@mindrian_os/cli 1.13.0-beta.10 → 1.13.0-beta.44

package/references/design/graph-visualization-standard.md

@@ -1,178 +0,0 @@
-# Graph Visualization Standard
-
-**Decision:** vis-network (vis.js) is the standard graph visualization library for ALL MindrianOS exports, snapshots, dashboards, and visual presentations.
-
-**Decided:** 2026-04-06
-**Supersedes:** Cytoscape.js for exports (Cytoscape.js retained for internal plugin dashboard only)
-
-## Why vis-network
-
-| Requirement | vis-network | Cytoscape.js |
-|-------------|-------------|--------------|
-| Physics simulation | Built-in ForceAtlas2, excellent | Available but less polished |
-| Drag & drop | Excellent out-of-box | Good |
-| Learning curve | Simple API | Steep |
-| Clustering | Built-in | Requires extensions |
-| Visual quality | Beautiful by default | Needs heavy styling |
-| Setup | `new Network(container, data, options)` | Verbose config |
-
-Cytoscape.js has superior graph algorithms (50+ built-in) but exports don't need algorithms -- they need beautiful interactive exploration.
-
-## When to Use What
-
-| Context | Library | Reason |
-|---------|---------|--------|
-| SnapshotHub exports | vis-network | Beauty + interaction for stakeholders |
-| /mos:present views | vis-network | Same as SnapshotHub |
-| /mos:dashboard live server | vis-network | Consistency with exports |
-| /mos:visualize command | vis-network | Standard graph output |
-| Plugin internal (Brain queries) | Cytoscape.js | Graph algorithms needed |
-
-## Standard Configuration
-
-```javascript
-var options = {
-  physics: {
-    enabled: true,
-    solver: 'forceAtlas2Based',
-    forceAtlas2Based: {
-      gravitationalConstant: -40,
-      centralGravity: 0.008,
-      springLength: 120,
-      springConstant: 0.04,
-      damping: 0.4
-    },
-    stabilization: { iterations: 200, fit: true }
-  },
-  interaction: {
-    hover: true,
-    tooltipDelay: 200,
-    zoomView: true,
-    dragView: true,
-    keyboard: { enabled: true }
-  },
-  nodes: {
-    font: {
-      color: '#ccc',
-      size: 11,
-      face: 'Inter, system-ui, sans-serif',
-      strokeWidth: 3,
-      strokeColor: '#0a0a0f'
-    },
-    borderWidth: 2,
-    shadow: { enabled: true, color: 'rgba(0,0,0,0.3)', size: 6 }
-  },
-  edges: {
-    smooth: { type: 'continuous', roundness: 0.3 },
-    hoverWidth: 2
-  },
-  layout: { improvedLayout: true }
-};
-```
-
-## Node Shapes
-
-| Node Type | Shape | Size | Description |
-|-----------|-------|------|-------------|
-| Section header | diamond | 20 | Room section nodes (problem-definition, market-analysis, etc.) |
-| Artifact | dot | 12 | Individual entries/documents |
-| Framework | triangle | 16 | Methodology framework nodes (for Brain views) |
-| Person | square | 14 | Team member or speaker nodes |
-
-## Edge Colors
-
-| Edge Type | Color | Opacity | Description |
-|-----------|-------|---------|-------------|
-| CONVERGES | #2ECC71 | 0.4 | Themes align across sections |
-| CONTRADICTS | #E74C3C | 0.4 | Tension detected between entries |
-| INFORMS | #3498DB | 0.4 | One entry informs another |
-| INVALIDATES | #E67E22 | 0.5 | One entry invalidates another |
-| FEEDS_INTO | #9B59B6 | 0.5 | Framework chains (Brain views) |
-
-## Section Colors
-
-| Section | Color | Hex |
-|---------|-------|-----|
-| problem-definition | Red | #E74C3C |
-| market-analysis | Yellow/Gold | #F39C12 |
-| solution-design | Blue | #3498DB |
-| business-model | Green | #2ECC71 |
-| competitive-analysis | Orange | #E67E22 |
-| team-execution | Purple | #9B59B6 |
-| legal-ip | Gold | #D4AC0D |
-| financial-model | Teal | #1ABC9C |
-| personas | Deep Purple | #8E44AD |
-| opportunity-bank | Forest Green | #27AE60 |
-| meetings | Gray | #7F8C8D |
-
-## CDN
-
-```html
-<script src="https://unpkg.com/vis-network@9.1.9/standalone/umd/vis-network.min.js"></script>
-```
-
-## Required UI Elements
-
-Every graph view MUST include:
-
-1. **Sidebar** with section filter toggles and edge type toggles
-2. **Detail panel** that appears on node click (shows connections)
-3. **Controls bar** at bottom: Fit, Zoom +/-, Physics toggle, Stabilize
-4. **Back to Hub** link in top bar
-5. **Mindrian branding** with Mondrian color bar
-6. **Legend** explaining edge types and node shapes
-7. **Stats** showing node/edge counts
-
-## Dark Theme (Standard)
-
-```css
-body { background: #0a0a0f; }
-sidebar { background: #0d0d14; border-right: 1px solid #1a1a2a; }
-top-bar { background: #0d0d12; }
-node-font-color: #ccc
-node-font-stroke: #0a0a0f (3px outline for readability)
-detail-panel: #12121a with backdrop-filter: blur(8px)
-```
-
-## Integration Points
-
-- `scripts/generate-hub.cjs` -- embeds vis-network graph in SnapshotHub
-- `scripts/generate-snapshot.cjs` -- constellation view uses vis-network
-- `scripts/generate-presentation.cjs` -- graph view uses vis-network
-- `lib/quickview/hub-server.cjs` -- live dashboard graph uses vis-network
-- `dashboard/index.html` -- localhost dashboard uses vis-network
-
----
-
-## Pitch Deck Standard (v1.9.3)
-
-The SnapshotHub pitch deck uses the `/slides` skill structure:
-- 10-slide YC Seed Deck format
-- Chart.js for all data visualizations (minimum 3 charts)
-- 16:9 aspect ratio with keyboard navigation (arrows + click)
-- Progress bar at top
-- De Stijl dark palette (#0a0a0f background, Mondrian accents)
-- Bebas Neue headings, Inter body
-- MINDRIAN logo + Back to Hub link
-- Mobile responsive (breakpoints at 900px, 600px)
-- Mondrian color bar footer
-
-### Slide Structure
-1. Title/Hook (AIDA formula)
-2. Problem (PAS formula)
-3. Convergence/IKA (Chart.js horizontal bar)
-4. Solution (TRL progress bars)
-5. Market & Timing (Chart.js S-curve lines)
-6. Competitive Landscape (grid with check/miss)
-7. Business Model (Chart.js stacked bar)
-8. Team (credential grid)
-9. Traction & Timeline (milestone cards)
-10. The Ask/CTA (AIDA urgency)
-
-### Generator Integration
-`generate-hub.cjs` should produce this deck as `views/deck.html` by:
-1. Reading room sections for content
-2. Extracting metrics from STATE.md
-3. Building Chart.js datasets from market-analysis/ and financial-model/
-4. Generating persona card from team/ data
-5. Using the slide template from references/templates/deck-template.html

package/references/document-generation.md

@@ -1,179 +0,0 @@
-# Document Generation Reference
-
-*Professional document structuring for MindrianOS — De Stijl formatted exports from the Data Room.*
-
----
-
-## Architecture
-
-```
-Room Markdown Artifacts (YAML frontmatter)
-    ↓
-markdown2 (parse to HTML + extract metadata)
-    ↓
-Jinja2 (inject into document-type template)
-    ↓
-De Stijl CSS stylesheet (shared across all templates)
-    ↓
-WeasyPrint (render to PDF)
-    ↓
-PyMuPDF (optional: TOC bookmarks, merge sections, watermark)
-    ↓
-room/exports/{document-type}.pdf
-```
-
-**Zero additional dependencies.** All tools already installed:
-- WeasyPrint 67.0 (HTML+CSS → PDF, CSS3 paged media)
-- markdown2 2.5.4 (Markdown → HTML with frontmatter)
-- Jinja2 3.1.6 (template engine)
-- PyMuPDF 1.26.6 (PDF manipulation, TOC, merge)
-- PyYAML 6.0.3 (frontmatter parsing)
-
----
-
-## Document Types
-
-| Document | Use Case | Template Style |
-|----------|----------|---------------|
-| **Investment Thesis** | Structured narrative for investors — problem, market, solution, financials | Multi-page portrait, section breaks, De Stijl accent bars |
-| **Executive Summary** | 1-2 page dense overview of entire Data Room | Two-column layout, tight margins, summary boxes |
-| **Due Diligence Report** | Comprehensive multi-section with TOC | Running headers, page numbers, section numbering |
-| **Research Paper** | Academic-style with citations and methodology | Two-column body, footnotes, bibliography |
-| **PWS Profile** | Professional profile/resume for cohort members | Single-page grid layout, accent bars, skill visualization |
-| **Pitch Deck** | Landscape slides for presentation | Landscape @page, large headings, one-concept-per-page |
-| **Venture Brief** | Quick 1-pager for stakeholder review | Constrained single page, key highlights only |
-
----
-
-## De Stijl CSS for PDF
-
-```css
-@page {
-  size: A4;
-  margin: 24mm 20mm;
-  background: #0D0D0D;
-
-  @top-center {
-    content: string(doctitle);
-    font-family: 'Bebas Neue', sans-serif;
-    color: #A09A90;
-    font-size: 10px;
-  }
-
-  @bottom-right {
-    content: counter(page) ' / ' counter(pages);
-    font-family: 'Inter', sans-serif;
-    color: #A09A90;
-    font-size: 10px;
-  }
-}
-
-:root {
-  --ds-bg: #0D0D0D;
-  --ds-surface: #1A1A1A;
-  --ds-elevated: #2A2A2A;
-  --ds-cream: #F5F0E8;
-  --ds-muted: #A09A90;
-  --ds-red: #A63D2F;
-  --ds-blue: #1E3A6E;
-  --ds-yellow: #C8A43C;
-  --ds-green: #2D6B4A;
-  --ds-sienna: #B5602A;
-  --ds-gray: #5C5A56;
-  --ds-amethyst: #6B4E8B;
-  --ds-teal: #2A6B5E;
-}
-
-body {
-  font-family: 'Inter', sans-serif;
-  color: var(--ds-cream);
-  background: var(--ds-bg);
-  line-height: 1.6;
-}
-
-h1, h2, h3 {
-  font-family: 'Bebas Neue', sans-serif;
-  letter-spacing: 0.05em;
-}
-
-* { border-radius: 0; }
-```
-
----
-
-## Room Section → Document Section Mapping
-
-| Room Section | Document Section | Accent Color |
-|-------------|-----------------|-------------|
-| problem-definition | Problem Statement / Opportunity | Red #A63D2F |
-| market-analysis | Market Analysis / TAM-SAM-SOM | Yellow #C8A43C |
-| solution-design | Solution Architecture / Technical Approach | Gray #5C5A56 |
-| business-model | Business Model / Revenue Strategy | Green #2D6B4A |
-| competitive-analysis | Competitive Landscape / Moat | Sienna #B5602A |
-| team-execution | Team / Execution Plan | Blue #1E3A6E |
-| legal-ip | Legal / IP Strategy | Amethyst #6B4E8B |
-| financial-model | Financial Projections / Investment Ask | Teal #2A6B5E |
-
----
-
-## Implementation Plan
-
-### Plugin Files Needed
-
-```
-templates/
-  destijl-base.css          # Shared De Stijl stylesheet for PDF
-  investment-thesis.html    # Jinja2 template
-  executive-summary.html    # Jinja2 template
-  due-diligence.html        # Jinja2 template
-  research-paper.html       # Jinja2 template
-  profile.html              # Jinja2 template (PWS profiles)
-  pitch-deck.html           # Jinja2 template (landscape)
-  venture-brief.html        # Jinja2 template (1-page)
-assets/
-  fonts/BebasNeue-Regular.ttf  # Bundled font (~50KB)
-scripts/
-  render-pdf                # Orchestrator: reads room, selects template, renders PDF
-commands/
-  export.md                 # /mos:export thesis|summary|report|profile|deck|brief
-```
-
-### Command UX
-
-```
-/mos:export thesis      → Investment thesis PDF from full room
-/mos:export summary     → 1-2 page executive summary
-/mos:export report      → Due diligence report with TOC
-/mos:export profile     → PWS profile for a cohort member
-/mos:export deck        → Landscape pitch deck
-/mos:export brief       → 1-page venture brief
-```
-
-### Tri-Polar Surface Behavior
-
-| Surface | Behavior |
-|---------|----------|
-| **CLI** | `render-pdf` script generates PDF, opens with default viewer |
-| **Desktop** | Larry offers "Want me to export this as a PDF?" after key milestones |
-| **Cowork** | Export to shared `00_Context/exports/` directory, visible to all team members |
-
----
-
-## LaTeX Skill Pattern Reference
-
-The "LaTeX Handouts" Claude Code skill (mcpmarket.com) demonstrates the pattern:
-- Skill reads source content (slides/markdown)
-- Expands bullets into research-backed prose
-- Generates structured professional document
-- Outputs as standalone file
-
-MindrianOS follows the same pattern but uses HTML→PDF (WeasyPrint) instead of LaTeX→PDF,
-keeping zero dependencies while achieving the same professional output quality.
-
----
-
-## Font Bundling Note
-
-Bebas Neue is a free Google Font (SIL Open Font License). Bundle the .ttf in the plugin's
-assets/ directory (~50KB). WeasyPrint loads it via @font-face in the CSS template.
-No system font installation required.

package/references/hsi/HSI-TOOLS-REFERENCE.md

@@ -1,222 +0,0 @@
-# HSI & Reverse Salient Discovery — Tool Reference
-
-*Computational engines for auto-relationship building in the Data Room knowledge graph.*
-
----
-
-## What These Tools Do for MindrianOS
-
-The HSI (Hybrid Similarity Index) and Reverse Salient Discovery framework provide the **computational backbone for auto-discovering cross-relationships** in the Data Room. Instead of relying only on keyword matching or explicit cross-references, these tools find HIDDEN connections between room artifacts using dual similarity analysis.
-
-### The Core Insight
-
-When two room artifacts share **structural similarity** (same methods/terms) but LOW **semantic similarity** (different meanings/applications), OR vice versa — that GAP is where hidden innovation connections live.
-
-```
-HSI(artifact_i, artifact_j) = |BERT_similarity - LSA_similarity| × Integrative_Factor
-
-High HSI = "These two artifacts are connected in ways nobody sees"
-```
-
-### Application to Data Room
-
-| Source Tool | Data Room Application |
-|-------------|----------------------|
-| LSA (TF-IDF + SVD) | Structural similarity between room artifacts (shared terminology) |
-| BERT embeddings | Semantic similarity between room artifacts (shared meaning) |
-| HSI differential | Hidden connections: artifacts that share structure but not meaning, or meaning but not structure |
-| Reverse Salient detection | Cross-subsystem innovation opportunities — where a solution in one room section addresses a problem in another |
-| Top pairs extraction | The most surprising connections to surface to the user |
-
-### Integration with Meeting Filing
-
-After meeting segments are filed to room sections, the HSI pipeline runs:
-1. Compute LSA similarity between ALL room artifacts (including new meeting segments)
-2. Compute BERT/embedding similarity between all artifacts
-3. Find high-differential pairs (|BERT - LSA| > threshold)
-4. Surface as ENABLES/INFORMS/CONTRADICTS edges in the knowledge graph
-5. Larry says: "I found a hidden connection between your mentor's advice and your market analysis that nobody mentioned in the meeting."
-
----
-
-## Tool 1: HSI Computational Pipeline
-
-### Architecture
-
-```
-Room artifacts (text) → TF-IDF vectorization → TruncatedSVD (80 components) → LSA similarity matrix
-Room artifacts (text) → BERT tokenization → segment embeddings → BERT similarity matrix
-|BERT - LSA| = differential matrix → HSI score × integrative factor → top pairs = hidden connections
-```
-
-### Key Parameters
-
-| Parameter | Value | Purpose |
-|-----------|-------|---------|
-| max_features | 2000 | TF-IDF vocabulary size |
-| n_components | 80 | SVD dimensions (topic space) |
-| max_df | 0.5 | Ignore terms in >50% of docs |
-| BERT model | bert-large-cased | Semantic embeddings |
-| max_tokens | 512 | BERT segment size |
-| threshold | 0.3 | Minimum differential for reverse salient |
-
-### Adaptation for Plugin
-
-**Problem:** BERT-large requires ~1.3GB memory + GPU. Plugin must work on CPU with low memory.
-
-**Solution (already proven):** Gemini-Native HSI — replace BERT with Claude/Gemini embedding API:
-- `text-embedding-004` or Claude's native embeddings
-- API-based, no local GPU needed
-- Minutes instead of hours
-- Fits within plugin constraints
-
-**Alternative:** Use Pinecone (already integrated as Brain MCP) for embedding similarity. Room artifacts get embedded at filing time. Cross-similarity is a Pinecone query.
-
-### LSA Component (lsa.py adapted)
-
-```python
-# Adapted for room artifacts instead of papers
-from sklearn.feature_extraction.text import TfidfVectorizer
-from sklearn.decomposition import TruncatedSVD
-
-def compute_lsa_similarity(artifacts: list[str]) -> np.ndarray:
-    vectorizer = TfidfVectorizer(stop_words='english', max_features=2000, max_df=0.5)
-    X = vectorizer.fit_transform(artifacts)
-    svd = TruncatedSVD(n_components=min(80, len(artifacts)-1), random_state=256)
-    Z = svd.fit_transform(X)
-    sim = cosine_similarity(Z)
-    # Normalize to [0,1]
-    sim = (sim - sim.min()) / (sim.max() - sim.min() + 1e-12)
-    return sim
-```
-
-### Semantic Component (adapted for plugin)
-
-```python
-# Option A: Pinecone embeddings (if Brain connected)
-def compute_semantic_similarity_pinecone(artifact_ids: list[str]) -> np.ndarray:
-    # Query Pinecone for existing embeddings
-    # Compute pairwise cosine similarity
-    pass
-
-# Option B: Local lightweight embeddings (Tier 0)
-def compute_semantic_similarity_local(artifacts: list[str]) -> np.ndarray:
-    from sentence_transformers import SentenceTransformer
-    model = SentenceTransformer('all-MiniLM-L6-v2')  # 80MB, CPU-friendly
-    embeddings = model.encode(artifacts)
-    sim = cosine_similarity(embeddings)
-    sim = (sim - sim.min()) / (sim.max() - sim.min() + 1e-12)
-    return sim
-```
-
-### HSI Computation
-
-```python
-def compute_hsi(artifacts: list[str]) -> dict:
-    lsa = compute_lsa_similarity(artifacts)
-    semantic = compute_semantic_similarity_local(artifacts)  # or Pinecone
-
-    # Differential = hidden connections
-    gap = np.abs(semantic - lsa)
-    gap = (gap - gap.min()) / (gap.max() - gap.min() + 1e-12)
-
-    return {"lsa": lsa, "semantic": semantic, "hsi": gap}
-
-def top_hidden_connections(hsi: np.ndarray, artifacts: list, k=10):
-    n = hsi.shape[0]
-    pairs = []
-    for i in range(n):
-        for j in range(i+1, n):
-            if hsi[i,j] > 0.3:  # threshold
-                pairs.append((i, j, float(hsi[i,j])))
-    pairs.sort(key=lambda x: x[2], reverse=True)
-    return pairs[:k]
-```
-
----
-
-## Tool 2: Reverse Salient Discovery Framework
-
-### The 4-Phase Pipeline
-
-```
-Phase 1: ACQUIRE     — gather all room artifacts as "documents"
-Phase 2: ANALYZE     — compute dual similarity (LSA + semantic)
-Phase 3: DETECT      — find high-differential pairs (reverse salients)
-Phase 4: SYNTHESIZE  — generate innovation thesis for each pair
-```
-
-### Adaptation for Data Room Auto-Relationships
-
-Instead of analyzing academic papers across domains, we analyze ROOM ARTIFACTS across sections:
-
-| Framework Concept | Data Room Equivalent |
-|-------------------|---------------------|
-| Domain A papers | Artifacts in section A (e.g., market-analysis) |
-| Domain B papers | Artifacts in section B (e.g., solution-design) |
-| Cross-domain reverse salient | Hidden connection between sections |
-| Innovation thesis | Larry's insight: "This market trend enables that technical approach" |
-
-### Edge Types Generated
-
-| HSI Pattern | Edge Type | Example |
-|-------------|-----------|---------|
-| High structural, low semantic | ENABLES | "Same method, different application — this technique in solution-design could address the gap in market-analysis" |
-| Low structural, high semantic | INFORMS | "Different words, same concept — the mentor's advice about timing maps to the S-curve analysis" |
-| High differential + contradiction | CONTRADICTS | "These two artifacts say opposite things using different language" |
-| Multiple artifacts → same concept | CONVERGES | "Three meetings, three speakers, all pointing to the same insight from different angles" |
-| Change in one → invalidates other | INVALIDATES | "This new finding makes the assumption in financial-model stale" |
-
-### Neo4j Storage (when Brain connected)
-
-```cypher
-// Store discovered relationships
-MERGE (a1:RoomArtifact {id: $artifact1_id})
-MERGE (a2:RoomArtifact {id: $artifact2_id})
-CREATE (a1)-[:HSI_CONNECTION {
-  hsi_score: $score,
-  lsa_sim: $lsa,
-  semantic_sim: $semantic,
-  connection_type: $type,
-  discovered: datetime(),
-  human_approved: null
-}]->(a2)
-```
-
----
-
-## Integration with Phase 6 (Cross-Relationship Discovery Loop)
-
-Plan 06-03 builds the cross-relationship discovery loop. The HSI tools integrate as:
-
-```
-Artifact filed (from meeting or methodology session)
-    ↓
-Step 6: Cross-relationship scan
-    ↓
-Option A (Tier 0, no deps): Keyword-based (existing analyze-room)
-Option B (Tier 1, lightweight): LSA + MiniLM embeddings (this reference)
-Option C (Tier 2, Brain): LSA + Pinecone + Neo4j storage
-    ↓
-Hidden connections surfaced → Larry presents → User APPROVE/REJECT/DEFER
-    ↓
-Graph edges created → Dashboard updated → Knowledge compounds
-```
-
----
-
-## Source Files
-
-Original HSI codebase (Jonathan's research):
-- `lsa.py` — LSA similarity computation (TF-IDF + TruncatedSVD)
-- `sts_bert.py` — BERT semantic similarity (segment-aware cosine)
-- `comparison.py` — Differential analysis + reverse salient extraction
-- `paper_gathering.py` — Scopus API document acquisition
-- `paper_cleaning.py` — Text preprocessing
-- `lsa_bert_similarity.py` — Combined LSA + BERT pipeline
-- `hybrid_index.py` — HSI computation with integrative scoring
-
-Enhanced framework:
-- Reverse Salient Discovery Agent (4-phase pipeline)
-- Neo4j integration schema for storing/querying discoveries
-- Dynamic threshold adjustment based on domain characteristics