project-biosciences-qms-session-log-2026-02-14

---

title: Session Log 2026-02-14 [BIO-QMS] type: reference component_type: session-log version: 1.0.0 audience: contributor status: active summary: Development session log for 2026-02-14 - Project: BIO-QMS (CODITECT Biosciences QMS Platform) keywords:

• session-log
• development-history
• biosciences
• qms
• fda
• hipaa project_id: 'BIO-QMS' tokens: ~500 created: '2026-02-14T01:17:25Z' updated: '2026-02-14T12:19:05Z' tags:
• session-log sessions:
• id: 'fc0f19e9-3a65-4bc2-8754-0f021106ef2c' start: '2026-02-14T01:17:25Z' focus: 'Project Initialization - Biosciences QMS Platform' moe_confidence: 0.900 moe_classified: 2026-02-14

---

Session Log - 2026-02-14 [BIO-QMS]

Consolidated development session log. All timestamps are ISO 8601 UTC. Project: BIO-QMS (CODITECT Biosciences QMS Platform) GitHub: https://github.com/coditect-ai/coditect-biosciences-qms-platform Path: submodules/dev/coditect-biosciences-qms-platform

---

2026-02-14T01:17:25Z - Session Start

Session ID: fc0f19e9-3a65-4bc2-8754-0f021106ef2c Author: Claude (Opus 4.6) Focus: Project Initialization - Biosciences QMS Platform

Project Genesis:

• Research artifacts created 2026-02-13 in coditect-core/analyze-new-artifacts/coditect-bioscience-workorders-research/
• 62 numbered artifacts: 34 markdown docs + 25 JSX dashboards + 3 meta documents
• Covers: executive/business case, market analysis (TAM $3.5B), architecture, compliance (FDA 21 CFR Part 11, HIPAA, SOC 2), agent orchestration, interactive dashboards
• Core architecture: 9-state FSM, 20+ PostgreSQL entities, 7 AI agent nodes, 3 regulatory frameworks, 6 RBAC roles

---

2026-02-14T01:17:25Z - [H.0] Project Setup Complete

Author: Claude (Opus 4.6)

Actions Completed:

Step	Detail	Evidence
GitHub repo created	coditect-ai/coditect-biosciences-qms-platform (private)	https://github.com/coditect-ai/coditect-biosciences-qms-platform
83 artifacts organized	Structured into docs/ (9 subdirs), dashboards/ (4 subdirs), prompts/, research/, config/	commit a8749c2
CODITECT symlinks	.coditect, .claude, CLAUDE.md — standard pattern matching coditect-cli	verified
Initial commit pushed	a8749c2 on origin/main — 87 files, 35,424 insertions	git push -u origin main
Git submodule added	submodules/dev/coditect-biosciences-qms-platform in rollout-master	git submodule status
projects.db registered	ID 5, UUID 4f62fde2-a18f-4e39-a28a-4ec8f20b87ca, type=submodule, parent=coditect-core	SELECT * FROM projects WHERE id=5
Session log created	BIO-QMS project-scoped log initialized	this file

Project Structure:

submodules/dev/coditect-biosciences-qms-platform/
├── .claude -> .coditect
├── .coditect -> ~/.coditect
├── CLAUDE.md -> ~/.coditect/CLAUDE.md
├── README.md
├── docs/
│   ├── executive/     (6)   ├── compliance/    (4)
│   ├── market/        (6)   ├── agents/        (3)
│   ├── product/       (2)   ├── reference/     (4)
│   ├── architecture/  (6)   ├── operations/   (13)
│   └── state-machine/ (2)
├── dashboards/
│   ├── system/        (8)   ├── business/      (8)
│   ├── compliance/    (4)   └── planning/      (5)
├── prompts/           (6)
├── research/          (3)
└── config/            (1)

Status: Project initialized, ready to build. Next: Begin implementation per 62-unified-execution-plan.md

• Task(s): H.0

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2026-02-14T01:25:49Z - [H.0] Document Compliance - Frontmatter, Footer, Classification (INCEPTION)

Author: Claude (Opus 4.6)

Instruction: Every document in BIO-QMS must be updated to comply with CODITECT coditect-core-standards:

1. Add/update YAML frontmatter per FRONTMATTER-STANDARD.md (type, title, version, status, created, updated, author, audience, summary, keywords, tags)
2. Add standard footer to every document: Copyright 2026 AZ1.AI Inc. | Developer: Hal Casteel, CEO/CTO | CODITECT-BIO-QMS is part of the CODITECT product suite
3. Run /classify on each document to populate MoE fields (component_type, moe_confidence, moe_classified)
4. Ensure all artifacts comply with coditect-core-standards templates

Scope: 83 artifacts (34 markdown + 25 JSX + remaining files)

---

2026-02-14T01:34:46Z - [H.0] Document Compliance Complete + Symlink Safety Directive

Author: Claude (Opus 4.6)

Frontmatter & Footer Updates:

• Bulk update script (/tmp/update-bio-qms-docs.py) processed all 83 files
• 57 markdown files: CODITECT-compliant YAML frontmatter added (type, title, version, status, author, audience, summary, category, keywords, tags, created, updated)
• 26 JSX files: metadata header comments added
• All files: copyright footer appended (Copyright 2026 AZ1.AI Inc. | CODITECT-BIO-QMS)
• Committed: f365495 — "docs: Add CODITECT-compliant frontmatter and copyright footers to all 83 artifacts"
• Pushed to origin/main

CRITICAL INCIDENT — Symlink Contamination (Resolved):

• The bulk update script followed CLAUDE.md symlink chain: CLAUDE.md → ~/.coditect/CLAUDE.md → ~/Library/Application Support/CODITECT/core/CLAUDE.md
• Protected installation CLAUDE.md was contaminated with BIO-QMS frontmatter and copyright footer
• Fix: Restored from submodules/core/coditect-core/CLAUDE.md (clean copy)
• Prevention: Added new safety directive to CLAUDE.md v3.3.0: "NEVER FOLLOW SYMLINKS WHEN BULK-PROCESSING FILES"
• Directive provides detection patterns: os.path.islink() (Python), [ -L "$file" ] (shell)
• Committed in coditect-core: bf02777a
• /sync pushed to all locations (GitHub, parent, protected installation)

Files Modified:

• 83 files in submodules/dev/coditect-biosciences-qms-platform/
• submodules/core/coditect-core/CLAUDE.md (v3.3.0 — symlink safety directive)

Remaining: Run /classify on each BIO-QMS document for MoE field population

---

2026-02-14T01:37:07Z - [H.0] MoE Classification Complete + CLAUDE.md v3.3.0 Safety Directive

Author: Claude (Opus 4.6)

MoE Classification:

• Ran /classify . -r --update-frontmatter --exclude "CLAUDE.md" on entire BIO-QMS project
• 56/56 markdown files classified (CLAUDE.md symlink correctly excluded)
• 26 JSX files: not classifiable (no YAML frontmatter — metadata in JSX comments)
• Classification breakdown: 43 reference (76.8%), 5 adr (8.9%), 5 workflow (8.9%), 3 guide (5.4%)
• All frontmatter updated with moe_confidence and moe_classified fields
• Generated internal/project/track-skills-index.md
• 0 errors, 0 escalations
• Committed: ecbbac9 — pushed to origin/main

CLAUDE.md v3.3.0 — New Safety Directive (lines 33-37):

NEVER FOLLOW SYMLINKS WHEN BULK-PROCESSING FILES. CLAUDE.md, .coditect, and .claude in project directories are symlinks to the protected installation. Any script, bulk edit, or batch operation that writes to files MUST skip symlinks: check with os.path.islink() (Python) or [ -L "$file" ] (shell).

• Live in: protected installation, coditect-core submodule, GitHub
• Committed: bf02777a via /sync

All Document Compliance Tasks Complete:

• YAML frontmatter per FRONTMATTER-STANDARD.md — 57 files
• Copyright footer — 83 files
• MoE classification — 56 files
• Symlink safety directive — CLAUDE.md v3.3.0
• All pushed to GitHub

---

2026-02-14T01:40:18Z - [H.0] Copyright in Frontmatter — All Documents Complete

Author: Claude (Opus 4.6)

What: Added copyright, developer, product, and classification fields to the frontmatter of every document and script in the BIO-QMS project. Copyright now exists in both the YAML/JSX frontmatter (machine-readable) and the document footer (human-readable).

Scope:

• 56 markdown files: 4 new YAML frontmatter fields
• 26 JSX files: 3 new JSDoc header fields (@copyright, @developer, @classification)
• 1 symlink skipped: CLAUDE.md (per v3.3.0 safety directive)

Example — Markdown YAML Frontmatter (final state):

---
title: 'Work Order Management System — Executive Summary'
type: reference
component_type: reference
version: 1.0.0
status: active
author: 'Hal Casteel'
audience: user
summary: 'Executive & Business: Work Order Management System — Executive Summary'
category: executive
keywords:
- bioscience-qms
- work-order
- coditect
- executive-summary
- business-case
- investment
tags:
- reference
- executive
- bio-qms
created: '2026-02-13'
updated: '2026-02-14'
moe_confidence: 0.583
moe_classified: 2026-02-14
copyright: 'Copyright 2026 AZ1.AI Inc. All rights reserved.'
developer: 'Hal Casteel, CEO/CTO'
product: 'CODITECT-BIO-QMS'
classification: 'Internal - Confidential'
---

Example — JSX Header Comment (final state):

/**
 * @title Tech Architecture Analyzer
 * @type reference
 * @category dashboard-system
 * @version 1.0.0
 * @status active
 * @author Hal Casteel
 * @product CODITECT-BIO-QMS
 * @created 2026-02-13
 * @updated 2026-02-14
 * @summary Interactive System Dashboard: Tech Architecture Analyzer
 * @keywords bioscience-qms, work-order, coditect, dashboard, react
 * @copyright Copyright 2026 AZ1.AI Inc. All rights reserved.
 * @developer Hal Casteel, CEO/CTO
 * @classification Internal - Confidential
 */

Evidence:

• BIO-QMS commit: eb58057 — pushed to origin/main
• Rollout-master submodule pointer updated and committed

---

2026-02-14T02:15:00Z - [H.0] Document Inventory Tracker Created (Artifact #30)

Author: Claude (Opus 4.6)

What: Created the interim document inventory tracker at docs/reference/30-document-inventory.md. This is the master reference for all 83 artifacts in the BIO-QMS initial data set.

Document Contents:

• Summary table by category (18 categories)
• 17 detailed sections with per-file tables tracking: name, type, description, version, created, modified
• Cross-reference index mapping all 83 artifact numbers to file paths
• Covers all 57 markdown files and 26 JSX dashboards
• Plain language descriptions suitable for both human review and agentic cross-reference

MoE Classification:

• Classifier assigned type: agent (67% confidence) — incorrect
• Manually corrected to type: reference (known MoE quirk with inventory/catalog documents)
• moe_confidence: 0.667, moe_classified: 2026-02-14

Evidence:

• BIO-QMS commits: 2b3aeaa (create), 0605845 (classify fix)
• Pushed to origin/main
• File: docs/reference/30-document-inventory.md (406 lines)

Status: Complete. This document fills artifact slot #30 and serves as the interim tracker for writing the final 30-document-inventory.

• Task(s): H.0

---

2026-02-14T02:20:07Z - [H.0] README.md v2.0.0 — Full Rewrite with Executive Summary, Directory Tree, and Correct Links

Author: Claude (Opus 4.6)

What: Complete rewrite of README.md (v1.0.0 → v2.0.0) for the BIO-QMS project. The previous README had broken links (flat paths instead of relative directory paths), outdated file counts (62 instead of 83), a missing executive summary, and no directory tree.

Changes:

• Added "What Is BIO-QMS?" executive summary — explains the product, problem ($650K–$3.95M/yr manual cost), solution (7 AI agents + 9-state FSM), core architecture, market opportunity (TAM $3.5B), and unit economics (ACV $150K–$500K, LTV:CAC 18.7x)
• Added full project directory tree showing all 83 artifacts organized into 7 top-level directories
• Fixed all internal links to use correct relative paths (docs/executive/01-executive-summary.md not 01-executive-summary.md)
• Fixed artifact #59 — was listed as 59-master-readme.md, actually config/59-coditect-system-prompt-v8.md
• Added 21 missing artifacts: operations docs (63–75), prompts (76–79), business model (60)
• Reorganized artifact index into 16 categories matching directory structure
• Added navigation rows for security architecture, API endpoints, testing, deployment
• Updated file count from 62 to 83
• All links are now clickable relative paths that work from GitHub

Evidence:

• BIO-QMS commit: 9407e27 — pushed to origin/main

• File: README.md (480 lines, up from 312)

• Task(s): H.0

---

2026-02-14T02:42:22Z - [H.0] Session Completion — All BIO-QMS Document Compliance and README Tasks Done

Author: Claude (Opus 4.6)

Session Summary: This session completed the full document compliance and project setup lifecycle for BIO-QMS:

1. Project setup — GitHub repo created, 83 artifacts organized, symlinks, projects.db registration
2. Frontmatter compliance — YAML frontmatter on 57 markdown files, JSDoc headers on 26 JSX files
3. Copyright & classification fields — Added to all 82 non-symlink files
4. MoE classification — 56 markdown files classified, symlink safety directive added to CLAUDE.md v3.3.0
5. Document inventory — Created docs/reference/30-document-inventory.md (406 lines, artifact #30)
6. README.md v2.0.0 — Full rewrite with executive summary, directory tree, 16 categorized sections, correct relative links
7. Final classify + push — README classified as reference (55%, Judge-approved), commit 5661c47 pushed

All Commits This Session:

Commit	Description
a8749c2	Initial commit — 87 files, structured layout
f365495	Frontmatter + copyright footers on 83 files
ecbbac9	MoE classification on 56 files
eb58057	Copyright fields in frontmatter of 82 files
2b3aeaa	Document inventory tracker (artifact #30)
0605845	Fix MoE classification agent→reference
9407e27	README.md v2.0.0 rewrite
5661c47	Track-skills-index timestamp from /classify

Status: All tasks complete. Project ready for implementation per docs/product/62-unified-execution-plan.md.

• Task(s): H.0

---

2026-02-14T03:33:18Z - [H.0] Dashboard Viewer Setup — Vite + Tailwind + Header/Footer/Dark Mode

Author: Claude (Opus 4.6)

What: Set up a local Vite dev server with Tailwind CSS to preview all 26 JSX dashboards in-browser. Added a polished viewer shell with CODITECT-branded header, copyright footer, and light/dark mode toggle.

Dashboard Viewer Features:

• Header: CODITECT logo (left), "CODITECT Bioscience Quality Management System" title, subtitle with compliance badges (FDA/HIPAA/SOC 2), sun/moon dark mode toggle (right)
• Sidebar: 4-category navigation (System 8, Compliance 4, Business 8, Planning 6) with active state highlighting
• Main area: Lazy-loaded dashboard rendering with Suspense fallback
• Footer: Copyright 2026 AZ1.AI Inc. | Developer: Hal Casteel, CEO/CTO | CODITECT-BIO-QMS | Internal — Confidential
• Dark mode: System preference detection + manual toggle, theme propagated to all viewer chrome

Dependencies Installed:

Package	Version	Purpose
react	19.2.4	Core React
react-dom	19.2.4	DOM rendering
lucide-react	0.564.0	Icons (dashboards + viewer)
vite	7.3.1	Dev server + HMR
@vitejs/plugin-react	5.1.4	JSX compilation
tailwindcss	4.1.18	Utility CSS (used by all 26 dashboards)
@tailwindcss/vite	4.1.18	Vite integration

JSX Code Review:

• All 26 dashboards analyzed for issues (parallel code-reviewer agents)
• 1 issue found and fixed: bare <1x> in 51-business-case-calculator.jsx:456 parsed as JSX tag — escaped to <1x
• Vite build: zero errors after fix

Files Created/Modified:

• package.json — project manifest with 3 deps + 4 devDeps
• package-lock.json — lockfile
• vite.config.js — Vite + React + Tailwind plugins
• index.html — HTML entry point
• viewer.jsx — Dashboard viewer app with header/footer/dark mode
• styles.css — Tailwind import
• assets/coditect-logo.png — 500x500 CODITECT logo
• dashboards/business/51-business-case-calculator.jsx — JSX escape fix

Usage: npm run dev → opens http://localhost:5173/

Commits:

Commit	Description
deb55c1	Initial package.json + react/lucide-react deps
dd8dd1e	Vite viewer with CODITECT header/footer, dark mode, lazy loading
2bf286f	Tailwind v4 CSS theme tokens across all 26 dashboards

• Task(s): H.0

---

2026-02-14T04:18:00Z - [H.0] Tailwind v4 CSS Theme Token System — Complete Conversion + Build + Push

Author: Claude (Opus 4.6)

What: Implemented a comprehensive Tailwind CSS v4 theme token system across all 26 dashboards. Converted all hardcoded Tailwind classes and inline hex colors to semantic CSS custom property tokens, enabling universal dark mode with zero additional CSS per dashboard.

Theme Token Architecture:

• Token file: styles.css with Tailwind v4 @theme directive
• Neutral tokens: --color-surface, --color-heading, --color-body, --color-label, --color-muted, --color-dim, --color-faint, --color-line, --color-line-soft, --color-line-hard
• 12 accent color groups: blue, red, amber, green, emerald, sky, indigo, purple, orange, teal, yellow, pink — each with -fg, -tint, -line variants
• Dark mode: All tokens overridden in .dark selector — toggle via document.documentElement.classList.toggle("dark")

Conversion Stats (5 passes):

Pass	Method	Scope	Lines Changed
1	Tailwind class→token batch script	23 dashboard files	2,236
2	Context-aware inline hex→var()	3 anomaly files (33, 42, 47)	230
3	Quoted hex→var() regex sweep	3 anomaly files	74
4	Manual #fff→var(--color-surface)	3 anomaly files (backgrounds)	4
5	CSS shorthand hex→var()	3 anomaly files	43
Total		26 files	2,587

Pink tokens added to styles.css (light + dark) for compliance category colors in file 33.

Remaining "#fff" (4 instances, intentional): White text on colored badges — converting would break contrast in dark mode.

Final verification: ZERO remaining 6-digit hex values in all 3 anomaly files.

Build: npx vite build — success in 10.75s, 64 chunks, zero errors.

Commits:

Commit	Description
dd8dd1e	feat: Add Vite dashboard viewer with CODITECT header/footer and dark mode
2bf286f	style: Convert all 26 dashboards to Tailwind v4 CSS theme tokens

Both pushed to origin/main.

Files Created/Modified:

• styles.css — Tailwind v4 @theme with 12 accent color groups (light/dark)
• viewer.jsx — Rewritten with semantic token classes
• index.html, vite.config.js — Viewer infrastructure
• public/coditect-logo.png — Brand asset
• .gitignore — Added nested submodules/ exclusion
• 26 dashboard files — All converted to semantic tokens

Status: Dashboard viewer and theme system complete. All 26 dashboards render correctly in both light and dark mode.

• Task(s): H.0

---

2026-02-14T04:28:31Z - [H.0] Website Content Plan Updated (56 → 83 Artifacts)

Author: Claude (Opus 4.6)

Updated docs/reference/31-website-plan.md (v1.0 → v1.1) to reflect expanded artifact inventory.

Changes made:

Section	What Changed
Header	"56 artifacts" → "83 artifacts (57 markdown + 26 JSX dashboards)"
Section 1.1 Nav	Added: Unified Execution Plan (62) to Product, Project Command Center (60) to Product dashboards, Research section (R1/R2), Configuration section (59)
Section 1.1 Reference	"81 artifacts" → "83 artifacts"
Section 1.2 URLs	Added 26 new routes: investor (60, 61), engineering operations (63-73), compliance (74, 70, 75), product (60 dashboard, 62), build (57-58, 76-79), research (R1, R2), config (59)
Section 4.1 Search	"56 documents" → "83 artifacts"
Section 4.2 Pipeline	Replaced flat file list with structured directory tree showing 10 doc directories, 4 dashboard directories, prompts, research, config
Section 4.5	NEW: Existing Viewer Implementation — documents Vite 7.3.1, React 19.2.4, Tailwind CSS v4 theme tokens, dark mode, CODITECT branding
Section 5 Phase 1	"31 markdown artifacts" → "57 markdown artifacts"
Section 5 Phase 2	"25 JSX dashboards" → "26 JSX dashboards"
Section 6 Metrics	"56 artifacts" → "83 artifacts"
Metadata	version 1.0.0 → 1.1.0, last updated 2026-02-14

Files Modified:

• docs/reference/31-website-plan.md

Classification: /classify confirmed reference type.

• Task(s): H.0

---

2026-02-14T05:30:14Z - [H.0] BIO-QMS Comprehensive Project Plan — TRACK Infrastructure + ADR-195/196

Author: Claude (Opus 4.6)

What: Built complete project plan infrastructure for BIO-QMS with 6 TRACK files (143 tasks), MASTER-TRACK-INDEX, and two ADRs in coditect-core.

TRACK Files Created (BIO-QMS):

Track	File	Tasks	Sprint	Agent
A	TRACK-A-PRESENTATION-PUBLISHING.md	34	S1-S3	frontend-react-typescript-expert
B	TRACK-B-COMPETITIVE-INTELLIGENCE-GTM.md	24	S2-S3	competitive-analyst
C	TRACK-C-TECHNICAL-FOUNDATION.md	30	S3-S6	senior-architect
D	TRACK-D-COMPLIANCE-SECURITY.md	21	S3-S6	security-specialist
E	TRACK-E-OPERATIONS-DEPLOYMENT.md	16	S5-S6	devops-engineer
F	TRACK-F-DOCUMENTATION-TRAINING.md	18	S3+	codi-documentation-writer
Index	MASTER-TRACK-INDEX.md	—	—	Keywords + dependencies

ADRs Created (coditect-core):

ADR	Title	Key Decisions
ADR-195	Push-Button Documentation Publishing Platform	D1: unified/remark pipeline, D2: publish.json manifest, D3: unified viewer, D4: MiniSearch/MCP search, D5: presentation mode, D6: Cloud Run deploy, D7: npm package
ADR-196	NDA-Gated Conditional Access Control	D1: NDARecord model, D2: DocumentViewToken + Redis cache, D3: AuditLog, D4: API endpoints, D5: client auth flow, D6: local bypass, D7: customer self-service

Sprint Plan (6 sprints, 12 weeks):

• S1 (wk 1-2): Presentation-grade local website (A.1-A.3)
• S2 (wk 3-4): Cloud publishing + competitive analysis (A.4, B.1, B.2)
• S3 (wk 5-6): Auth + GTM + technical foundation start (A.5-A.6, B.2-B.4, C.1, D.1)
• S4-S6 (wk 7-12): Full technical build (C.1-C.5, D.2-D.5, E.1-E.4, F.1-F.4)

Files Created:

• internal/project/plans/tracks/MASTER-TRACK-INDEX.md
• internal/project/plans/tracks/TRACK-A-PRESENTATION-PUBLISHING.md
• internal/project/plans/tracks/TRACK-B-COMPETITIVE-INTELLIGENCE-GTM.md
• internal/project/plans/tracks/TRACK-C-TECHNICAL-FOUNDATION.md
• internal/project/plans/tracks/TRACK-D-COMPLIANCE-SECURITY.md
• internal/project/plans/tracks/TRACK-E-OPERATIONS-DEPLOYMENT.md
• internal/project/plans/tracks/TRACK-F-DOCUMENTATION-TRAINING.md
• coditect-core/internal/architecture/adrs/ADR-195-push-button-documentation-publishing.md
• coditect-core/internal/architecture/adrs/ADR-196-nda-gated-conditional-access.md

Status: All TRACK files and ADRs written. Ready for commit and push.

• Task(s): H.0

---

2026-02-14T05:39:46Z - [H.0] BIO-QMS Project Plan — Commits & Sync Complete

Author: Claude (Opus 4.6)

Step 9: BIO-QMS Track Files Committed & Pushed

• Commit: 8705d4e — feat: Add 6 TRACK files with 143 tasks + MASTER-TRACK-INDEX
• 7 files, 1,339 insertions
• Pushed to github.com/coditect-ai/coditect-biosciences-qms-platform

Step 10: coditect-core ADRs Synced via /sync

• Core commit: 5855b958 — feat(docs): Update 2 docs (ADR-195 + ADR-196)
• Parent commit: 37890f80 — submodule pointer update
• Protected installation updated to 5855b958
• Integrity scan: 5,697 files scanned, 2 created, 0 errors

All 10 execution plan steps complete.

Summary of BIO-QMS Project Plan Deliverables:

Deliverable	Location	Status
MASTER-TRACK-INDEX	internal/project/plans/tracks/MASTER-TRACK-INDEX.md	Committed 8705d4e
TRACK-A (34 tasks)	internal/project/plans/tracks/TRACK-A-PRESENTATION-PUBLISHING.md	Committed 8705d4e
TRACK-B (24 tasks)	internal/project/plans/tracks/TRACK-B-COMPETITIVE-INTELLIGENCE-GTM.md	Committed 8705d4e
TRACK-C (30 tasks)	internal/project/plans/tracks/TRACK-C-TECHNICAL-FOUNDATION.md	Committed 8705d4e
TRACK-D (21 tasks)	internal/project/plans/tracks/TRACK-D-COMPLIANCE-SECURITY.md	Committed 8705d4e
TRACK-E (16 tasks)	internal/project/plans/tracks/TRACK-E-OPERATIONS-DEPLOYMENT.md	Committed 8705d4e
TRACK-F (18 tasks)	internal/project/plans/tracks/TRACK-F-DOCUMENTATION-TRAINING.md	Committed 8705d4e
ADR-195	coditect-core/internal/architecture/adrs/ADR-195-push-button-documentation-publishing.md	Synced 5855b958
ADR-196	coditect-core/internal/architecture/adrs/ADR-196-nda-gated-conditional-access.md	Synced 5855b958

Next Session: Execute Track B (Prompts 76/77/78) for competitive intelligence & GTM strategy.

• Task(s): H.0

---

2026-02-14T06:23:00Z - [H.0] Full Specification Complete — 10 New TRACK Files (G-P), 198 New Tasks, 341 Total

Author: Claude (Opus 4.6)

What: Expanded BIO-QMS project plan from 6 tracks (A-F, 143 tasks) to 16 tracks (A-P, 341 tasks) covering complete regulated SaaS product scope. All 10 new tracks written, classified, and verified per plan v3.0.0.

Gap Analysis Findings: Original 6 tracks covered only frontend, competitive intel, backend, compliance, ops, and docs — missing revenue operations, customer lifecycle, sales, product analytics, platform reliability, data/BI, security operations, legal, partner ecosystem, and accessibility/i18n. 43 BIO-QMS research documents were analyzed by 3 parallel Explore agents to extract detailed specifications.

New TRACK Files Created:

Track	File	Tasks	Sprint	Primary Agent
G	TRACK-G-REVENUE-BILLING-OPERATIONS.md	24	S5-S7	payment-systems-specialist
H	TRACK-H-CUSTOMER-OPERATIONS.md	22	S5-S8	customer-onboarding
I	TRACK-I-SALES-BUSINESS-DEVELOPMENT.md	20	S4-S7	sales-workflow
J	TRACK-J-PRODUCT-MANAGEMENT-ANALYTICS.md	22	S6-S8	product-analytics-specialist
K	TRACK-K-PLATFORM-RELIABILITY-MAINTENANCE.md	20	S6-S9	sre-on-call-assistant
L	TRACK-L-DATA-BUSINESS-INTELLIGENCE.md	20	S7-S9	data-pipeline-specialist
M	TRACK-M-SECURITY-OPERATIONS.md	18	S6-S9	incident-response-specialist
N	TRACK-N-LEGAL-REGULATORY-OPERATIONS.md	18	S5-S8	regulatory-change-monitor
O	TRACK-O-PARTNER-ECOSYSTEM.md	16	S7-S10	partner-onboarding
P	TRACK-P-ACCESSIBILITY-I18N.md	18	S4-S10	accessibility-testing-specialist

Updated Files:

• MASTER-TRACK-INDEX.md — v1.0.0 → v2.0.0: 16 tracks, keyword index, 18 cross-track dependencies, 10-sprint plan
• track-skills-index.md — Updated by /classify
• TRACK-A through TRACK-F — Frontmatter updated by /classify

Verification:

• ls TRACK-*.md | wc -l → 16 files
• grep -c '\[ \]' TRACK-*.md → 341 total tasks (34+24+30+21+16+18+24+22+20+22+20+20+18+18+16+18)
• /classify → 17 files classified, 0 errors, all reference type

Sprint Plan (10 sprints, 20 weeks):

• S1-S3: Presentation, competitive intel, frontend, auth
• S4-S5: Backend core, billing, onboarding, sales enablement, legal, a11y audit
• S6-S7: Operations, payments, security, i18n, data warehouse, SLA, partners
• S8-S9: Docs, BI dashboards, marketplace, l10n, chaos engineering, regulatory reporting
• S10: Feedback systems, partner ops, accessibility automation

Commits:

Commit	Repo	Description
a5b9e8f	BIO-QMS	feat: Add 10 new TRACK files (G-P) expanding plan to 341 tasks across 16 tracks
7d94e55c	rollout-master	chore(submodules): Update coditect-biosciences-qms-platform to a5b9e8f

Status: All 16 TRACK files committed and pushed. Full specification complete.

• Task(s): H.0

---

2026-02-14T09:01:18Z - [H.0] Agent-to-Subtask Mapping Document — 341 Tasks → 78 Agents

Author: Claude (Opus 4.6)

What: Created comprehensive MoE agent-to-subtask mapping document at internal/project/plans/AGENT-SUBTASK-MAPPING.md (1,085 lines). Maps every one of the 341 subtasks across all 16 tracks (A-P) to specific primary and secondary CODITECT agents.

Document Contents:

• Agent Roster: Top 15 agents by task count + full 78-agent reference list
• Per-Track Mapping Tables: 16 sections with task ID, description, primary agent, secondary agent for every subtask
• Cross-Track Utilization Summary: Agent concurrency analysis per sprint
• Bottleneck Analysis: Identifies frontend-react-typescript-expert (38 tasks, peaks S6-S7) and backend-development (28 tasks, peaks S5-S6) as highest concurrency risks
• Sprint Distribution: Task counts per sprint (S1-S10)
• Verification Table: 16 tracks with task counts summing to 341

Key Statistics:

Metric	Value
Total subtasks mapped	341
Unique agents assigned	78
Tasks with secondary agent	142 (42%)
Tasks with single agent	199 (58%)
Top agent	frontend-react-typescript-expert (38 tasks)
Peak concurrency sprint	S6-S7

Files Created:

• internal/project/plans/AGENT-SUBTASK-MAPPING.md (1,085 lines)

• Task(s): H.0

---

2026-02-14T09:16:07Z - [H.0] Sprint Cross-Check Analysis Complete

Author: Claude (Opus 4.6)

Analysis Document: bio-qms-sprint-crosscheck-2026-02-14.md Full Path: internal/analysis/bio-qms-sprint-crosscheck/bio-qms-sprint-crosscheck-2026-02-14.md

Summary: Comprehensive cross-check of all 16 tracks (A-P), 78 sections, 341 tasks, and 10 sprints. All tasks have descriptions, dependencies, sprint assignments, and agent mappings (100% coverage). 81% of tracks rated HIGH detail, 19% MEDIUM-HIGH. Primary risk: S7 overload (32 tasks, 11 tracks). Critical path: C.1 gates 11+ downstream sections.

Cross-Check Results:

Metric	Result
Tracks	16 (A-P)
Sections	78
Tasks	341
Sprints	10 (S1-S10, 20 weeks)
Agent coverage	341/341 (100%)
Unique agents	78
Dependencies	18 cross-track
Detail level	13 HIGH, 3 MEDIUM-HIGH, 0 gaps
Heaviest sprint	S7 (32 tasks, 11 tracks)
Critical path	C.1 → 11+ downstream sections

Sprint Load: S1:15 | S2:12 | S3:22 | S4:20 | S5:28 | S6:24 | S7:32 | S8:24 | S9:12 | S10:7

Recommendations: No blockers for Sprint 1. Consider extending S7 or shifting tasks to S8. C.1 must be #1 priority in S3.

Files Created:

• internal/analysis/bio-qms-sprint-crosscheck/bio-qms-sprint-crosscheck-2026-02-14.md

• Task(s): H.0

---

2026-02-14T09:37:43Z - [H.0] Comprehensive Completeness Analysis & Sprint Rebalancing

Author: Claude (Opus 4.6)

Summary: Executed 3-agent comprehensive completeness analysis (research doc gaps, structural issues, regulated SaaS gaps). Created standalone analysis document, new Track Q, updated 10 existing tracks with 64 new tasks, and rebalanced sprint allocation to address S7 overload.

Analysis Document: bio-qms-completeness-analysis-2026-02-14.md Full Path: internal/analysis/bio-qms-completeness/bio-qms-completeness-analysis-2026-02-14.md

Outcome:

Metric	Before	After	Delta
Tracks	16 (A-P)	17 (A-Q)	+1
Tasks	341	405	+64
Sections	78	88	+10
S7 tasks (peak)	32	38 (K.1, L.1, N.3, O.1 moved out)	Relieved

New Track Created:

• Track Q: AI & Automation Governance — 12 tasks, 3 sections (Q.1-Q.3), Sprint S8-S10

Tracks Updated (new sections/tasks):

• Track C (30→41): C.2.7-C.2.11 (change governance), C.3.6-C.3.7 (agent audit), C.5.7-C.5.10 (HL7 FHIR, EBR, batch traceability, quality hold)
• Track D (21→33): D.5.5-D.5.8 (ALCOA+ controls), D.6 (multi-tenancy, 4 tasks), D.7 (validation execution, 4 tasks)
• Track E (16→20): E.5 (DR validation & automation, 4 tasks)
• Track F (18→24): F.4.4-F.4.5 (GxP training, qualification prerequisites), F.6 (training records, 4 tasks)
• Track H (22→24): H.3.6-H.3.7 (predictive health analytics, intervention playbook)
• Track K (20→24): K.6 (multi-site coordination, 4 tasks)
• Track L (20→22): L.5.4-L.5.5 (audit readiness dashboard, regulatory submission automation)
• Track N (18→26): N.3.4-N.3.6 (BAA lifecycle), N.4.4-N.4.6 (compliance intelligence), N.5.4-N.5.5 (vendor SLA prediction)
• Track O (16→19): O.2.5-O.2.7 (vendor portal, integration sandbox, dependency management)

Sprint Rebalancing (S7 Relief):

• K.1 (SLA Management): S7→S6
• L.1 (Data Warehouse): S7→S6
• N.3 (Contracts): S7→S6
• O.1 (Partner Foundation): S7→S8
• C.5 split: core (S5), healthcare (S6)

MASTER-TRACK-INDEX: Updated to v3.0.0 with Track Q, all new counts, 7 new cross-track dependencies, sprint load analysis table

Files Modified: TRACK-C, TRACK-D, TRACK-E, TRACK-F, TRACK-H, TRACK-K, TRACK-L, TRACK-N, TRACK-O, MASTER-TRACK-INDEX Files Created: TRACK-Q-AI-AUTOMATION-GOVERNANCE.md, bio-qms-completeness-analysis-2026-02-14.md

• Task(s): H.0

---

2026-02-14T09:59:26Z - [A.1-A.3] Sprint 1 Implementation Complete — Presentation-Grade Document Viewer

Author: Claude (Opus 4.6)

What: Implemented Sprint 1 (A.1-A.3) of the BIO-QMS project plan — a presentation-grade document viewer rendering 75 artifacts (49 markdown docs + 26 JSX dashboards) with unified markdown rendering, full-text search, navigation, and presentation mode.

Sprint 1 Task Completion (15/15):

Task	Description	Status
A.1.1	Install unified/remark/rehype markdown pipeline + MiniSearch	Done
A.1.2	MarkdownRenderer with frontmatter, syntax highlighting, GFM, math	Done
A.1.3	publish.json manifest generator (75 artifacts, 13 categories)	Done
A.1.4	Hash-based URL routing (/#/doc-id)	Done
A.1.5	Metadata bar with audience badges, word count, category	Done
A.1.6	Print-friendly CSS with @media print	Done
A.2.1	Full-text search via MiniSearch (fuzzy, title 3x boost)	Done
A.2.2	Keyboard shortcuts (/ search, ? help, P presentation)	Done
A.2.3	Sidebar navigation tree with category grouping, collapse/expand	Done
A.2.4	Breadcrumbs + Table of Contents with scroll spy	Done
A.2.5	Search panel with keyboard navigation (Arrow keys, Enter, Esc)	Done
A.3.1	Presentation mode with H2-based slide splitting	Done
A.3.2	Keyboard navigation (arrows, Space, Home/End, Escape)	Done
A.3.3	Presenter timer toggle (T key)	Done
A.3.4	Section overview grid (O key) with slide picker	Done

Dependencies Installed (14 packages): unified, remark-parse, remark-gfm, remark-frontmatter, remark-math, remark-rehype, rehype-stringify, rehype-highlight, rehype-slug, rehype-autolink-headings, rehype-katex, rehype-raw, katex, minisearch, gray-matter, vite-plugin-static-copy

Files Created (8 new):

File	Lines	Purpose
scripts/generate-publish-manifest.js	72	Auto-generate publish.json from docs/research/dashboards
components/MarkdownRenderer.jsx	162	unified pipeline + frontmatter + code copy + heading extraction
components/SearchPanel.jsx	144	MiniSearch integration + keyboard-navigable overlay
components/Sidebar.jsx	78	Category-grouped nav tree with collapse/expand
components/Breadcrumbs.jsx	26	Home > Category > Title breadcrumbs
components/TableOfContents.jsx	64	Auto-generated TOC with scroll spy
components/PresentationMode.jsx	189	Fullscreen slides, timer, overview grid
public/publish.json	1	Generated manifest (75 docs, 13 categories)

Files Modified (4):

File	Changes
viewer.jsx	Complete rewrite (144 to 364 lines) — integrates all 7 components
styles.css	Added 200+ lines: markdown prose, code highlighting, print CSS
vite.config.js	Added vite-plugin-static-copy for production builds
package.json	Added type:module, build scripts, 14 new dependencies

Build Verification:

• npx vite build — 2,344 modules, 19.21s, zero errors
• npx vite — dev server starts in 341ms
• node scripts/generate-publish-manifest.js — 75 documents, 13 categories

Issues Resolved:

1. Research file miscategorization — fixed with directory depth check
2. Node.js ESM warning — added "type": "module" to package.json
3. CSS @import layer() broke PostCSS — moved imports to JavaScript
4. package.json stale read after npm install — re-read before edit

• Task(s): A.1.1-A.3.4

---

Overall BIO-QMS Project Status (2026-02-14T09:59:26Z)

Author: Claude (Opus 4.6)

Project Lifecycle:

Phase	Status	Detail
Research	Complete	83 artifacts organized from research analysis
Project Setup	Complete	GitHub repo, symlinks, projects.db registration
Document Compliance	Complete	Frontmatter, footers, MoE classification (83 files)
Full Specification	Complete	17 tracks (A-Q), 405 tasks, 10 sprints, 78 agents
Sprint 1	Complete	A.1-A.3 (15 tasks): viewer, search, nav, presentation
Sprint 2+	Pending	A.4-A.6, B.1-B.4 next

Sprint Timeline:

Sprint	Scope	Tasks	Status
S1	Presentation-grade viewer (A.1-A.3)	15	DONE
S2	Cloud publishing + competitive intel (A.4, B.1-B.2)	12	Pending
S3	Auth + GTM + technical foundation (A.5-A.6, B.2-B.4, C.1, D.1)	22	Pending
S4	Backend core + sales + a11y (C.1-C.2, I.1, P.1)	20	Pending
S5	Billing + onboarding + legal (C.3-C.4, G.1-G.2, H.1, N.1-N.2)	28	Pending
S6	Operations + security + data (C.5, D.3-D.5, K.1, L.1, M.1-M.2, N.3)	38	Pending
S7	Advanced operations (D.6-D.7, G.3-G.4, J.1-J.3, K.2-K.3, M.3)	28	Pending
S8	Docs + partners + AI governance (E.3-E.5, F.3-F.6, H.3-H.4, O.1-O.2, Q.1)	24	Pending
S9	BI + reliability + regulatory (K.4-K.6, L.4-L.5, M.4, Q.2)	12	Pending
S10	Partner ops + a11y automation (O.3-O.4, P.4, Q.3)	7	Pending

All Commits This Session:

Commit	Description
a8749c2	Initial commit — 87 files
f365495	Frontmatter + copyright footers (83 files)
ecbbac9	MoE classification (56 files)
eb58057	Copyright fields in frontmatter (82 files)
2b3aeaa	Document inventory tracker (artifact #30)
0605845	Fix MoE classification
9407e27	README.md v2.0.0 rewrite
5661c47	Track-skills-index timestamp
deb55c1	package.json + react/lucide-react deps
dd8dd1e	Vite viewer with header/footer, dark mode
2bf286f	Tailwind v4 CSS theme tokens (26 dashboards)
8705d4e	6 TRACK files (143 tasks) + MASTER-TRACK-INDEX
a5b9e8f	10 new TRACK files (G-P), 341 total tasks
2e7e3f6	Completeness analysis, Track Q, sprint rebalancing, 405 tasks
a5d3c80	Sprint 1: 7 components + viewer rewrite + CSS + manifest
70665ac	TRACK-A: Mark A.1.1-A.3.4 complete with evidence

Next: Sprint 2 (A.4 Cloud Publishing, B.1-B.2 Competitive Intelligence).

• Task(s): A.1.1-A.3.4

---

2026-02-14T10:06:08Z - [A.1-A.3] Sprint 1 Housekeeping Complete

Author: Claude (Opus 4.6)

Completed Sprint 1 post-implementation housekeeping:

1. TRACK-A updated: All 15 tasks (A.1.1-A.3.4) marked [x] with commit evidence (a5d3c80). Track A progress: 44% (15/34).
2. Committed and pushed: 70665ac to BIO-QMS repo.
3. Rollout-master updated: Submodule pointer commit a623ef7f, pushed.
4. Classified: TRACK-A file reclassified (judge-approved, reference type).

Commits:

• BIO-QMS: 70665ac — docs(track-a): Mark Sprint 1 tasks A.1.1-A.3.4 complete

• Rollout-master: a623ef7f — chore(submodules): Update coditect-biosciences-qms-platform to 70665ac

• Task(s): A.1.1-A.3.4

---

2026-02-14T10:08:15Z - [H.0] Regulated SaaS Platform Gap Analysis Complete

Author: Claude (Opus 4.6)

Analysis Document: regulated-saas-gap-analysis-2026-02-14.md Full Path: internal/analysis/regulated-saas-gaps/regulated-saas-gap-analysis-2026-02-14.md

Summary: Comprehensive gap analysis of all 16 TRACK files against regulated SaaS requirements (FDA Part 11, HIPAA, SOC 2). Found 8 gap areas (1 CRITICAL, 4 HIGH, 3 MEDIUM) totaling 41 proposed new tasks. Most critical gap: AI/ML Governance (no track covers model validation, bias monitoring, or AI decision audit trails). Recommends creating Track Q (AI Governance, 12 tasks) and extending Tracks C, D, E, F with new sections.

Key Findings:

Gap	Severity	Proposed Tasks
AI/ML Governance	CRITICAL	12
Multi-Tenancy Data Segregation	HIGH	4
Disaster Recovery Validation	HIGH	4
QMS Change Management	HIGH	5
Validation Execution (IQ/OQ/PQ)	HIGH	4
ALCOA+ Implementation	MEDIUM	4
User Qualification Tracking	MEDIUM	4
Healthcare Integration (HL7 FHIR)	MEDIUM	4

Impact: 41 new tasks would bring project total from 405 to ~446 across 17-18 tracks.

• Task(s): H.0

---

2026-02-14T10:13:31Z - [H.0] Analysis Preservation: Research Coverage & TRACK Consistency

Author: Claude (Opus 4.6)

Saved remaining two background agent analysis findings as standalone documents per Analysis Preservation Protocol. All three cross-check analyses now persisted, committed, and pushed.

Analysis Document 1: bio-qms-research-coverage-analysis-2026-02-14.md Full Path: internal/analysis/bio-qms-research-coverage/bio-qms-research-coverage-analysis-2026-02-14.md Summary: 57 research documents cross-referenced against 16 TRACKs. 91% overall completeness. 12 gaps identified requiring ~80-100 additional tasks, predominantly Phase 4-5 features intentionally deferred.

Analysis Document 2: bio-qms-track-consistency-audit-2026-02-14.md Full Path: internal/analysis/bio-qms-track-consistency/bio-qms-track-consistency-audit-2026-02-14.md Summary: 341 tasks, 78 sections, zero numbering gaps, perfect INDEX alignment. 3 CRITICAL issues: Sprint S7 overloaded (60 tasks/2 weeks), ~40+ intra-track dependencies missing from INDEX, 20+ referenced docs unverified. 8 HIGH issues including task decomposition needs in F, L, C.

Commits:

Repo	Hash	Description
BIO-QMS	d233c8b	3 analysis documents (regulated SaaS gaps, research coverage, TRACK consistency)
rollout-master	c0098a18	Submodule pointer update

• Task(s): H.0

---

2026-02-14T11:03:54Z - [H.0] Resolved 4 Critical Issues: Sprint Rebalancing, Doc Verification, Intra-Track Dependencies

Author: Claude (Opus 4.6)

Resolved all 4 critical issues identified by the 3 parallel cross-check analysis agents. MASTER-TRACK-INDEX updated to v3.1.0.

Issue 1 — Sprint S7 Overload (RESOLVED): Rebalanced S7-S10 by moving 4 sections to later sprints:

Section	From	To	Tasks Moved
K.3	S7	S9	~8
M.2	S7	S9	4
M.5	S8-S9	S10	3
N.5	S8	S9	5

Result: S7: 38→30, S8: 42→34, S9: 16→29, S10: 11→14

Issue 2 — AI/ML Governance Gap (RESOLVED): Track Q (AI & Automation Governance) already created in prior session — 12 tasks across Q.1-Q.3. No additional work needed.

Issue 3 — 20+ Referenced Documents Unverified (RESOLVED): Added B.0 Pre-Sprint Document Verification section to TRACK-B with 4 tasks (B.0.1-B.0.4). Assigned to S1 as a gate before S2 execution. Track B task count: 24→28.

Issue 4 — ~40+ Intra-Track Dependencies Missing (RESOLVED): Added Intra-Track Dependencies table to MASTER-TRACK-INDEX with 44 rows covering all 17 tracks (A-Q). Each row specifies From section, To section(s), and Description.

Files Modified:

• internal/project/plans/tracks/TRACK-K-PLATFORM-RELIABILITY-MAINTENANCE.md — K.3 sprint S7→S9
• internal/project/plans/tracks/TRACK-M-SECURITY-OPERATIONS.md — M.2 S7→S9, M.5 S8-S9→S10
• internal/project/plans/tracks/TRACK-N-LEGAL-REGULATORY-OPERATIONS.md — N.5 S8→S9
• internal/project/plans/tracks/TRACK-B-COMPETITIVE-INTELLIGENCE-GTM.md — Added B.0 section (4 tasks)
• internal/project/plans/tracks/MASTER-TRACK-INDEX.md — v3.1.0: sprint rebalancing, B.0, intra-track deps, updated task counts (~405→~409, 88→89 sections)

Commits:

Repo	Hash	Description
BIO-QMS	7a8f6f9	Sprint rebalancing, B.0 doc verification, intra-track deps
rollout-master	7c6bc41e	Submodule pointer update

• Task(s): H.0

---

2026-02-14T11:30:58Z - [H.0] Sprint Dependency Map + v3.2 Violation Fixes

Author: Claude (Opus 4.6)

Sprint Dependency Mapping: Created comprehensive Sprint Dependency Map in MASTER-TRACK-INDEX covering all 10 sprints (S1-S10). Each sprint has a per-section dependency verification table showing: Section, Depends On, Dep Sprint, Status (✅ earlier/⚠️ same/❌ later). Identified 3 forward-reference violations from v3.0 rebalancing.

v3.2 Dependency Violation Fixes (3 violations → 0):

Section	Was	Now	Reason
K.1 (SLA Management)	S6	S7	Depends on E.3 (S7) — was forward-referencing
N.3 (Contract Lifecycle)	S6	S7	Depends on I.4 (S7) — was forward-referencing
F.6 (Training Records)	S7	S8	Depends on F.4 (S8) — was forward-referencing

Load impact: S6: 42→33 (-9), S7: 30→35 (+5), S8: 34→38 (+4). Range: 12-38.

Files Modified:

• TRACK-K-PLATFORM-RELIABILITY-MAINTENANCE.md — K.1 sprint S6→S7
• TRACK-N-LEGAL-REGULATORY-OPERATIONS.md — N.3 sprint S6→S7
• TRACK-F-DOCUMENTATION-TRAINING.md — F.6 sprint S7→S8
• MASTER-TRACK-INDEX.md — v3.2.0: Sprint Dependency Map (10 tables), violation fixes, sprint allocation updates, load analysis v3.2 column, Track K sprint range S6-S9→S7-S9

Commits:

Repo	Hash	Description
BIO-QMS	9e35612	Track files (F, K, N) sprint updates
BIO-QMS	5f9baaf	INDEX v3.2 dep map completion
rollout-master	20ead2ca	Submodule pointer update

• Task(s): H.0

---

2026-02-14T11:48:02Z - [B.0.1-B.0.4] Sprint 1 Completion — B.0 Pre-Sprint Document Verification

Author: Claude (Opus 4.6)

Session Focus: Complete Sprint 1 by executing B.0 Pre-Sprint Document Verification (4 tasks). Sprint 1 = A.1+A.2+A.3 (complete, 15/15 tasks, commit a5d3c80) + B.0 (4 tasks, pending). B.0 gates Sprint 2.

Plan: Approved plan at /Users/halcasteel/.claude/plans/witty-drifting-sunrise.md

Discovery Findings:

• 47 unique paths referenced across 17 TRACK files
• 32/47 exist (68%), 15 missing (32%)
• Missing categories: ~6 naming mismatches, ~6 future B.1/B.2/B.3 outputs, ~3 truly missing
• Key mismatches: 05-market-analysis.md→05-market-opportunity.md, 22-rbac-role-based-access-control.md→21-rbac-model.md+22-rbac-permissions-matrix.md, 17-security-architecture.md→17-e-signature-architecture.md

Execution: B.0.1 (audit report) → B.0.2 (fix refs + stubs) → B.0.3 (cross-refs) → B.0.4 (gate script) → commit + push

---

2026-02-14T11:59:29Z - [B.0.1-B.0.3] Verification Report + Mismatch Fixes + Cross-References Complete

Author: Claude (Opus 4.6)

B.0.1 — Audit Report (COMPLETE):

• Created internal/analysis/doc-verification/doc-verification-report.md
• 38 unique paths audited: 20 exact match (53%), 6 naming mismatch (16%), 9 future outputs (24%), 3 truly missing (8%)

B.0.2 — Naming Fixes + Stubs (COMPLETE):

• 10 naming mismatch corrections across 4 TRACK files (B, C, D, Q)
• 3 stub documents created: 58-gap-analysis-framework.md, compliance-readiness-matrix.md, 66-multi-site-management.md
• All naming mismatches now resolved — TRACK references point to correct existing files

B.0.3 — Cross-References (COMPLETE):

• 18 existing docs updated with referenced_by frontmatter
• 3 stubs already had referenced_by from creation
• 100% bidirectional coverage achieved
• Cross-reference matrix appended to verification report (Section 8)

Files Modified:

• internal/analysis/doc-verification/doc-verification-report.md (created + updated)
• 4 TRACK files: TRACK-B, TRACK-C, TRACK-D, TRACK-Q (naming mismatch fixes)
• 3 stub docs created in docs/compliance/ and docs/operations/
• 18 existing docs: referenced_by frontmatter added

Remaining: B.0.4 (readiness gate script) → commit + push

• Task(s): B.0.1, B.0.2, B.0.3

---

2026-02-14T12:06:52Z - [B.0.1-B.0.4] Sprint 1 B.0 Pre-Sprint Document Verification COMPLETE

Author: Claude (Opus 4.6) Phase: COMPLETION

Summary: All 4 B.0 tasks complete. Sprint 1 fully done (A.1-A.3 + B.0 = 19/19 tasks).

Results:

Task	Description	Status	Evidence
B.0.1	Audit TRACK-referenced documents	COMPLETE	38 paths audited, verification report created
B.0.2	Fix naming mismatches + create stubs	COMPLETE	10 corrections, 3 stubs
B.0.3	Bidirectional cross-references	COMPLETE	18 docs updated, 100% coverage
B.0.4	Document readiness gate script	COMPLETE	scripts/check-doc-readiness.sh (bash 3.x)

Commits:

• BIO-QMS: 67a65fd — Main B.0 work (29 files, +906 lines)
• BIO-QMS: 20e037f — Evidence hash + INDEX progress update
• rollout-master: e91891c4 — Submodule pointer update

Key Artifacts:

• internal/analysis/doc-verification/doc-verification-report.md — Full audit report with cross-reference matrix
• scripts/check-doc-readiness.sh — Sprint readiness gate (31 PASS, 13 future outputs)
• TRACK-B updated: B.0 marked Complete (4/4), progress 14% (4/28)
• MASTER-TRACK-INDEX updated: Track B → In Progress

Sprint 1 Final Status: 19/19 tasks complete (A.1 + A.2 + A.3 + B.0) Sprint 2 Gate: Document readiness verified — ready to begin B.1, C.1, C.2

• Task(s): B.0.1, B.0.2, B.0.3, B.0.4

---

2026-02-14T12:09:38Z - [B.0] Create S2-S3 Stub Documents with Frontmatter Scaffolding

Author: Claude (Opus 4.6)

Created 12 stub documents for the 13 missing future outputs (1 is scripts/deploy.sh — C.6, S6, not a doc). Each stub has:

• status: stub in frontmatter
• generated_by: B.x.x task reference
• referenced_by cross-references where applicable
• "Intended Content" section describing what prompt execution will generate

Stubs Created (12):

• docs/market/market-sizing.md (B.1.1)
• docs/market/customer-segmentation.md (B.1.2)
• docs/market/competitive-landscape.md (B.1.3)
• docs/market/competitive-positioning.md (B.1.4)
• docs/market/gtm-foundation.md (B.2.1)
• docs/market/gtm-channels.md (B.2.2)
• docs/market/gtm-marketing.md (B.2.3)
• docs/market/gtm-customer-success.md (B.2.4)
• docs/market/gtm-execution-plan.md (B.2.5)
• docs/market/gtm-metrics.md (B.2.6)
• docs/reference/cross-artifact-impact-register.md (B.3.1)
• dashboards/system/impact-register-dashboard.jsx (B.3.3)

Readiness Gate Result: 44/45 PASS (only scripts/deploy.sh remains — C.6, Sprint 6)

Commits:

• BIO-QMS: a1ab1ce — 12 stub documents (+552 lines)
• rollout-master: 0f431d77 — Submodule pointer update

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2026-02-14T12:11:05Z - [B.0.1-B.0.4] B.0 Pre-Sprint Document Verification — COMPLETE (User Summary)

Author: Claude (Opus 4.6)

Commit	Repo	Description
67a65fd	BIO-QMS	Main B.0 work (29 files, +906 lines)
20e037f	BIO-QMS	Evidence hash + INDEX progress
a1ab1ce	BIO-QMS	12 stub documents for S2-S3 (+552 lines)
e91891c4	rollout-master	Submodule → 20e037f
0f431d77	rollout-master	Submodule → a1ab1ce

Stubs created: 12 documents with proper frontmatter (status: stub, generated_by, referenced_by, intended content descriptions). Each will be superseded when their corresponding B.1/B.2/B.3 prompt tasks execute during Sprint 2-3.

Readiness gate: 44/45 PASS. Only scripts/deploy.sh missing (C.6, Sprint 6 — not a doc, deliberately not stubbed).

Sprint 1: 19/19 tasks complete. Sprint 2 ready to begin (B.1, C.1, C.2).

• Task(s): B.0.1, B.0.2, B.0.3, B.0.4

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2026-02-14T12:19:05Z - [B.0] Sprint 1 Checkpoint Created

Author: Claude (Opus 4.6)

Checkpoint File: 2026-02-14T12-13-57Z-sprint-1-complete-b0-verification.md Full Path: context-storage/checkpoints/2026-02-14T12-13-57Z-sprint-1-complete-b0-verification.md Checkpoint ID: chk-2026-02-14T12-13-57Z ISO Datetime: 2026-02-14T12:13:57Z

Summary: Sprint 1 completion checkpoint capturing all 19/19 tasks (A.1, A.2, A.3, B.0). Contains full sprint summary, commit history, key artifacts inventory (~97 artifacts), document inventory, and Sprint 2 next steps with context for session continuity.

All Session Commits (BIO-QMS):

Hash	Description
67a65fd	Main B.0 work (29 files, +906 lines)
20e037f	Evidence hash + MASTER-TRACK-INDEX progress
a1ab1ce	12 stub documents for S2-S3 (+552 lines)

All Session Commits (rollout-master):

Hash	Description
e91891c4	Submodule → 20e037f
0f431d77	Submodule → a1ab1ce

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2026-02-14T12:42:22Z - [H.9] Plan: Local Dev Server Lifecycle Management

Author: Claude (Opus 4.6)

Context: BIO-QMS has a full Vite viewer at localhost:5173 (viewer.jsx + 27 JSX dashboards + markdown renderer), and coditect-core has 4+ tools with dev servers (component-viewer:5173, trajectory-dashboard:5174, bi-dashboard, trajectory-visualizer). But there's no centralized way to launch, manage ports, or lifecycle-manage these project-local servers. The /port-check command exists as documentation (commands/port-check.md) but scripts/port-check.sh was never implemented. The /start-viewer command copies components TO coditect-core's viewer — it doesn't launch a project's own server.

Need: A /serve command that detects a project's existing Vite/dev server, manages port conflicts (check, kill, restart), installs deps if needed, and launches — working with any project that has package.json + npm run dev.

Project: PILOT (coditect-core framework components) Track: H.9 (new section added to TRACK-H-FRAMEWORK-AUTONOMY)

Components to Create (6 total):

Task	File	Description
H.9.1	scripts/port-check.sh	Port management utility (check, kill, range, JSON output)
H.9.2	scripts/frontend/serve.sh	Project server launcher (detect, install deps, launch)
H.9.3	commands/serve.md	/serve slash command definition
H.9.4	skills/local-dev-server/SKILL.md	Server lifecycle skill (detection, launch, troubleshooting)
H.9.5	agents/local-dev-server.md	Server management agent persona
H.9.6	TRACK-H edit	H.9 section added to TRACK-H ✅

Status: H.9.6 (TRACK update) complete. H.9.1-H.9.5 implementation in progress.

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2026-02-14T13:12:25Z - [H.0] Markdown + JSX Serving Options Research

Author: Claude (Opus 4.6)

Context: Investigated options for serving markdown documents alongside JSX dashboards with the current BIO-QMS Vite dev server. Found the 30-document inventory and website plan from the original document set.

Key Documents Found:

• docs/reference/30-document-inventory.md — Master inventory of all 83 artifacts (57 markdown + 26 JSX) across 17 categories
• docs/reference/31-website-plan.md — Full website content plan with site architecture, URL structure, Next.js 14+ recommendation, MDX page templates, and 4-phase build plan

Finding: Current Viewer Already Serves Both The existing viewer.jsx already has a complete markdown+JSX serving capability:

• Hash-based routing with manifest-driven discovery (publish.json)
• Full unified rendering pipeline: remark-parse + remark-gfm + remark-math + remark-frontmatter + rehype-highlight + rehype-katex + rehype-slug + rehype-autolink-headings + gray-matter + minisearch
• 26 dashboards lazy-loaded via React.lazy() + Suspense
• vite-plugin-static-copy copies docs/ and research/ to dist for runtime markdown loading

Enhancement Options Identified (3 Tiers):

Tier	Approach	Effort	What It Adds
1. Keep Current	Viewer already works	Zero	Nothing needed — already serving 75 artifacts
2. Add MDX to Vite	@mdx-js/rollup v3.1.1 in vite.config.js	Low (1-2 hrs)	Embed JSX components directly inside .mdx files
3. Next.js + MDX	Per doc 31 website plan	Medium (weeks)	SSR, SEO, production URL structure, Algolia search

Research Sources:

• Web search: 6 Vite markdown approaches compared (vite-plugin-markdown, MDX, react-markdown, vite-plugin-pages, ?raw suffix, vite-plugin-md)
• Codebase: viewer.jsx architecture, vite.config.js plugins, package.json dependencies
• Doc 31 Section 4.1: Recommends Next.js 14+ App Router + MDX + Tailwind for production
• Doc 31 Section 4.3: MDX page template with dashboard embedding pattern

Decision Pending: User has not yet selected which tier to pursue.

• Task(s): H.0

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2026-02-14T13:30:00Z - [H.0] MDX vs Runtime Markdown — Graded Analysis with MoE Judges

Author: Claude (Opus 4.6)

Analysis Document: bio-qms-tier1-vs-tier2-graded-analysis-2026-02-14.md Full Path: internal/analysis/mdx-vs-runtime-markdown/bio-qms-tier1-vs-tier2-graded-analysis-2026-02-14.md

Summary: BIO-QMS-specific graded comparison of Tier 1 (current runtime markdown) vs Tier 2 (MDX addition to Vite config). 10 weighted attributes scored: Full-Text Search (15%), Component Embedding (15%), Content Control (12%), Migration Effort (12%), Security Model (10%), Build Performance (8%), Runtime Performance (8%), Developer Experience (8%), Bundle Size (6%), Future Extensibility (6%). Tier 1 scored 6.27/10, Tier 2 scored 7.16/10 (14.2% advantage). MoE Judge Panel: all 3 judges (Consistency, Quality, Domain/FDA) APPROVED Hybrid Tier 2 recommendation — keep regulatory .md docs, convert ~14 interactive docs to .mdx.

Also created (companion document):

• mdx-vs-runtime-markdown-technical-comparison-2026-02-14.md (generic technical comparison, 1,225 lines)

• Full Path: internal/analysis/mdx-vs-runtime-markdown/mdx-vs-runtime-markdown-technical-comparison-2026-02-14.md

• Task(s): H.0

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2026-02-14T13:36:12Z - [A.1.2] Fix Buffer is not defined crash in MarkdownRenderer

Author: Claude (Opus 4.6)

Issue: gray-matter library crashes in browser with Uncaught ReferenceError: Buffer is not defined at MarkdownRenderer.jsx:104. gray-matter uses Node.js Buffer.from() internally; Vite 7 does not polyfill Node.js globals in the browser.

Root Cause: gray-matter is a Node.js-only library imported at MarkdownRenderer.jsx:18 and called at lines 104 and 147. Vite 7.3.1 does not ship browser polyfills for Buffer.

Fix: Replaced gray-matter import with browser-native parseFrontmatter() function:

• Regex-based --- delimiter matching
• Simple YAML key-value + list parsing
• Returns { data, content } matching gray-matter's API
• Zero dependencies, no polyfills needed

Files Modified:

• components/MarkdownRenderer.jsx — Removed import matter from "gray-matter", added parseFrontmatter() function, updated both call sites (line 138 render effect, line 181 extractSections export)

Note: gray-matter stays in package.json — scripts/generate-publish-manifest.js (Node.js build script) still uses it correctly.

Commits:

• BIO-QMS: 938b072 — fix(viewer): Replace gray-matter with browser-native frontmatter parser

• rollout-master: 0ae6d2e4 — chore(submodules): Update coditect-biosciences-qms-platform to 938b072

• Task(s): A.1.2

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2026-02-14T14:03:44Z - [H.0] Architecture Decision: Stay with Tier 1 (Runtime Markdown)

Author: Claude (Opus 4.6)

Decision: After completing the MDX vs Runtime Markdown graded analysis (Tier 1 = 6.27, Tier 2 = 7.16), the decision is to stay with Tier 1 (runtime markdown conversion) rather than adopting MDX. The current unified/remark/rehype pipeline with runtime fetch is sufficient for the BIO-QMS document viewer's needs.

Rationale: The 14.2% weighted advantage of Tier 2 does not justify the migration complexity for a regulated document platform where content stability and compliance narrative integrity are paramount. The existing pipeline already serves 75 artifacts (49 markdown + 26 JSX dashboards) effectively.

Next Feature Request — Dynamic Category Landing Pages: User requested enhanced breadcrumb navigation where:

1. Breadcrumbs become active links (not just text labels)
2. Clicking a folder/category in breadcrumbs lands on a dynamic landing page
3. Each folder provides a content-type-aware listing of its contents
4. Navigation becomes more intuitive — users can browse by folder hierarchy, not just flat search

Example flow: Home > Compliance > State Machine > [doc] — clicking "Compliance" shows all compliance docs, clicking "State Machine" shows state machine docs with type-appropriate presentation (references get table layout, guides get card layout, etc.)

Implementation considerations:

• Currently breadcrumbs are text-only (Breadcrumbs.jsx, 26 lines)

• Category pages would need to filter publish.json by category

• Content-type-aware layouts: reference docs (table), guides (cards), dashboards (grid with previews)

• Could reuse existing Sidebar.jsx category grouping logic

• Hash routing: #/category/compliance → dynamic landing page

• Task(s): H.0

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2026-02-14T14:11:40Z - [A.2.4-A.2.5] Dynamic Category Landing Pages with Active Breadcrumbs

Author: Claude (Opus 4.6)

Implemented the feature request from the previous entry: category names in sidebar and breadcrumbs are now clickable links that navigate to content-type-aware landing pages. Each category shows its documents as a filterable list and dashboards in a 2-column grid, with audience badges and artifact stats.

Architecture decision: Stay with Tier 1 runtime markdown rendering (not MDX). MoE judges scored Tier 1 at 6.27 vs Tier 2 at 7.16, but Tier 1's advantages in zero-build-step iteration and runtime publish.json flexibility outweigh the marginal score difference for the BIO-QMS use case.

What was done:

• Created components/CategoryLanding.jsx (~155 lines) — dynamic category landing with content-type-aware layouts, audience badges, category descriptions for all 13 categories
• Rewrote components/Breadcrumbs.jsx (26→45 lines) — clickable category links: Home > Category (link) > Doc Title
• Updated components/Sidebar.jsx (78→85 lines) — dual-action headers: chevron toggles collapse, category name navigates to landing
• Updated viewer.jsx (364→393 lines) — hash-based category routing (#/category/{name}), parseHash() replacing getDocFromHash(), navigateToCategory callback
• Fixed Buffer is not defined crash in MarkdownRenderer.jsx — replaced gray-matter with browser-native parseFrontmatter()

Hash routing scheme:

• #/ or empty → home landing page
• #/{docId} → document view
• #/category/{categoryName} → category landing page (NEW)

Commits:

• 938b072 — fix: Replace gray-matter with browser-native frontmatter parser
• f89dd0c — feat: Dynamic category landing pages with active breadcrumb navigation
• c8ae3646 — chore(submodules): Update BIO-QMS pointer in rollout-master

Vite build: Zero errors, 11.39s

Files Modified:

• components/CategoryLanding.jsx (NEW)

• components/Breadcrumbs.jsx

• components/Sidebar.jsx

• viewer.jsx

• components/MarkdownRenderer.jsx (gray-matter fix)

• Task(s): A.2.4, A.2.5

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2026-02-14T14:17:30Z - [H.0] Viewer Navigation Confirmed Working + New Mermaid Requirement

Author: Claude (Opus 4.6)

Status update: The new viewer with dynamic category landing pages and active breadcrumb navigation is working correctly. Hash-based routing (#/category/{name}) loads content-type-aware landing pages, sidebar dual-action headers function as expected, and breadcrumb links navigate properly through the Home > Category > Document hierarchy.

New requirement logged: Embedded Mermaid charts in markdown documents need to be viewable as rendered PNG images. Currently, Mermaid code blocks in markdown source are rendered as syntax-highlighted code text by the remark/rehype pipeline but not as visual diagrams. The requirement is to detect Mermaid fenced code blocks (```mermaid) and render them as PNG diagram images inline within the document view.

Implementation considerations:

• Current markdown pipeline: unified → remark-parse → remark-gfm → remark-math → rehype → rehype-katex → rehype-raw → rehype-stringify

• Option A: Client-side rendering via mermaid.js library — renders SVG in browser, no build step

• Option B: Build-time PNG generation via @mermaid-js/mermaid-cli (mmdc) — pre-renders to PNG during generate-publish-manifest.js

• Option C: Custom rehype plugin (rehype-mermaid) — integrates into existing pipeline

• BIO-QMS docs contain Mermaid diagrams in: state machine docs, architecture docs, workflow docs, compliance process flows

• Need to confirm: render as SVG inline (scalable, interactive) vs PNG (static but universally compatible)?

• Task(s): H.0

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2026-02-14T14:24:20Z - [A.1.2] Implementing Mermaid.js Client-Side SVG Rendering

Author: Claude (Opus 4.6)

Decision: Option A selected — client-side mermaid.js rendering to inline SVG. Mermaid fenced code blocks (```mermaid) in 3 BIO-QMS markdown files will be detected post-render and replaced with SVG diagrams. Follows the same DOM mutation pattern as existing addCopyButtons() in MarkdownRenderer.jsx.

Approach:

1. npm install mermaid in BIO-QMS project
2. Add renderMermaidBlocks(container) function to MarkdownRenderer.jsx
3. Hook into existing useEffect chain after HTML render
4. Detect <code class="language-mermaid"> elements, render via mermaid.run()

Files with Mermaid content:

• docs/architecture/14-c4-architecture.md (4 diagrams: graph, classDiagram)

• docs/architecture/15-mermaid-diagrams.md (4+ diagrams: graph, sequenceDiagram, flowchart)

• config/59-coditect-system-prompt-v8.md (incidental)

• Task(s): A.1.2

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2026-02-14T14:27:07Z - [A.1.2] Mermaid.js Client-Side Rendering Complete

Author: Claude (Opus 4.6)

Implemented client-side Mermaid diagram rendering. Fenced ```mermaid code blocks in markdown docs are now rendered as inline SVG diagrams with dark theme matching the viewer palette.

Implementation:

• Installed mermaid@11.12.2 — diagram type chunks are lazy-loaded (sequence, class, flowchart, gantt, etc.)
• Added initMermaid() with dark theme variables matching BIO-QMS viewer color palette
• Added renderMermaidBlocks(container) — finds <code class="language-mermaid"> elements, calls mermaid.render(), replaces <pre> with SVG wrapper
• Hooked into existing useEffect after HTML render (same pattern as addCopyButtons)
• Copy buttons now skip mermaid code blocks
• Added .mermaid-diagram CSS (centered, rounded container with subtle border) and .mermaid-error CSS

Commits:

• 03fa78d — feat: Add client-side Mermaid diagram rendering via mermaid.js
• 8d827117 — chore(submodules): Update BIO-QMS pointer in rollout-master

Vite build: Zero errors, 15.09s. Mermaid chunks properly code-split.

Files Modified:

• components/MarkdownRenderer.jsx (import + init + render function + useEffect hook)

• styles.css (mermaid-diagram + mermaid-error styles)

• package.json / package-lock.json (mermaid@11.12.2)

• Task(s): A.1.2

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