{"type":"thinking_level_change","id":"97ebb812","parentId":null,"timestamp":"2026-04-03T00:54:28.313Z","thinkingLevel":"medium"}
{"type":"model_change","id":"b92c8a07","parentId":"97ebb812","timestamp":"2026-04-03T00:54:28.315Z","provider":"anthropic","modelId":"claude-opus-4-6"}
{"type":"custom_message","customType":"gsd-auto","content":"You are executing GSD auto-mode.\n\n## Working Directory\n\nYour working directory is `/home/aux/projects/content-to-kb-automator`. All file reads, writes, and shell commands MUST operate relative to this directory. Do NOT `cd` to any other directory.\n\n## UNIT: Complete Slice S01 (\"Synthesis Prompt v5 — Nested Sections + Citations\") — Milestone M014\n\n## Your Role in the Pipeline\n\nExecutor agents built each task and wrote task summaries. You are the closer — verify the assembled work actually delivers the slice goal, then compress everything into a slice summary. After you finish, a **reassess-roadmap agent** reads your slice summary to decide if the remaining roadmap still makes sense. The slice summary is also the primary record of what this slice achieved — future slice researchers and planners read it as a dependency summary when their work builds on yours.\n\nWrite the summary for those downstream readers. What did this slice actually deliver? What patterns did it establish? What should the next slice know?\n\nAll relevant context has been preloaded below — the slice plan, all task summaries, and the milestone roadmap are inlined. Start working immediately without re-reading these files.\n\n## Inlined Context (preloaded — do not re-read these files)\n\n### Milestone Roadmap\nSource: `.gsd/milestones/M014/M014-ROADMAP.md`\n\n# M014: \n\n## Vision\nRestructure technique pages to be broader (per-creator+category across videos), deeper (H2/H3 nesting with TOC), multi-source (compose new video content into existing pages), with inline citations linking prose claims to source moments, admin multi-source management, and section-level search with deep linking.\n\n## Slice Overview\n| ID | Slice | Risk | Depends | Done | After this |\n|----|-------|------|---------|------|------------|\n| S01 | Synthesis Prompt v5 — Nested Sections + Citations | high | — | ⬜ | Run test harness with new prompt → output has list-of-objects body_sections with H2/H3 nesting, citation markers on key claims, broader page scope. |\n| S02 | Composition Prompt + Test Harness Compose Mode | high | S01 | ⬜ | Run test harness --compose mode with existing page + new moments → merged output with deduplication, new sections, updated citations. |\n| S03 | Data Model + Migration | low | — | ⬜ | Alembic migration runs clean. API response includes body_sections_format and source_videos fields. |\n| S04 | Pipeline Compose-or-Create Logic | high | S01, S02, S03 | ⬜ | Process two COPYCATT videos. Second video's moments composed into existing page. technique_page_videos has both video IDs. |\n| S05 | Frontend — Nested Rendering, TOC, Citations | medium | S03 | ⬜ | Format-2 page renders with TOC, nested sections, clickable citations. Format-1 pages unchanged. |\n| S06 | Admin UI — Multi-Source Pipeline Management | medium | S03, S04 | ⬜ | Admin view for multi-source page shows source dropdown, composition history, per-video chunking inspection. |\n| S07 | Search — Per-Section Embeddings + Deep Linking | medium | S04, S05 | ⬜ | Search 'LFO grain position' → section-level result → click → navigates to page#section and scrolls. |\n\n---\n\n### Slice Plan\nSource: `.gsd/milestones/M014/slices/S01/S01-PLAN.md`\n\n# S01: Synthesis Prompt v5 — Nested Sections + Citations\n\n**Goal:** Stage 5 synthesis prompt produces body_sections as a list of BodySection objects with H2/H3 nesting and inline [N] citation markers, validated by schema and test harness.\n**Demo:** After this: Run test harness with new prompt → output has list-of-objects body_sections with H2/H3 nesting, citation markers on key claims, broader page scope.\n\n## Tasks\n- [x] **T01: Added BodySection/BodySubSection schema models, changed SynthesizedPage.body_sections to list[BodySection] with v2 format tag, and created citation_utils with 15 passing tests** — Add BodySubSection and BodySection Pydantic models to schemas.py. Change SynthesizedPage.body_sections from dict to list[BodySection]. Add body_sections_format field. Create a small citation validation utility (validate_citations) that checks [N] markers in section content against a moment count. This utility is reused by the test harness in T03.\n\n## Steps\n\n1. Read `backend/pipeline/schemas.py` fully.\n2. Add `BodySubSection` model with `heading: str` and `content: str` fields.\n3. Add `BodySection` model with `heading: str`, `content: str`, and `subsections: list[BodySubSection]` (default_factory=list).\n4. Change `SynthesizedPage.body_sections` type from `dict` to `list[BodySection]` with updated description.\n5. Add `body_sections_format: str = Field(default='v2')` to `SynthesizedPage`.\n6. Create `backend/pipeline/citation_utils.py` with:\n   - `extract_citations(text: str) -> list[int]` — regex extracts all `[N]` and `[N,M]` markers, returns sorted unique indices.\n   - `validate_citations(sections: list[BodySection], moment_count: int) -> dict` — returns `{valid: bool, total_citations: int, invalid_indices: list[int], uncited_moments: list[int], coverage_pct: float}`.\n7. Add unit tests in `backend/pipeline/test_citation_utils.py` covering: valid citations, out-of-range indices, multi-citation markers `[0,2]`, no citations, empty sections.\n\n## Must-Haves\n\n- [ ] BodySubSection and BodySection models exist with correct field types\n- [ ] SynthesizedPage.body_sections is list[BodySection]\n- [ ] body_sections_format field defaults to 'v2'\n- [ ] extract_citations parses [N] and [N,M] markers correctly\n- [ ] validate_citations returns coverage stats and flags invalid indices\n- [ ] Unit tests pass\n  - Estimate: 30m\n  - Files: backend/pipeline/schemas.py, backend/pipeline/citation_utils.py, backend/pipeline/test_citation_utils.py\n  - Verify: cd /home/aux/projects/content-to-kb-automator && python -m pytest backend/pipeline/test_citation_utils.py -v\n- [x] **T02: Rewrote stage5_synthesis.txt with v2 body_sections (list-of-objects with heading/content/subsections), citation rules ([N] and [N,M] format), body_sections_format tag, and H3 subsection guidance** — Rewrite the output format section of `prompts/stage5_synthesis.txt` to produce the new list-of-objects body_sections structure with inline [N] citation markers. Preserve all voice, tone, synthesis philosophy, and body section naming guidance. Back up the current prompt before editing.\n\n## Steps\n\n1. Back up: `cp prompts/stage5_synthesis.txt prompts/stage5_synthesis.$(date +%Y%m%d_%H%M%S).bak`\n2. Read the full prompt file.\n3. Update the `## Body sections structure` section (line ~46): add a paragraph about H3 subsections. Sections can contain 2-3 subsections when a topic has distinct sub-aspects. Subsections are optional — flat sections (no subsections) are fine when the topic doesn't warrant splitting.\n4. Add a new `## Citation rules` section after `## Body sections structure`:\n   - `[N]` after specific factual claims (settings, values, frequencies, routing decisions) where N is the zero-indexed moment from the input.\n   - `[N,M]` when a claim draws from multiple moments.\n   - Place citation at end of sentence before period: \"Set the LFO to 3/16th timing [2].\"\n   - Every section must have at least one citation.\n   - Citations only on technical/factual claims, not general observations.\n   - A moment can be cited multiple times.\n5. Rewrite `## Output format` section (line ~163): replace the JSON example with new structure using `body_sections` as a list of objects with heading/content/subsections. Include citation markers in the example prose. Add `body_sections_format: \"v2\"` field.\n6. Update `## Field rules` section (line ~199): change body_sections description from \"Dict of section_name → prose\" to \"List of section objects with heading, content, and optional subsections. Each section's content contains inline [N] citation markers.\"\n7. Verify: the prompt file is valid text, contains the new JSON example structure, has citation rules, and all other sections (voice, tone, plugin rules, etc.) are unchanged.\n\n## Must-Haves\n\n- [ ] Current prompt backed up before changes\n- [ ] body_sections in JSON example is a list of objects with heading/content/subsections\n- [ ] Citation rules section exists with [N] and [N,M] format\n- [ ] body_sections_format: \"v2\" in JSON example\n- [ ] All non-output-format sections preserved unchanged\n- [ ] Subsections shown as optional (empty array or omitted in some example sections)\n  - Estimate: 45m\n  - Files: prompts/stage5_synthesis.txt\n  - Verify: cd /home/aux/projects/content-to-kb-automator && python -c \"import json; t=open('prompts/stage5_synthesis.txt').read(); assert 'body_sections_format' in t; assert 'Citation rules' in t or 'citation rules' in t.lower(); assert '\\\"subsections\\\"' in t; print('Prompt v5 structure OK')\"\n- [x] **T03: Updated test_harness.py word-count/section-count logic for list[BodySection] v2 format and added per-page citation coverage reporting with 13 new tests passing** — Update the test harness word-count and section-count logic to walk the new list-of-objects body_sections structure instead of dict.values(). Add citation coverage reporting using the citation_utils from T01. This closes the slice — the harness can parse and report on v2 synthesis output.\n\n## Steps\n\n1. Read `backend/pipeline/test_harness.py` fully.\n2. Read `backend/pipeline/schemas.py` (updated in T01) and `backend/pipeline/citation_utils.py` (created in T01).\n3. Update line ~283-289 (per-page summary in `run_synthesis`): replace `sections.values()` iteration with walking `BodySection` objects. Word count = sum of `section.content` words + sum of all `subsection.content` words. Section count = len(body_sections). Report subsection count too.\n4. Update line ~457 (metadata total_words): same dict→list-of-objects change for the output metadata calculation.\n5. Add citation reporting after per-page summary: import `validate_citations` from citation_utils, call it with `page.body_sections` and `len(page.moment_indices)`, log citation coverage % and any invalid indices.\n6. Create a small test script `backend/pipeline/test_harness_v2_format.py` that:\n   - Constructs a mock SynthesisResult with the new body_sections format (list of BodySection objects)\n   - Verifies word counting works correctly (known content → expected count)\n   - Verifies citation validation integrates correctly\n   - Does NOT require an LLM call\n\n## Must-Haves\n\n- [ ] Word count logic handles list[BodySection] including subsection content\n- [ ] Section count reports H2 count and subsection count\n- [ ] Citation coverage logged per-page\n- [ ] Metadata total_words uses new structure\n- [ ] Test script passes with mock v2 data\n  - Estimate: 30m\n  - Files: backend/pipeline/test_harness.py, backend/pipeline/test_harness_v2_format.py\n  - Verify: cd /home/aux/projects/content-to-kb-automator && python -m pytest backend/pipeline/test_harness_v2_format.py -v && python -m pytest backend/pipeline/test_citation_utils.py -v\n\n---\n\n### Requirements\nSource: `.gsd/REQUIREMENTS.md`\n\n# Requirements\n\n## R001 — Whisper Transcription Pipeline\n**Status:** validated\n**Description:** Desktop Python script that accepts video files (MP4/MKV), extracts audio via ffmpeg, runs Whisper large-v3 on RTX 4090, and outputs timestamped transcript JSON with segment-level timestamps and word-level timing. Must be resumable.\n**Validation:** Script processes a sample video and produces valid JSON with timestamped segments.\n**Primary Owner:** M001/S01\n\n## R002 — Transcript Ingestion API\n**Status:** validated\n**Description:** FastAPI endpoint that accepts transcript JSON uploads, creates/updates Creator and Source Video records, and stores transcript data in PostgreSQL. Handles new creator detection from folder names.\n**Validation:** POST transcript JSON → 200 OK, records created in DB, file stored on filesystem.\n**Primary Owner:** M001/S02\n\n## R003 — LLM-Powered Extraction Pipeline (Stages 2-5)\n**Status:** validated\n**Description:** Background worker pipeline: transcript segmentation → key moment extraction → classification/tagging → technique page synthesis. Uses OpenAI-compatible API with primary (DGX Sparks Qwen) and fallback (local Ollama) endpoints. Pipeline must be resumable per-video per-stage.\n**Validation:** End-to-end: transcript JSON in → technique pages with key moments, tags, and cross-references out.\n**Primary Owner:** M001/S03\n\n## R004 — Review Queue UI\n**Status:** validated\n**Description:** Admin interface for reviewing extracted key moments: approve, edit+approve, split, merge, reject. Organized by source video for contextual review. Includes mode toggle (review vs auto-publish).\n**Validation:** Admin can review, edit, and approve/reject moments; mode toggle controls whether new moments require review.\n**Primary Owner:** M001/S04\n\n## R005 — Search-First Web UI\n**Status:** validated\n**Description:** Landing page with prominent search bar, live typeahead (results after 2-3 chars), scope toggle (All/Topics/Creators), and two navigation cards (Topics, Creators). Recently added section. Search powered by Qdrant semantic search with keyword fallback.\n**Validation:** User types query → results appear within 500ms, grouped by type, with clickable navigation.\n**Primary Owner:** M001/S05\n\n## R006 — Technique Page Display\n**Status:** validated\n**Description:** Core content unit: header (tags, title, creator, meta), study guide prose (organized by sub-aspects with signal chain blocks and quotes), key moments index (timestamped list), related techniques, plugins referenced. Amber banner for livestream-sourced content.\n**Validation:** Technique page renders with all sections populated from synthesized data.\n**Primary Owner:** M001/S05\n\n## R007 — Creators Browse Page\n**Status:** validated\n**Description:** Filterable creator list with genre filter pills, type-to-narrow, sort options (randomized default, alphabetical, view count). Each row: name, genre tags, technique count, video count, view count. Links to creator detail page.\n**Validation:** Page loads with randomized order, genre filtering works, clicking row navigates to creator detail.\n**Primary Owner:** M001/S05\n\n## R008 — Topics Browse Page\n**Status:** validated\n**Description:** Two-level topic hierarchy (7 top-level categories → sub-topics). Filter input, genre filter pills. Each sub-topic shows technique count and creator count. Clicking sub-topic loads a dedicated page with creator-grouped techniques and breadcrumbs.\n**Validation:** Hierarchy renders, filtering works, sub-topics have dedicated pages at /topics/:category/:subtopic with backend filtering and creator grouping. Verified: M010/S01.\n**Primary Owner:** M001/S05\n\n## R009 — Qdrant Vector Search Integration\n**Status:** validated\n**Description:** Embed key moment summaries, technique page content, and transcript segments in Qdrant using configurable embedding model (nomic-embed-text default). Power semantic search with metadata filtering.\n**Validation:** Semantic search returns relevant results for natural language queries; embeddings update when content changes.\n**Primary Owner:** M001/S03\n\n## R010 — Docker Compose Deployment\n**Status:** validated\n**Description:** Single docker-compose.yml packaging API, web UI, PostgreSQL, and worker services. Follows XPLTD conventions: bind mounts at /vmPool/r/services/, compose at /vmPool/r/compose/chrysopedia/, xpltd_chrysopedia project name, dedicated Docker network.\n**Validation:** `docker compose up -d` brings up all services; data persists across restarts.\n**Primary Owner:** M001/S01\n\n## R011 — Canonical Tag System\n**Status:** validated\n**Description:** Editable canonical tag list (config file) with aliases. Pipeline references tags during classification. New tags can be proposed by LLM and queued for admin approval or auto-added within existing categories.\n**Validation:** Tag list is editable; pipeline uses canonical tags consistently; alias normalization works.\n**Primary Owner:** M001/S03\n\n## R012 — Incremental Content Addition\n**Status:** validated\n**Description:** System handles ongoing content: new videos processed through pipeline, new creators auto-detected, existing technique pages updated when new moments are added for same creator+topic.\n**Validation:** Adding a new video for an existing creator updates their technique pages; new creator folder creates new Creator record.\n**Primary Owner:** M001/S03\n\n## R013 — Prompt Template System\n**Status:** validated\n**Description:** Extraction prompts (stages 2-5) stored as editable configuration files, not hardcoded. Admin can edit prompts and re-run extraction on specific or all videos for calibration.\n**Validation:** Prompt files are editable; re-processing a video with updated prompts produces different output.\n**Primary Owner:** M001/S03\n\n## R014 — Creator Equity\n**Status:** validated\n**Description:** No creator is privileged in the UI. Default sort on Creators page is randomized on every page load. All creators get equal visual weight.\n**Validation:** Refreshing Creators page shows different order each time; no creator gets larger/bolder display.\n**Primary Owner:** M001/S05\n\n## R015 — 30-Second Retrieval Target\n**Status:** active\n**Description:** A producer mid-session can find a specific technique in under 30 seconds from Alt+Tab to reading the key insight.\n**Validation:** Timed test: Alt+Tab → search → read technique → under 30 seconds.\n**Primary Owner:** M001/S05\n\n## R016 — Card Hover Animations & Staggered Entrance\n**Status:** validated\n**Description:** All technique/content cards animate on hover (scale + shadow transition). Card grids use staggered fade-in-up entrance animations on page load.\n**Validation:** Cards visually respond to hover with smooth 200ms transition. Grid cards appear sequentially on page load.\n**Primary Owner:** M011/S01\n\n## R017 — Featured Technique Visual Redesign\n**Status:** validated\n**Description:** Featured Technique section on homepage has a visually distinct treatment (gradient border, glow, or full-bleed) that differentiates it from ordinary cards.\n**Validation:** Featured technique is visually prominent and clearly distinct from regular technique cards.\n**Primary Owner:** M011/S01\n\n## R018 — Random Technique Discovery\n**Status:** validated\n**Description:** A \"Random Technique\" button exists that navigates to a randomly selected technique page.\n**Validation:** Clicking the button loads a different technique each time.\n**Primary Owner:** M011/S01\n\n## R019 — Topics Page Default-Collapsed\n**Status:** validated\n**Description:** Topics page loads with all categories collapsed, showing only category cards. Clicking a category expands its sub-topics with a smooth slide animation.\n**Validation:** Page loads collapsed. Click expands with animation. Click again collapses.\n**Primary Owner:** M011/S02\n\n## R020 — Global Search in Navigation\n**Status:** validated\n**Description:** A compact search input in the navigation bar is available on all pages except the homepage. Cmd+K (or /) keyboard shortcut focuses it from any page.\n**Validation:** Search bar visible in nav on Topics, Creators, Technique, About pages. Cmd+K focuses it.\n**Primary Owner:** M011/S03\n\n## R021 — Mobile Hamburger Menu\n**Status:** validated\n**Description:** Navigation uses a hamburger menu on viewports below 768px with generous touch targets (44×44px minimum).\n**Validation:** Mobile viewport shows hamburger icon. Tapping reveals nav items. Touch targets meet minimum size.\n**Primary Owner:** M011/S03\n\n## R022 — Heading Hierarchy Fix\n**Status:** validated\n**Description:** Every page has exactly one H1 element. Heading levels are sequential (no skips from H1 to H3).\n**Validation:** DOM inspection confirms single H1 per page and sequential heading levels.\n**Primary Owner:** M011/S04\n\n## R023 — Skip-to-Content Link\n**Status:** validated\n**Description:** A visually hidden skip link is the first focusable element on every page, visible on keyboard focus.\n**Validation:** Tab from page load shows \"Skip to content\" link. Clicking it jumps to main content area.\n**Primary Owner:** M011/S04\n\n## R024 — Text Contrast AA Compliance\n**Status:** validated\n**Description:** All text meets WCAG AA contrast ratios (4.5:1 for normal text, 3:1 for large text) against the dark background.\n**Validation:** Secondary text color passes 4.5:1 contrast check against page background.\n**Primary Owner:** M011/S04\n\n## R025 — Page-Specific Document Titles\n**Status:** validated\n**Description:** Each route sets a descriptive document title (e.g., \"Bass — Sound Design — Chrysopedia\", \"COPYCATT — Chrysopedia\").\n**Validation:** Browser tab shows distinct title per page. Navigating between pages updates the title.\n**Primary Owner:** M011/S04\n\n## R026 — Creator Stats Topic-Colored Pills\n**Status:** validated\n**Description:** Creator detail page stats line rendered as topic-colored pill badges instead of run-on text.\n**Validation:** Stats show as visually distinct colored pills grouped by topic category.\n**Primary Owner:** M011/S02\n\n## R027 — Tag Overflow Limit on Cards\n**Status:** validated\n**Description:** Technique cards show a maximum of 4 tags, with a \"+N more\" indicator for additional tags.\n**Validation:** Cards with >4 tags show exactly 4 plus a \"+N more\" badge.\n**Primary Owner:** M011/S02\n\n## R028 — Empty Subtopic Handling\n**Status:** validated\n**Description:** Sub-topics with 0 techniques either hidden by default or display a \"Coming soon\" badge.\n**Validation:** Empty subtopics are visually distinguished or hidden. No dead-end clicks.\n**Primary Owner:** M011/S02\n\n## Denied / Out of Scope\n\n## R029 — Beginner Learning Paths\n**Status:** out-of-scope\n**Description:** Curated beginner learning paths with skill-level tags and \"New to Production?\" section.\n**Validation:** n/a\n**Notes:** Denied — audience knows what they're looking for. Assessment F01.\n\n## R030 — YouTube Deep Links on Key Moments\n**Status:** out-of-scope\n**Description:** Key moment timestamps link to source YouTube videos at the correct time.\n**Validation:** n/a\n**Notes:** Denied — no video URLs in data model / don't want to link out. Assessment F02.\n\n## R031 — Hide Admin Dropdown\n**Status:** out-of-scope\n**Description:** Admin dropdown hidden from public visitors behind auth or flag.\n**Validation:** n/a\n**Notes:** Denied — fine as-is. Assessment F03.\n\n## R032 — CTA Label Changes\n**Status:** out-of-scope\n**Description:** Change \"Start Exploring\" to more descriptive CTA text.\n**Validation:** n/a\n**Notes:** Denied — skipped. Assessment F15.\n\n---\n\n[...truncated 32 sections]\n\n**Match effort to complexity.** A simple slice with 1-2 tasks needs a brief summary and lightweight verification. A complex slice with 5 tasks across multiple subsystems needs thorough verification and a detailed summary. Scale the work below accordingly.\n\nThen:\n1. Use the **Slice Summary** and **UAT** output templates from the inlined context above\n2. If a `GSD Skill Preferences` block is present in system context, use it and the `<available_skills>` catalog in your system prompt to decide which skills to load and follow for this unit, without relaxing required verification or artifact rules.\n3. Run all slice-level verification checks defined in the slice plan. All must pass before marking the slice done. If any fail, fix them first.\n4. If the slice plan includes observability/diagnostic surfaces, confirm they work. Skip this for simple slices that don't have observability sections.\n5. If the slice involved runtime behavior, fill the **Operational Readiness** section (Q8) in the slice summary: health signal, failure signal, recovery procedure, and monitoring gaps. Omit entirely for simple slices with no runtime concerns.\n6. If this slice produced evidence that a requirement changed status (Active → Validated, Active → Deferred, etc.), call `gsd_save_decision` with scope=\"requirement\", decision=\"{requirement-id}\", choice=\"{new-status}\", rationale=\"{evidence}\". Do NOT write `.gsd/REQUIREMENTS.md` directly — the engine renders it from the database.\n7. Write `/home/aux/projects/content-to-kb-automator/.gsd/milestones/M014/slices/S01/S01-SUMMARY.md` (compress all task summaries).\n8. Write `/home/aux/projects/content-to-kb-automator/.gsd/milestones/M014/slices/S01/S01-UAT.md` — a concrete UAT script with real test cases derived from the slice plan and task summaries. Include preconditions, numbered steps with expected outcomes, and edge cases. This must NOT be a placeholder or generic template — tailor every test case to what this slice actually built.\n9. Review task summaries for `key_decisions`. Append any significant decisions to `.gsd/DECISIONS.md` if missing.\n10. Review task summaries for patterns, gotchas, or non-obvious lessons learned. If any would save future agents from repeating investigation or hitting the same issues, append them to `.gsd/KNOWLEDGE.md`. Only add entries that are genuinely useful — don't pad with obvious observations.\n11. Call `gsd_complete_slice` with milestone_id, slice_id, the slice summary, and the UAT result. Do NOT manually mark the roadmap checkbox — the tool writes to the DB and renders the ROADMAP.md projection automatically.\n12. Do not run git commands — the system commits your changes and handles any merge after this unit succeeds.\n13. Update `.gsd/PROJECT.md` if it exists — refresh current state if needed.\n\n**You MUST call `gsd_complete_slice` with the slice summary and UAT content before finishing. The tool persists to both DB and disk and renders `/home/aux/projects/content-to-kb-automator/.gsd/milestones/M014/slices/S01/S01-SUMMARY.md` and `/home/aux/projects/content-to-kb-automator/.gsd/milestones/M014/slices/S01/S01-UAT.md` automatically.**\n\nWhen done, say: \"Slice S01 complete.\"","display":false,"id":"09477337","parentId":"b92c8a07","timestamp":"2026-04-03T00:54:28.318Z"}
{"type":"message","id":"af6799d8","parentId":"09477337","timestamp":"2026-04-03T00:54:36.246Z","message":{"role":"assistant","content":[{"type":"thinking","thinking":"Let me start by reading the task summaries to understand what was actually delivered, then run verification checks.","thinkingSignature":"Eq8CClkIDBgCKkDtyQ7ty5p1Hy/+Aiq2dixwbPKf1ut5XgN6+//L2Ja831/iFZQQKUBsxaimszznYLz+OhZ3KHAjhNVqCbqgnThhMg9jbGF1ZGUtb3B1cy00LTY4ABIMTD96mVy4/LwC+LJkGgwDe/QP5N/j4H4rkiAiMF3cp/CypWPLgSJlL0Zbf92LResvntn/zq5bPgqJSKV1RI0APpPwxYR6M0Y3GN6tpSqDAYSvUrIPpiB63+A4MrIOrJdsn/uofdVR4WBmmNwj0PCTKWP2P9lwhTYWY+HTyMewNlot5W2tBScOwNs+fWyJUSNRYvR8vR748PoK4OJRv+uHJUTCdVH5JmU/3DssQa0slqF7benyJ+9w67hjiwgMN9HP2lxUYFnR9VF+JnHvDvoo4Tl8GAE="},{"type":"text","text":"Let me read the task summaries and verify the slice deliverables."},{"type":"toolCall","id":"toolu_01V3QKAB8AeePmdma7nuBnLs","name":"bash","arguments":{"command":"ls .gsd/milestones/M014/slices/S01/tasks/"}},{"type":"toolCall","id":"toolu_016zPvSUbNnSTcNrFsCVXegr","name":"bash","arguments":{"command":"cd /home/aux/projects/content-to-kb-automator && python -m pytest backend/pipeline/test_citation_utils.py -v 2>&1 | tail -30"}},{"type":"toolCall","id":"toolu_018Fp3QdEccsdxnPnQjJ9GwN","name":"bash","arguments":{"command":"cd /home/aux/projects/content-to-kb-automator && python -m pytest backend/pipeline/test_harness_v2_format.py -v 2>&1 | tail -30"}},{"type":"toolCall","id":"toolu_01EXqoFGgCBkKtCEPw2Gi9YH","name":"bash","arguments":{"command":"cd /home/aux/projects/content-to-kb-automator && python -c \"import json; t=open('prompts/stage5_synthesis.txt').read(); assert 'body_sections_format' in t; assert 'Citation rules' in t or 'citation rules' in t.lower(); assert '\\\"subsections\\\"' in t; print('Prompt v5 structure OK')\""}}],"api":"anthropic-messages","provider":"anthropic","model":"claude-opus-4-6","usage":{"input":3,"output":408,"cacheRead":59865,"cacheWrite":7068,"totalTokens":67344,"cost":{"input":0.000015000000000000002,"output":0.0102,"cacheRead":0.029932499999999997,"cacheWrite":0.044175,"total":0.0843225}},"stopReason":"toolUse","timestamp":1775177668316}}
{"type":"message","id":"a8791526","parentId":"af6799d8","timestamp":"2026-04-03T00:54:36.272Z","message":{"role":"toolResult","toolCallId":"toolu_01V3QKAB8AeePmdma7nuBnLs","toolName":"bash","content":[{"type":"text","text":"T01-PLAN.md\nT01-SUMMARY.md\nT01-VERIFY.json\nT02-PLAN.md\nT02-SUMMARY.md\nT02-VERIFY.json\nT03-PLAN.md\nT03-SUMMARY.md\nT03-VERIFY.json\n"}],"isError":false,"timestamp":1775177676272}}
{"type":"message","id":"13204da9","parentId":"a8791526","timestamp":"2026-04-03T00:54:36.600Z","message":{"role":"toolResult","toolCallId":"toolu_016zPvSUbNnSTcNrFsCVXegr","toolName":"bash","content":[{"type":"text","text":"============================= test session starts ==============================\nplatform linux -- Python 3.12.3, pytest-8.4.2, pluggy-1.6.0 -- /usr/local/bin/python\ncachedir: .pytest_cache\nrootdir: /home/aux/projects/content-to-kb-automator/backend\nconfigfile: pytest.ini\nplugins: asyncio-0.24.0, anyio-4.13.0\nasyncio: mode=Mode.AUTO, default_loop_scope=None\ncollecting ... collected 15 items\n\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_single_markers PASSED [  6%]\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_multi_marker PASSED [ 13%]\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_multi_marker_with_spaces PASSED [ 20%]\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_no_citations PASSED [ 26%]\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_duplicate_indices_deduplicated PASSED [ 33%]\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_returns_sorted PASSED [ 40%]\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_adjacent_markers PASSED [ 46%]\nbackend/pipeline/test_citation_utils.py::TestExtractCitations::test_does_not_match_non_numeric_brackets PASSED [ 53%]\nbackend/pipeline/test_citation_utils.py::TestValidateCitations::test_all_moments_cited PASSED [ 60%]\nbackend/pipeline/test_citation_utils.py::TestValidateCitations::test_out_of_range_index PASSED [ 66%]\nbackend/pipeline/test_citation_utils.py::TestValidateCitations::test_multi_citation_markers PASSED [ 73%]\nbackend/pipeline/test_citation_utils.py::TestValidateCitations::test_no_citations_at_all PASSED [ 80%]\nbackend/pipeline/test_citation_utils.py::TestValidateCitations::test_empty_sections PASSED [ 86%]\nbackend/pipeline/test_citation_utils.py::TestValidateCitations::test_subsection_citations_counted PASSED [ 93%]\nbackend/pipeline/test_citation_utils.py::TestValidateCitations::test_zero_moment_count_with_citations PASSED [100%]\n\n============================== 15 passed in 0.08s ==============================\n"}],"isError":false,"timestamp":1775177676600}}
{"type":"message","id":"44735094","parentId":"13204da9","timestamp":"2026-04-03T00:54:36.601Z","message":{"role":"toolResult","toolCallId":"toolu_018Fp3QdEccsdxnPnQjJ9GwN","toolName":"bash","content":[{"type":"text","text":"============================= test session starts ==============================\nplatform linux -- Python 3.12.3, pytest-8.4.2, pluggy-1.6.0 -- /usr/local/bin/python\ncachedir: .pytest_cache\nrootdir: /home/aux/projects/content-to-kb-automator/backend\nconfigfile: pytest.ini\nplugins: asyncio-0.24.0, anyio-4.13.0\nasyncio: mode=Mode.AUTO, default_loop_scope=None\ncollecting ... collected 13 items\n\nbackend/pipeline/test_harness_v2_format.py::TestWordCounting::test_flat_sections_no_subsections PASSED [  7%]\nbackend/pipeline/test_harness_v2_format.py::TestWordCounting::test_sections_with_subsections PASSED [ 15%]\nbackend/pipeline/test_harness_v2_format.py::TestWordCounting::test_empty_sections_list PASSED [ 23%]\nbackend/pipeline/test_harness_v2_format.py::TestWordCounting::test_section_with_empty_content PASSED [ 30%]\nbackend/pipeline/test_harness_v2_format.py::TestWordCounting::test_metadata_word_count_matches PASSED [ 38%]\nbackend/pipeline/test_harness_v2_format.py::TestSectionCounting::test_section_and_subsection_counts PASSED [ 46%]\nbackend/pipeline/test_harness_v2_format.py::TestCitationIntegration::test_full_coverage PASSED [ 53%]\nbackend/pipeline/test_harness_v2_format.py::TestCitationIntegration::test_partial_coverage PASSED [ 61%]\nbackend/pipeline/test_harness_v2_format.py::TestCitationIntegration::test_invalid_index PASSED [ 69%]\nbackend/pipeline/test_harness_v2_format.py::TestCitationIntegration::test_citations_in_subsections PASSED [ 76%]\nbackend/pipeline/test_harness_v2_format.py::TestCitationIntegration::test_multi_citation_markers PASSED [ 84%]\nbackend/pipeline/test_harness_v2_format.py::TestCitationIntegration::test_no_sections PASSED [ 92%]\nbackend/pipeline/test_harness_v2_format.py::TestSynthesisResultV2::test_round_trip_model_dump PASSED [100%]\n\n============================== 13 passed in 0.08s ==============================\n"}],"isError":false,"timestamp":1775177676600}}
{"type":"message","id":"9853a3d8","parentId":"44735094","timestamp":"2026-04-03T00:54:36.605Z","message":{"role":"toolResult","toolCallId":"toolu_01EXqoFGgCBkKtCEPw2Gi9YH","toolName":"bash","content":[{"type":"text","text":"Prompt v5 structure OK\n"}],"isError":false,"timestamp":1775177676601}}
{"type":"message","id":"a7ffd853","parentId":"9853a3d8","timestamp":"2026-04-03T00:54:41.682Z","message":{"role":"assistant","content":[{"type":"text","text":"All three verification gates pass: 15 citation tests, 13 harness v2 format tests, and prompt structure checks. Let me read the task summaries to build the slice summary."},{"type":"toolCall","id":"toolu_01P42JV1umesxd8nDF42mQTd","name":"bash","arguments":{"command":"cat .gsd/milestones/M014/slices/S01/tasks/T01-SUMMARY.md"}},{"type":"toolCall","id":"toolu_01CNFLEbFXiudoHRgYanJbah","name":"bash","arguments":{"command":"cat .gsd/milestones/M014/slices/S01/tasks/T02-SUMMARY.md"}},{"type":"toolCall","id":"toolu_01K6AM9hLctoG8tBqDmcbtEu","name":"bash","arguments":{"command":"cat .gsd/milestones/M014/slices/S01/tasks/T03-SUMMARY.md"}}],"api":"anthropic-messages","provider":"anthropic","model":"claude-opus-4-6","usage":{"input":1,"output":242,"cacheRead":66933,"cacheWrite":1851,"totalTokens":69027,"cost":{"input":0.000005,"output":0.006050000000000001,"cacheRead":0.033466499999999996,"cacheWrite":0.011568750000000001,"total":0.05109025}},"stopReason":"toolUse","timestamp":1775177676602}}
{"type":"message","id":"89f8d743","parentId":"a7ffd853","timestamp":"2026-04-03T00:54:41.708Z","message":{"role":"toolResult","toolCallId":"toolu_01P42JV1umesxd8nDF42mQTd","toolName":"bash","content":[{"type":"text","text":"---\nid: T01\nparent: S01\nmilestone: M014\nprovides: []\nrequires: []\naffects: []\nkey_files: [\"backend/pipeline/schemas.py\", \"backend/pipeline/citation_utils.py\", \"backend/pipeline/test_citation_utils.py\"]\nkey_decisions: [\"Citations use 0-based indices matching moment list position\", \"validate_citations returns a dict for flexible downstream use\"]\npatterns_established: []\ndrill_down_paths: []\nobservability_surfaces: []\nduration: \"\"\nverification_result: \"Ran python -m pytest backend/pipeline/test_citation_utils.py -v — all 15 tests passed (0.09s). Verified schema instantiation confirms body_sections defaults to list and body_sections_format defaults to 'v2'.\"\ncompleted_at: 2026-04-03T00:50:26.993Z\nblocker_discovered: false\n---\n\n# T01: Added BodySection/BodySubSection schema models, changed SynthesizedPage.body_sections to list[BodySection] with v2 format tag, and created citation_utils with 15 passing tests\n\n> Added BodySection/BodySubSection schema models, changed SynthesizedPage.body_sections to list[BodySection] with v2 format tag, and created citation_utils with 15 passing tests\n\n## What Happened\n---\nid: T01\nparent: S01\nmilestone: M014\nkey_files:\n  - backend/pipeline/schemas.py\n  - backend/pipeline/citation_utils.py\n  - backend/pipeline/test_citation_utils.py\nkey_decisions:\n  - Citations use 0-based indices matching moment list position\n  - validate_citations returns a dict for flexible downstream use\nduration: \"\"\nverification_result: passed\ncompleted_at: 2026-04-03T00:50:26.994Z\nblocker_discovered: false\n---\n\n# T01: Added BodySection/BodySubSection schema models, changed SynthesizedPage.body_sections to list[BodySection] with v2 format tag, and created citation_utils with 15 passing tests\n\n**Added BodySection/BodySubSection schema models, changed SynthesizedPage.body_sections to list[BodySection] with v2 format tag, and created citation_utils with 15 passing tests**\n\n## What Happened\n\nAdded BodySubSection and BodySection Pydantic models to schemas.py for H2/H3 nested page structure. Changed SynthesizedPage.body_sections from dict to list[BodySection] and added body_sections_format='v2'. Created citation_utils.py with extract_citations (regex-based [N] and [N,M] parsing) and validate_citations (coverage stats, invalid/uncited detection). Wrote 15 unit tests covering all edge cases.\n\n## Verification\n\nRan python -m pytest backend/pipeline/test_citation_utils.py -v — all 15 tests passed (0.09s). Verified schema instantiation confirms body_sections defaults to list and body_sections_format defaults to 'v2'.\n\n## Verification Evidence\n\n| # | Command | Exit Code | Verdict | Duration |\n|---|---------|-----------|---------|----------|\n| 1 | `python -m pytest backend/pipeline/test_citation_utils.py -v` | 0 | ✅ pass | 90ms |\n| 2 | `python -c 'from pipeline.schemas import BodySection, BodySubSection, SynthesizedPage; ...'` | 0 | ✅ pass | 500ms |\n\n\n## Deviations\n\nNone.\n\n## Known Issues\n\nNone.\n\n## Files Created/Modified\n\n- `backend/pipeline/schemas.py`\n- `backend/pipeline/citation_utils.py`\n- `backend/pipeline/test_citation_utils.py`\n\n\n## Deviations\nNone.\n\n## Known Issues\nNone.\n"}],"isError":false,"timestamp":1775177681708}}
{"type":"message","id":"a34ed420","parentId":"89f8d743","timestamp":"2026-04-03T00:54:41.709Z","message":{"role":"toolResult","toolCallId":"toolu_01CNFLEbFXiudoHRgYanJbah","toolName":"bash","content":[{"type":"text","text":"---\nid: T02\nparent: S01\nmilestone: M014\nprovides: []\nrequires: []\naffects: []\nkey_files: [\"prompts/stage5_synthesis.txt\", \"prompts/stage5_synthesis.20260403_005044.bak\"]\nkey_decisions: [\"Citations placed end-of-sentence before period, matching academic convention\", \"Sections with subsections use empty-string content field, substance lives in subsections\"]\npatterns_established: []\ndrill_down_paths: []\nobservability_surfaces: []\nduration: \"\"\nverification_result: \"Ran task verification command: python -c asserting body_sections_format, Citation rules, and subsections presence in prompt file — all passed. Ran comprehensive check verifying all 15 original section headings preserved, v2 JSON example has both empty and populated subsections arrays, field rules updated.\"\ncompleted_at: 2026-04-03T00:52:45.317Z\nblocker_discovered: false\n---\n\n# T02: Rewrote stage5_synthesis.txt with v2 body_sections (list-of-objects with heading/content/subsections), citation rules ([N] and [N,M] format), body_sections_format tag, and H3 subsection guidance\n\n> Rewrote stage5_synthesis.txt with v2 body_sections (list-of-objects with heading/content/subsections), citation rules ([N] and [N,M] format), body_sections_format tag, and H3 subsection guidance\n\n## What Happened\n---\nid: T02\nparent: S01\nmilestone: M014\nkey_files:\n  - prompts/stage5_synthesis.txt\n  - prompts/stage5_synthesis.20260403_005044.bak\nkey_decisions:\n  - Citations placed end-of-sentence before period, matching academic convention\n  - Sections with subsections use empty-string content field, substance lives in subsections\nduration: \"\"\nverification_result: passed\ncompleted_at: 2026-04-03T00:52:45.317Z\nblocker_discovered: false\n---\n\n# T02: Rewrote stage5_synthesis.txt with v2 body_sections (list-of-objects with heading/content/subsections), citation rules ([N] and [N,M] format), body_sections_format tag, and H3 subsection guidance\n\n**Rewrote stage5_synthesis.txt with v2 body_sections (list-of-objects with heading/content/subsections), citation rules ([N] and [N,M] format), body_sections_format tag, and H3 subsection guidance**\n\n## What Happened\n\nBacked up the current prompt, then made four targeted edits: added H3 subsection guidance under Body sections structure, added a new Citation rules section with [N] and [N,M] format definitions, rewrote the Output format JSON example with list-of-objects body_sections showing both flat and nested sections with inline citation markers and body_sections_format: v2, and updated the Field rules to describe the new format. All non-output sections preserved unchanged. Prompt grew from 206 to 252 lines.\n\n## Verification\n\nRan task verification command: python -c asserting body_sections_format, Citation rules, and subsections presence in prompt file — all passed. Ran comprehensive check verifying all 15 original section headings preserved, v2 JSON example has both empty and populated subsections arrays, field rules updated.\n\n## Verification Evidence\n\n| # | Command | Exit Code | Verdict | Duration |\n|---|---------|-----------|---------|----------|\n| 1 | `python -c \"...assert 'body_sections_format' in t; assert 'Citation rules' in t...\"` | 0 | ✅ pass | 50ms |\n| 2 | `python3 -c \"...check all sections preserved, new content present...\"` | 0 | ✅ pass | 50ms |\n\n\n## Deviations\n\nNone.\n\n## Known Issues\n\nNone.\n\n## Files Created/Modified\n\n- `prompts/stage5_synthesis.txt`\n- `prompts/stage5_synthesis.20260403_005044.bak`\n\n\n## Deviations\nNone.\n\n## Known Issues\nNone.\n"}],"isError":false,"timestamp":1775177681708}}
{"type":"message","id":"39b67e08","parentId":"a34ed420","timestamp":"2026-04-03T00:54:41.715Z","message":{"role":"toolResult","toolCallId":"toolu_01K6AM9hLctoG8tBqDmcbtEu","toolName":"bash","content":[{"type":"text","text":"---\nid: T03\nparent: S01\nmilestone: M014\nprovides: []\nrequires: []\naffects: []\nkey_files: [\"backend/pipeline/test_harness.py\", \"backend/pipeline/test_harness_v2_format.py\"]\nkey_decisions: [\"Word count includes both section.content and subsection.content; heading text excluded\", \"Citation report uses CITE log tag for grep-friendly structured output\"]\npatterns_established: []\ndrill_down_paths: []\nobservability_surfaces: []\nduration: \"\"\nverification_result: \"Ran both test suites — 28 tests total, all passing: test_harness_v2_format.py (13 passed), test_citation_utils.py (15 passed).\"\ncompleted_at: 2026-04-03T00:54:24.346Z\nblocker_discovered: false\n---\n\n# T03: Updated test_harness.py word-count/section-count logic for list[BodySection] v2 format and added per-page citation coverage reporting with 13 new tests passing\n\n> Updated test_harness.py word-count/section-count logic for list[BodySection] v2 format and added per-page citation coverage reporting with 13 new tests passing\n\n## What Happened\n---\nid: T03\nparent: S01\nmilestone: M014\nkey_files:\n  - backend/pipeline/test_harness.py\n  - backend/pipeline/test_harness_v2_format.py\nkey_decisions:\n  - Word count includes both section.content and subsection.content; heading text excluded\n  - Citation report uses CITE log tag for grep-friendly structured output\nduration: \"\"\nverification_result: passed\ncompleted_at: 2026-04-03T00:54:24.347Z\nblocker_discovered: false\n---\n\n# T03: Updated test_harness.py word-count/section-count logic for list[BodySection] v2 format and added per-page citation coverage reporting with 13 new tests passing\n\n**Updated test_harness.py word-count/section-count logic for list[BodySection] v2 format and added per-page citation coverage reporting with 13 new tests passing**\n\n## What Happened\n\nTwo locations in test_harness.py treated body_sections as a dict. Updated both to walk BodySection objects: per-page summary now counts words from section.content + subsection.content, reports H2/subsection counts separately, and logs citation coverage via validate_citations(). Metadata total_words uses the same structure on serialized dicts. Created test_harness_v2_format.py with 13 tests covering word counting, section counting, citation integration, and SynthesisResult v2 round-trip.\n\n## Verification\n\nRan both test suites — 28 tests total, all passing: test_harness_v2_format.py (13 passed), test_citation_utils.py (15 passed).\n\n## Verification Evidence\n\n| # | Command | Exit Code | Verdict | Duration |\n|---|---------|-----------|---------|----------|\n| 1 | `python -m pytest backend/pipeline/test_harness_v2_format.py -v` | 0 | ✅ pass | 80ms |\n| 2 | `python -m pytest backend/pipeline/test_citation_utils.py -v` | 0 | ✅ pass | 80ms |\n\n\n## Deviations\n\nNone.\n\n## Known Issues\n\nNone.\n\n## Files Created/Modified\n\n- `backend/pipeline/test_harness.py`\n- `backend/pipeline/test_harness_v2_format.py`\n\n\n## Deviations\nNone.\n\n## Known Issues\nNone.\n"}],"isError":false,"timestamp":1775177681713}}
{"type":"message","id":"b9832bab","parentId":"39b67e08","timestamp":"2026-04-03T00:54:49.858Z","message":{"role":"assistant","content":[{"type":"thinking","thinking":"All verifications pass, task summaries are clean with no blockers or deviations. Let me check for any decisions that should be appended.\n\nKey decisions from tasks:\n- T01: Citations use 0-based indices matching moment list position; validate_citations returns a dict\n- T02: Citations placed end-of-sentence before period; Sections with subsections use empty-string content field\n- T03: Word count includes section.content + subsection.content, heading text excluded; CITE log tag for grep-friendly output\n\nLet me check DECISIONS.md for any of these already recorded.","thinkingSignature":"EvEFClkIDBgCKkBIwlvOq+8yJAjzC1+ghE5XuRLBUlGCZYHs+W4G8v3hWrqjPzKT4ZsxYcFxoOMDT8wGTFxe1CaxwTTxip9hfoLnMg9jbGF1ZGUtb3B1cy00LTY4ABIMyITZg0q4IRyNS8thGgx1CMZ0btRLooUHDYgiMBzD7rqEkgnAdZABthurAqIKCcArEFbUZqy80dtPjuuyHOP8G4b0uzx9vrrdhzhYzCrFBB7We457LfJWsQOWtAsMjmITxpR/N4QWU9s77FoBnPDb/3dPWKmJnqejEknmf+qjQOI7w0XhW/nUYJ1sjOcY4BI/SwqkVeS7r0zhOc7hWnbaWsWtBNgOr6ylEKjDB0YFh41QDMut2PFsk89jrULTQGou04qzpxlYibhk3HIihbIZ/Qg1obmJ0e2BOeUlHS3UXIK7T/3oH+iYiHzJBOno/U6PFRnNyDs61Fzy96tbGQ6exRR3v2g7n/fbaqJmclqzaZtT5Yt4i/AD0ecEnbh6A8bQ0DwSFaGAHvcsoC6YmF3eT7SzPxALd2R8eB8Dk2eUmF6JiWL1psGpsxqVlRaz3yHXZrGMUmqPLbZL7qBAAc1hseGg6m0HIAtnCiOAdv9vWo0SMos2TiesMMzhoVpjXfTmUNp27Ctiqo4vUI0EcABD2oOBmPr1ytyB6p3fb8D8xwr4dGG9ZeI/O38PXFfcKCWgMMrcZ3nxXhlBHkA0iYz4qBAjUPcKIi4kyZABYM+MNmCj+8sBRZALdR6L9vQBh2H1rlgTBU1nXhAlkJTypplxlKpKnvmwUngBSQ9CzUm3JTI8hD9b5HiSf5aIFZuMocFF+Na2dYCDKz/vXCWVT/RwPeUaEW7lSZIE/lIhkLWNFmcw3gPjXBs9+4U7HODYLSGxCr88c+FKf7Fp1KqgjrqKVc5t9B8APjfolVlLAJTl8LypoOoCbQOBIo15rvMm6U8xriYBuZ2PzxTYGbe+5eUugxQw/qxojf5CB9CkBcAmGuxodP5uGAE="},{"type":"text","text":"All 28 tests pass, prompt structure validates, no blockers or deviations across any task. Let me check existing decisions before completing."},{"type":"toolCall","id":"toolu_01KYPadCJA9pJncj3ggAUrbf","name":"bash","arguments":{"command":"grep -c \"M014\" .gsd/DECISIONS.md 2>/dev/null || echo \"0\""}},{"type":"toolCall","id":"toolu_01QzHA4MoLNsJqnmtTSYass6","name":"bash","arguments":{"command":"ls backend/pipeline/schemas.py backend/pipeline/citation_utils.py backend/pipeline/test_citation_utils.py backend/pipeline/test_harness.py backend/pipeline/test_harness_v2_format.py prompts/stage5_synthesis.txt prompts/stage5_synthesis.*.bak 2>&1"}}],"api":"anthropic-messages","provider":"anthropic","model":"claude-opus-4-6","usage":{"input":1,"output":365,"cacheRead":68784,"cacheWrite":3133,"totalTokens":72283,"cost":{"input":0.000005,"output":0.009125000000000001,"cacheRead":0.034392,"cacheWrite":0.01958125,"total":0.06310325}},"stopReason":"toolUse","timestamp":1775177681714}}
{"type":"message","id":"48502e15","parentId":"b9832bab","timestamp":"2026-04-03T00:54:49.870Z","message":{"role":"toolResult","toolCallId":"toolu_01KYPadCJA9pJncj3ggAUrbf","toolName":"bash","content":[{"type":"text","text":"0\n0\n"}],"isError":false,"timestamp":1775177689870}}
{"type":"message","id":"279e8bab","parentId":"48502e15","timestamp":"2026-04-03T00:54:49.874Z","message":{"role":"toolResult","toolCallId":"toolu_01QzHA4MoLNsJqnmtTSYass6","toolName":"bash","content":[{"type":"text","text":"backend/pipeline/citation_utils.py\nbackend/pipeline/schemas.py\nbackend/pipeline/test_citation_utils.py\nbackend/pipeline/test_harness.py\nbackend/pipeline/test_harness_v2_format.py\nprompts/stage5_synthesis.20260401_101518.bak\nprompts/stage5_synthesis.20260403_005044.bak\nprompts/stage5_synthesis.txt\n"}],"isError":false,"timestamp":1775177689872}}
{"type":"message","id":"03f9c6c4","parentId":"279e8bab","timestamp":"2026-04-03T00:54:59.156Z","message":{"role":"assistant","content":[{"type":"text","text":"All files present. Two key decisions worth recording from the task summaries: citation index convention and subsection content model."},{"type":"toolCall","id":"toolu_01RRSmB3FtKTz14yBnpnfEho","name":"gsd_decision_save","arguments":{"choice":"0-based indices matching moment list position","decision":"Citation index convention for body_sections v2","made_by":"agent","rationale":"Aligns [N] markers directly with the zero-indexed input moment array from the LLM prompt, avoiding off-by-one errors between prompt input and output parsing.","scope":"architecture","when_context":"M014/S01"}},{"type":"toolCall","id":"toolu_014qu22itjvRvnNJuVvvretu","name":"gsd_decision_save","arguments":{"choice":"Sections with subsections use empty-string content field; substance lives in subsections","decision":"Content model for sections with subsections","made_by":"agent","rationale":"Avoids duplication between section-level content and subsection content. The section heading serves as H2 container; all prose lives in subsection content fields. Sections without subsections use the section content field directly.","scope":"architecture","when_context":"M014/S01"}}],"api":"anthropic-messages","provider":"anthropic","model":"claude-opus-4-6","usage":{"input":1,"output":424,"cacheRead":71917,"cacheWrite":387,"totalTokens":72729,"cost":{"input":0.000005,"output":0.0106,"cacheRead":0.0359585,"cacheWrite":0.0024187500000000003,"total":0.04898224999999999}},"stopReason":"toolUse","timestamp":1775177689873}}
{"type":"message","id":"d50e955b","parentId":"03f9c6c4","timestamp":"2026-04-03T00:54:59.162Z","message":{"role":"toolResult","toolCallId":"toolu_01RRSmB3FtKTz14yBnpnfEho","toolName":"gsd_decision_save","content":[{"type":"text","text":"Saved decision D024"}],"details":{"operation":"save_decision","id":"D024"},"isError":false,"timestamp":1775177699162}}
{"type":"message","id":"e32be56c","parentId":"d50e955b","timestamp":"2026-04-03T00:54:59.165Z","message":{"role":"toolResult","toolCallId":"toolu_014qu22itjvRvnNJuVvvretu","toolName":"gsd_decision_save","content":[{"type":"text","text":"Saved decision D024"}],"details":{"operation":"save_decision","id":"D024"},"isError":false,"timestamp":1775177699163}}
{"type":"message","id":"7e7beb9d","parentId":"e32be56c","timestamp":"2026-04-03T00:55:48.819Z","message":{"role":"assistant","content":[{"type":"text","text":"Now complete the slice."},{"type":"toolCall","id":"toolu_01WokhbtzEMw1Fqx4hGYdVfe","name":"gsd_complete_slice","arguments":{"affects":["S02 — uses updated test harness and prompt for compose mode testing","S04 — pipeline uses the v2 prompt and parses v2 output via BodySection models","S05 — frontend renders list[BodySection] with TOC and citation links"],"deviations":"None.","drillDownPaths":[".gsd/milestones/M014/slices/S01/tasks/T01-SUMMARY.md",".gsd/milestones/M014/slices/S01/tasks/T02-SUMMARY.md",".gsd/milestones/M014/slices/S01/tasks/T03-SUMMARY.md"],"filesModified":[{"description":"Added BodySubSection, BodySection models; changed SynthesizedPage.body_sections to list[BodySection]; added body_sections_format='v2'","path":"backend/pipeline/schemas.py"},{"description":"New file: extract_citations() and validate_citations() functions","path":"backend/pipeline/citation_utils.py"},{"description":"New file: 15 unit tests for citation utilities","path":"backend/pipeline/test_citation_utils.py"},{"description":"Updated word-count and metadata logic from dict iteration to BodySection object walking; added citation coverage reporting","path":"backend/pipeline/test_harness.py"},{"description":"New file: 13 tests for v2 format word counting, section counting, citation integration, round-trip","path":"backend/pipeline/test_harness_v2_format.py"},{"description":"Added Citation rules section, H3 subsection guidance, rewrote Output format to v2 list-of-objects with citations, updated Field rules","path":"prompts/stage5_synthesis.txt"}],"followUps":"None.","keyDecisions":["D024: Citations use 0-based indices matching moment list position","D024: Sections with subsections use empty-string content; substance lives in subsections","Word count includes section.content + subsection.content; heading text excluded","Citation report uses CITE log tag for grep-friendly structured output"],"keyFiles":["backend/pipeline/schemas.py","backend/pipeline/citation_utils.py","backend/pipeline/test_citation_utils.py","backend/pipeline/test_harness.py","backend/pipeline/test_harness_v2_format.py","prompts/stage5_synthesis.txt"],"knownLimitations":"The v2 format is schema-validated and test-harnessed but has not been run against a live LLM yet — that happens when the pipeline compose logic (S04) exercises the prompt end-to-end.","milestoneId":"M014","narrative":"This slice replaced the flat dict-based body_sections format with a structured list-of-objects format supporting H2/H3 nesting and inline citation markers.\n\n**T01 — Schema & Citation Utils:** Added BodySection and BodySubSection Pydantic models to schemas.py. BodySection has heading, content, and optional subsections list. Changed SynthesizedPage.body_sections from dict to list[BodySection] and added body_sections_format='v2' discriminator field. Created citation_utils.py with extract_citations() (regex parser for [N] and [N,M] markers) and validate_citations() (returns coverage stats, invalid indices, uncited moments). 15 unit tests cover all edge cases including multi-citation markers, out-of-range indices, subsection citations, and zero-moment edge case.\n\n**T02 — Prompt Rewrite:** Backed up the existing prompt, then made four targeted edits to stage5_synthesis.txt: (1) H3 subsection guidance in the body sections structure section, (2) new Citation rules section defining [N] and [N,M] format with placement conventions, (3) rewrote the Output format JSON example with v2 structure showing both flat and nested sections with inline citations, (4) updated Field rules to describe the new format. All non-output sections (voice, tone, synthesis philosophy) preserved unchanged.\n\n**T03 — Test Harness Update:** Updated two locations in test_harness.py where body_sections was iterated as a dict — now walks BodySection objects for word counting and metadata. Added subsection count reporting and per-page citation coverage logging with a CITE log tag for grep-friendly output. Created test_harness_v2_format.py with 13 tests covering word counting (flat and nested), section counting, citation integration, and SynthesisResult round-trip serialization.","observabilitySurfaces":["CITE log tag in test harness output for per-page citation coverage reporting"],"oneLiner":"Introduced body_sections v2 format (list-of-objects with H2/H3 nesting and inline [N] citation markers), backed by Pydantic schema, citation validation utility, updated synthesis prompt, and v2-aware test harness — all verified with 28 passing tests.","patternsEstablished":["body_sections v2 format: list[BodySection] with heading/content/subsections, discriminated by body_sections_format='v2'","Citation validation as reusable utility — validate_citations() returns a dict with coverage_pct, invalid_indices, uncited_moments for any consumer","Prompt backup convention: .bak with timestamp suffix before destructive edits"],"provides":["BodySection/BodySubSection Pydantic models for downstream rendering (S05) and DB storage (S03)","citation_utils.extract_citations() and validate_citations() for pipeline quality checks","stage5_synthesis.txt v5 prompt with v2 output format for pipeline execution (S04)","test_harness v2 format support for composition testing (S02)"],"requirementsAdvanced":[],"requirementsInvalidated":[],"requirementsSurfaced":[],"requirementsValidated":[],"requires":[],"sliceId":"S01","sliceTitle":"Synthesis Prompt v5 — Nested Sections + Citations","uatContent":"## UAT: S01 — Synthesis Prompt v5 — Nested Sections + Citations\n\n### Preconditions\n- Working directory: `/home/aux/projects/content-to-kb-automator`\n- Python 3.12+ with pytest available\n- All slice files committed\n\n---\n\n### Test 1: BodySection schema models exist and validate\n\n**Steps:**\n1. Run: `python -c \"from pipeline.schemas import BodySection, BodySubSection; s = BodySubSection(heading='Sub', content='text'); b = BodySection(heading='Main', content='body', subsections=[s]); print(b.model_dump())\"`\n\n**Expected:** Outputs a dict with heading, content, and subsections list containing one subsection object. No import or validation errors.\n\n---\n\n### Test 2: SynthesizedPage uses v2 format\n\n**Steps:**\n1. Run: `python -c \"from pipeline.schemas import SynthesizedPage; p = SynthesizedPage(title='T', slug='t', summary='s', body_sections=[], moment_indices=[], tags=[]); assert p.body_sections_format == 'v2'; assert isinstance(p.body_sections, list); print('v2 format confirmed')\"`\n\n**Expected:** Prints \"v2 format confirmed\". body_sections is list type, body_sections_format defaults to 'v2'.\n\n---\n\n### Test 3: Citation extraction parses all marker formats\n\n**Steps:**\n1. Run: `python -c \"from pipeline.citation_utils import extract_citations; assert extract_citations('claim [0] and [2,3] here') == [0, 2, 3]; assert extract_citations('no markers') == []; assert extract_citations('[1][1][5]') == [1, 5]; print('extraction OK')\"`\n\n**Expected:** All assertions pass. Single markers, multi-markers, deduplication, and empty input handled correctly.\n\n---\n\n### Test 4: Citation validation returns coverage stats\n\n**Steps:**\n1. Run: `python -c \"from pipeline.citation_utils import validate_citations; from pipeline.schemas import BodySection; secs = [BodySection(heading='H', content='claim [0] and [1] here')]; r = validate_citations(secs, 3); assert r['valid'] == True; assert r['total_citations'] == 2; assert r['uncited_moments'] == [2]; assert abs(r['coverage_pct'] - 66.67) < 0.1; print('validation OK')\"`\n\n**Expected:** valid=True (no out-of-range), 2 citations found, moment index 2 uncited, ~66.67% coverage.\n\n---\n\n### Test 5: Full citation test suite passes\n\n**Steps:**\n1. Run: `cd /home/aux/projects/content-to-kb-automator && python -m pytest backend/pipeline/test_citation_utils.py -v`\n\n**Expected:** 15 tests pass, 0 failures.\n\n---\n\n### Test 6: Full harness v2 format test suite passes\n\n**Steps:**\n1. Run: `cd /home/aux/projects/content-to-kb-automator && python -m pytest backend/pipeline/test_harness_v2_format.py -v`\n\n**Expected:** 13 tests pass, 0 failures.\n\n---\n\n### Test 7: Prompt file contains v2 structure\n\n**Steps:**\n1. Run: `python -c \"t=open('prompts/stage5_synthesis.txt').read(); assert 'body_sections_format' in t; assert 'Citation rules' in t; assert '\\\"subsections\\\"' in t; assert '\\\"heading\\\"' in t; print('Prompt v5 OK')\"`\n\n**Expected:** All assertions pass — prompt contains v2 JSON structure, citation rules, and subsection definitions.\n\n---\n\n### Test 8: Prompt backup exists\n\n**Steps:**\n1. Run: `ls prompts/stage5_synthesis.*.bak`\n\n**Expected:** At least one .bak file exists (timestamped backup of pre-v5 prompt).\n\n---\n\n### Edge Case 9: Out-of-range citation index flagged\n\n**Steps:**\n1. Run: `python -c \"from pipeline.citation_utils import validate_citations; from pipeline.schemas import BodySection; secs = [BodySection(heading='H', content='bad ref [99]')]; r = validate_citations(secs, 3); assert r['valid'] == False; assert 99 in r['invalid_indices']; print('out-of-range caught')\"`\n\n**Expected:** valid=False, invalid_indices contains 99.\n\n---\n\n### Edge Case 10: Empty sections produce zero coverage\n\n**Steps:**\n1. Run: `python -c \"from pipeline.citation_utils import validate_citations; r = validate_citations([], 5); assert r['total_citations'] == 0; assert r['coverage_pct'] == 0.0; print('empty OK')\"`\n\n**Expected:** Zero citations, 0% coverage, no crashes on empty input.","verification":"All three task verification commands pass:\n- `python -m pytest backend/pipeline/test_citation_utils.py -v` — 15/15 passed (0.08s)\n- `python -m pytest backend/pipeline/test_harness_v2_format.py -v` — 13/13 passed (0.08s)\n- Prompt structure assertion (body_sections_format, Citation rules, subsections present) — passed\n\nTotal: 28 tests passing, prompt validates structurally."}}],"api":"anthropic-messages","provider":"anthropic","model":"claude-opus-4-6","usage":{"input":1,"output":3087,"cacheRead":72304,"cacheWrite":503,"totalTokens":75895,"cost":{"input":0.000005,"output":0.07717500000000001,"cacheRead":0.036152,"cacheWrite":0.0031437500000000003,"total":0.11647575000000002}},"stopReason":"toolUse","timestamp":1775177699164}}
{"type":"message","id":"822357e9","parentId":"7e7beb9d","timestamp":"2026-04-03T00:55:48.864Z","message":{"role":"toolResult","toolCallId":"toolu_01WokhbtzEMw1Fqx4hGYdVfe","toolName":"gsd_complete_slice","content":[{"type":"text","text":"Completed slice S01 (M014)"}],"details":{"operation":"complete_slice","sliceId":"S01","milestoneId":"M014","summaryPath":"/home/aux/projects/content-to-kb-automator/.gsd/milestones/M014/slices/S01/S01-SUMMARY.md","uatPath":"/home/aux/projects/content-to-kb-automator/.gsd/milestones/M014/slices/S01/S01-UAT.md"},"isError":false,"timestamp":1775177748863}}
{"type":"message","id":"ee172cc8","parentId":"822357e9","timestamp":"2026-04-03T00:55:51.591Z","message":{"role":"assistant","content":[{"type":"text","text":"Slice S01 complete."}],"api":"anthropic-messages","provider":"anthropic","model":"claude-opus-4-6","usage":{"input":1,"output":10,"cacheRead":72807,"cacheWrite":3125,"totalTokens":75943,"cost":{"input":0.000005,"output":0.00025,"cacheRead":0.0364035,"cacheWrite":0.01953125,"total":0.05618975}},"stopReason":"stop","timestamp":1775177748864}}
