T19:23:16.802030-07:00", "updated_at": "2026-04-22T19:23:16.802030-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":90,\"files\":[\"paper_library/markdown_writer.py\",\"paper_library/arxiv_fetcher.py\",\"paper_library/web_fetcher.py\",\"paper_library/doi_fetcher.py\",\"paper_library/batch_process.py\",\"paper_library/cli.py\",\"paper_library/citation_context.py\",\"paper_library/orchestrator.py\",\"tests/test_markdown_writer.py\"]}" }, { "id": 72, "change_id": "6153e374-d0fe-4514-b37e-6c05bbb12d0b", "node_type": "outcome", "title": "Issue #10 closed: mojibake bullet fixed in 4889147 with TestArticleByline regression tests (159 tests now passing, was 157). Issue #27 closed across 3 commits (2f2b30a ruff+E402, a05dc8c dead code removal, a42ce47 batch_process.py deletion + doc updates). ruff clean, 65 lines of dead code removed, 1 redundant file deleted.", "description": null, "status": "pending", "created_at": "2026-04-22T19:28:19.385571-07:00", "updated_at": "2026-04-22T19:28:19.385571-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"a42ce47\",\"confidence\":95}" }, { "id": 73, "change_id": "fe614f06-c623-4295-bb57-496eaec00c17", "node_type": "action", "title": "Grind through code-review issues: start with small independent fixes (R10 HTTPS, R8 raise-on-unknown-source, R9 Unpaywall email, R12 skills cache, R11 version unify, R5 PDF date, R6 filename stable), then year trio (R3+R4+R15), then R2 data-loss pair. One commit per logical unit. Stop before limits rather than forcing.", "description": null, "status": "pending", "created_at": "2026-04-23T06:39:21.235764-07:00", "updated_at": "2026-04-23T06:39:21.235764-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":85}" }, { "id": 74, "change_id": "ff2ed075-7743-44d5-bb3b-2e0b4f85f90d", "node_type": "action", "title": "Atomic state writes + corrupt-state backup (R2)", "description": null, "status": "pending", "created_at": "2026-04-23T10:37:02.824823-07:00", "updated_at": "2026-04-23T10:37:02.824823-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"a18407c\",\"confidence\":95}" }, { "id": 75, "change_id": "72feb730-c077-4d19-ad7b-aaa86c7bf9cb", "node_type": "outcome", "title": "R2 landed: #11 closed, 185 tests pass (was 177, +8 new)", "description": null, "status": "pending", "created_at": "2026-04-23T10:37:20.776444-07:00", "updated_at": "2026-04-23T10:37:20.776444-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"a18407c\",\"confidence\":95}" }, { "id": 76, "change_id": "fdd8e382-85f8-4201-a06f-c460fd4170b8", "node_type": "outcome", "title": "Pushed R2 + graph sync to origin/claude (c23f468..74dba50)", "description": null, "status": "pending", "created_at": "2026-04-23T10:37:38.778876-07:00", "updated_at": "2026-04-23T10:37:38.778876-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"74dba50\",\"confidence\":95}" }, { "id": 77, "change_id": "022097db-a968-4dd0-a06f-5a55b7382878", "node_type": "goal", "title": "Finish remaining 5 code-review issues: R7 R13 R14 R16 R17", "description": null, "status": "pending", "created_at": "2026-04-24T22:49:04.449458-07:00", "updated_at": "2026-04-24T22:49:04.449458-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95,\"prompt\":\"A then B sounds great, go for it.\\n\\n(Context: \\\"A\\\" = finish the 5 remaining code-review issues from epic #9 before opening the PR to merge claude→main. Issues: #16 R7 cached PDF verification, #22 R13 single GET, #23 R14 acronym protection, #25 R16 author suffixes/honorifics, #26 R17 validate/init split.)\"}" }, { "id": 78, "change_id": "a33b0a51-648d-4fd4-a2e4-f61c95eaa608", "node_type": "action", "title": "Implement R14, R13, R17, R16, R7 — 5 remaining code-review issues", "description": null, "status": "pending", "created_at": "2026-04-24T22:55:59.567049-07:00", "updated_at": "2026-04-24T22:55:59.567049-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95}" }, { "id": 79, "change_id": "e818616b-0f45-45df-9a9d-1b213ada3f6e", "node_type": "outcome", "title": "All 5 code-review issues fixed: R14 #23, R17 #26, R13 #22, R16 #25, R7 #16 — 218 tests passing", "description": null, "status": "pending", "created_at": "2026-04-24T22:57:02.969114-07:00", "updated_at": "2026-04-24T22:57:02.969114-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"4d117bd\",\"confidence\":98}" }, { "id": 80, "change_id": "6dd64449-f6d9-4d00-821b-c41ecfcef272", "node_type": "goal", "title": "Test suite + telemetry hardening: A1-A4 + issue #7", "description": null, "status": "pending", "created_at": "2026-04-29T00:07:19.420106-07:00", "updated_at": "2026-04-29T00:07:19.420106-07:00", "metadata_json": "{\"branch\":\"claude\",\"confidence\":95,\"prompt\":\"Let's keep going!\\n\\n(Context: code review hardening merged via PR #28. Remaining work: test suite remediation A1-A4 from docs/test-audit-2026-04.md, plus issue #7 instrumentation hardening. A1=delete legacy tests, A2=fix test_pipeline, A3=rewrite test_telemetry, A4=synthesis_generator unit tests, #7=TracerProvider shutdown + meter lazy-init + token_utils structlog import + orchestrator span pattern.)\"}" }, { "id": 81, "change_id": "a34540b0-9aa3-45a5-95b1-e62bd68d6cd1", "node_type": "action", "title": "Implement A1 legacy deletion, A2 pipeline fix, #7 hardening, A3 telemetry rewrite, A4 synthesis unit tests", "description": null, "status": "pending", "created_at": "2026-04-29T01:07:07.305110-07:00", "updated_at": "2026-04-29T01:07:07.305110-07:00", "metadata_json": "{\"branch\":\"claude\",\"commit\":\"629442a\",\"confidence\":95}" }, { "id": 82, "change_id": "1261ce5b-833d-440c-8ce8-43a13986b35f", "node_type": "outcome", "title": "A1-A4 + #7 done: 250 unit tests passing (was 217), PR #29 open", "description": null, "status": "pending", "created_at": "2026-04-29T01:09:39.669737-07:00", "updated_at": "2026-04-29T01:09:39.669737-07:00", "metadata_json": 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