monomind 1.19.0 → 2.0.1

package/.claude/commands/monograph/monograph-build.md

@@ -1,79 +0,0 @@
----
-name: monograph:monograph-build
-description: Build the knowledge graph from code, docs (md/txt/rst), and PDFs — full index with optional Claude LLM semantic extraction
----
-
-# monograph build
-
-Build the knowledge graph from code, docs (md/txt/rst), and PDFs.
-
-## Usage
-
-```bash
-npx monomind monograph build [options]
-```
-
-## Options
-
-| Flag | Short | Type | Default | Description |
-|---|---|---|---|---|
-| `--path` | `-p` | string | cwd | Root path to index |
-| `--code-only` | — | boolean | `false` | Index only code files, skip documents |
-| `--llm` | — | boolean | `false` | Enable Claude semantic extraction (requires `ANTHROPIC_API_KEY`) |
-| `--llm-sections` | — | number | `50` | Max sections to enrich with LLM |
-| `--force` | `-f` | boolean | `false` | Force full rebuild even if index is fresh |
-
-## Examples
-
-```bash
-# Build code + all documents (default)
-npx monomind monograph build
-
-# Code only — skip docs and PDFs
-npx monomind monograph build --code-only
-
-# With Claude semantic extraction
-npx monomind monograph build --llm
-
-# Enrich up to 200 sections with Claude
-npx monomind monograph build --llm --llm-sections 200
-
-# Index a specific path
-npx monomind monograph build -p ./src
-
-# Force full rebuild
-npx monomind monograph build --force
-```
-
-## What Gets Indexed
-
-- **Code files** — functions, classes, imports, exports → structured graph nodes
-- **Markdown/MDX** — headings become `Section` nodes; links become edges
-- **Plain text / RST** — chunked into `Section` nodes
-- **PDFs** — text extracted and chunked into nodes
-
-Ignored directories: `node_modules`, `.git`, `dist`, `build`, `__pycache__`, `.cache`, `coverage`, `.monomind`, `vendor`, `target`
-
-## LLM Enrichment
-
-When `--llm` is passed and `ANTHROPIC_API_KEY` is set, Claude extracts typed semantic relationships between sections (e.g. `DESCRIBES`, `CAUSES`, `PART_OF`). These become `INFERRED` edges in the graph, enabling richer semantic search.
-
-## Output
-
-After build, the graph is stored at `.monomind/monograph.db`. Run `monograph stats` to see node/edge counts.
-
-## MCP Tool
-
-```javascript
-mcp__monomind__monograph_build({
-  path: "./",
-  codeOnly: false,
-  force: false
-})
-```
-
-## See Also
-
-- `monograph wiki` — doc/PDF-focused build with better output for documentation projects
-- `monograph stats` — view what was indexed
-- `monograph watch` — auto-rebuild on file changes

package/.claude/commands/monograph/monograph-search.md

@@ -1,96 +0,0 @@
----
-name: monograph:monograph-search
-description: Search the knowledge graph using BM25 keyword search, semantic (embedding) search, or hybrid RRF-merged results — filter by node type (Section, Function, Class, File, Concept)
----
-
-# monograph search
-
-Search the knowledge graph using BM25 keyword search, semantic (embedding) search, or hybrid RRF-merged results.
-
-## Usage
-
-```bash
-npx monomind monograph search [options]
-```
-
-## Options
-
-| Flag | Short | Type | Default | Required | Description |
-|---|---|---|---|---|---|
-| `--query` | `-q` | string | — | yes | Search query text |
-| `--limit` | `-l` | number | `15` | no | Maximum results to return |
-| `--label` | — | string | — | no | Filter by node type: `Section`, `Function`, `Concept`, `File`, `Class` |
-| `--mode` | `-m` | string | `hybrid` | no | Search mode: `bm25`, `semantic`, `hybrid` |
-| `--path` | `-p` | string | cwd | no | Root path (location of `.monomind/monograph.db`) |
-
-## Examples
-
-```bash
-# Hybrid search (default) — best general-purpose
-npx monomind monograph search -q "authentication flow"
-
-# Keyword search — exact term matching
-npx monomind monograph search -q "JWT" --mode bm25
-
-# Semantic search — concept/meaning matching
-npx monomind monograph search -q "pipeline architecture" --mode semantic
-
-# Filter to doc sections only
-npx monomind monograph search -q "API design" --label Section
-
-# Find function definitions
-npx monomind monograph search -q "parseToken" --label Function
-
-# More results
-npx monomind monograph search -q "error handling" -l 30
-```
-
-## Search Modes
-
-| Mode | Algorithm | Best For |
-|---|---|---|
-| `hybrid` | RRF merge of BM25 + semantic | General purpose (recommended) |
-| `bm25` | Full-text BM25 ranking | Exact term matching, known symbol names |
-| `semantic` | Embedding cosine similarity | Conceptual queries, meaning-based lookup |
-
-Hybrid mode runs both BM25 and semantic internally, then merges with Reciprocal Rank Fusion (RRF).
-
-## Node Labels (--label filter)
-
-| Label | Represents |
-|---|---|
-| `File` | Source or document files |
-| `Section` | Markdown headings / doc sections |
-| `Function` | Code functions and methods |
-| `Class` | Code classes and interfaces |
-| `Concept` | Extracted semantic concepts |
-
-## Prerequisites
-
-Run `monograph build` or `monograph wiki` first to create the index.
-
-```bash
-# If you see "No knowledge graph found":
-npx monomind monograph build
-```
-
-## MCP Tool
-
-The MCP equivalent for Claude Code integration:
-
-```javascript
-mcp__monomind__monograph_query({
-  query: "authentication flow",
-  limit: 15,
-  label: "Section",
-  mode: "hybrid"
-})
-```
-
-Use `mcp__monomind__monograph_suggest` for task-oriented lookup that returns files ranked by relevance to your current work.
-
-## See Also
-
-- `monograph build` — build the graph index
-- `monograph stats` — see what's indexed
-- `monograph wiki` — doc-focused build

package/.claude/commands/monograph/monograph-stats.md

@@ -1,53 +0,0 @@
----
-name: monograph:monograph-stats
-description: Show knowledge graph statistics — node counts by type, edge type breakdown, and top concepts by importance score
----
-
-# monograph stats
-
-Show knowledge graph statistics — node counts by type, edge type breakdown, and top concepts by importance.
-
-## Usage
-
-```bash
-npx monomind monograph stats [options]
-```
-
-## Options
-
-| Flag | Short | Type | Default | Description |
-|---|---|---|---|---|
-| `--path` | `-p` | string | cwd | Root path (location of `.monomind/monograph.db`) |
-| `--top` | — | number | `10` | Number of top concepts to show |
-
-## Examples
-
-```bash
-# Show graph statistics
-npx monomind monograph stats
-
-# Show top 20 concepts
-npx monomind monograph stats --top 20
-
-# Stats for a different project path
-npx monomind monograph stats -p ./other-project
-```
-
-## Output
-
-- **Nodes table** — count per node type (`File`, `Section`, `Function`, `Class`, `Concept`) with bar chart
-- **Edges table** — count per relation type (`IMPORTS`, `TAGGED_AS`, `CO_OCCURS`, `INFERRED`, etc.)
-- **Top N Concepts** — ranked by importance score and section count, shown with star ratings
-- **Summary line** — CO_OCCURS edge count and LLM-inferred edge count
-
-## MCP Tool
-
-```javascript
-mcp__monomind__monograph_stats()
-```
-
-## See Also
-
-- `monograph build` — build or rebuild the graph
-- `monograph search` — search across nodes
-- `monograph watch` — auto-rebuild on changes

package/.claude/commands/monograph/monograph-watch.md

@@ -1,63 +0,0 @@
----
-name: monograph:monograph-watch
-description: Watch for file changes and incrementally rebuild the knowledge graph — keeps the graph fresh during active development or documentation writing
----
-
-# monograph watch
-
-Watch for file changes and incrementally rebuild the knowledge graph. Keeps the graph fresh during active development.
-
-## Usage
-
-```bash
-npx monomind monograph watch [options]
-```
-
-## Options
-
-| Flag | Short | Type | Default | Description |
-|---|---|---|---|---|
-| `--path` | `-p` | string | cwd | Root path to watch |
-| `--llm` | — | boolean | `false` | Enable LLM enrichment on each rebuild (requires `ANTHROPIC_API_KEY`) |
-
-## Examples
-
-```bash
-# Watch and rebuild on any file change
-npx monomind monograph watch
-
-# Watch with Claude semantic enrichment on each rebuild
-npx monomind monograph watch --llm
-
-# Watch a specific path
-npx monomind monograph watch -p ./docs
-```
-
-## Behavior
-
-- Runs until `Ctrl+C`
-- Detects changes to code files, markdown, text, RST, and PDFs
-- Triggers incremental rebuild (only changed files re-processed)
-- Outputs progress per phase as changes are detected
-
-## When to Use
-
-- During active documentation writing — graph stays current as you write
-- During refactoring — relationships update as imports change
-- CI environments — run in background to keep graph fresh for search queries
-
-## MCP Tools
-
-```javascript
-// Start watch via MCP
-mcp__monomind__monograph_watch({ path: "./" })
-
-// Stop watch via MCP
-mcp__monomind__monograph_watch_stop()
-```
-
-## See Also
-
-- `monograph build` — one-time full build
-- `monograph wiki` — doc-focused build
-- `monograph stats` — check current graph state

package/.claude/commands/monograph/monograph-wiki.md

@@ -1,91 +0,0 @@
----
-name: monograph:monograph-wiki
-description: Scan all docs and PDFs and build a searchable knowledge graph — optimized for documentation-heavy projects with Claude LLM semantic extraction
----
-
-# monograph wiki
-
-Scan all docs and PDFs in the project and build a searchable knowledge graph. Optimized for documentation-heavy projects.
-
-## Usage
-
-```bash
-npx monomind monograph wiki [options]
-```
-
-## Options
-
-| Flag | Short | Type | Default | Description |
-|---|---|---|---|---|
-| `--path` | `-p` | string | cwd | Root path to scan |
-| `--llm` | — | boolean | `false` | Enrich with Claude semantic extraction (requires `ANTHROPIC_API_KEY`) |
-| `--llm-sections` | — | number | `100` | Max sections for LLM enrichment |
-| `--force` | `-f` | boolean | `false` | Force full rebuild |
-
-## Examples
-
-```bash
-# Build knowledge graph from all docs and PDFs
-npx monomind monograph wiki
-
-# With Claude semantic extraction
-npx monomind monograph wiki --llm
-
-# Deep enrichment — process 200 sections with Claude
-npx monomind monograph wiki --llm --llm-sections 200
-
-# Specific docs folder
-npx monomind monograph wiki -p ./docs
-
-# Force full rebuild
-npx monomind monograph wiki --force
-```
-
-## What Gets Indexed
-
-Scans for files with extensions: `.md`, `.mdx`, `.txt`, `.rst`, `.pdf`
-
-| Type | Processing |
-|---|---|
-| `.md` / `.mdx` | Headings → `Section` nodes with hierarchical structure |
-| `.txt` / `.rst` | Chunked → `Section` nodes |
-| `.pdf` | Text extracted → PDF chunk nodes |
-
-## Difference from `build`
-
-| | `build` | `wiki` |
-|---|---|---|
-| Code files | Yes | No |
-| Documents | Yes | Yes |
-| PDFs | Yes | Yes |
-| LLM default sections | 50 | 100 |
-| Best for | Mixed projects | Doc-heavy / knowledge bases |
-
-## LLM Enrichment
-
-With `--llm`, Claude extracts semantic relationships between sections:
-- `DESCRIBES` — section explains a concept
-- `CAUSES` — one event leads to another
-- `PART_OF` — hierarchical membership
-- `CO_OCCURS` — concepts appear together
-
-These `INFERRED` edges make semantic search significantly more accurate.
-
-## After Build
-
-```bash
-# Search your wiki
-npx monomind monograph search -q "your query"
-
-# View statistics
-npx monomind monograph stats
-
-# Auto-rebuild on edits
-npx monomind monograph watch
-```
-
-## See Also
-
-- `monograph build` — full build including code files
-- `monograph search` — search the graph
-- `monograph stats` — node/edge breakdown

package/.claude/commands/optimization/auto-topology.md

@@ -1,85 +0,0 @@
----
-name: optimization:auto-topology
-description: Automatically select the optimal swarm topology based on task complexity — use pre-task hook recommendations, swarm init flags, and performance optimize CLI
----
-
-# Auto Topology Selection
-
-Automatically select the optimal swarm topology based on task complexity so you don't have to configure it manually.
-
-## How It Works
-
-### 1. Get a Routing Recommendation
-
-Before spawning agents, run the `pre-task` hook. It analyzes task complexity and recommends a topology:
-
-```bash
-npx monomind hooks pre-task -d "Refactor authentication system with JWT, add tests, update docs"
-```
-
-Output includes agent and topology suggestions.
-
-### 2. Initialize the Swarm With the Recommended Topology
-
-```bash
-# Simple/medium tasks — hierarchical (anti-drift, tight control)
-npx monomind swarm init --topology hierarchical --max-agents 6 --strategy specialized
-
-# Complex multi-domain tasks — hierarchical-mesh (peer communication + queen)
-npx monomind swarm init --topology hierarchical-mesh --max-agents 12 --strategy specialized
-```
-
-### Topology Selection Guide
-
-| Complexity | Agents Needed | Recommended Topology |
-|---|---|---|
-| Simple (single file) | 1–2 | `star` — skip swarm, use Edit tool directly |
-| Medium | 3–5 | `hierarchical` |
-| Complex (multi-module) | 6–8 | `hierarchical` |
-| Large (10+ agents) | 10–15 | `hierarchical-mesh` |
-| Sequential pipeline | any | `ring` |
-
-## Optimize Existing Swarm Topology
-
-If a swarm is already running, optimize its topology via the coordination MCP tool:
-
-```javascript
-mcp__monomind__coordination_topology({
-  swarmId: "current",
-  optimize: true
-})
-```
-
-Or via the performance CLI:
-
-```bash
-# Analyze and recommend optimizations (dry run)
-npx monomind performance optimize --target all --dry-run
-
-# Apply recommended optimizations
-npx monomind performance optimize --target all --apply
-```
-
-## Hook Integration
-
-`pre-task` fires automatically if wired in `settings.json`:
-
-```json
-{
-  "hooks": {
-    "PreToolUse": [{
-      "matcher": "^Task$",
-      "hooks": [{
-        "type": "command",
-        "command": "npx monomind hooks pre-task -d '${tool.params.description}'"
-      }]
-    }]
-  }
-}
-```
-
-## See Also
-
-- `swarm init` — initialize swarm with explicit topology
-- `performance optimize` — system-level performance tuning
-- `hooks pre-task` — get routing and topology recommendations

package/.claude/commands/optimization/performance-optimize.md

@@ -1,79 +0,0 @@
----
-name: optimization:performance-optimize
-description: Analyze and apply system-level performance optimizations — memory, CPU, and latency using npx monomind performance optimize
----
-
-# performance optimize
-
-Analyze and apply system-level performance optimizations — memory, CPU, and latency.
-
-## Usage
-
-```bash
-npx monomind performance optimize [options]
-```
-
-## Options
-
-| Flag | Short | Type | Default | Description |
-|---|---|---|---|---|
-| `--target` | `-t` | string | `all` | Optimization target: `memory`, `cpu`, `latency`, `all` |
-| `--apply` | `-a` | boolean | `false` | Apply recommended optimizations |
-| `--dry-run` | `-d` | boolean | `false` | Show recommended changes without applying |
-
-## Examples
-
-```bash
-# Analyze and show recommendations (no changes)
-npx monomind performance optimize --dry-run
-
-# Optimize everything and apply
-npx monomind performance optimize --target all --apply
-
-# Memory-specific optimization
-npx monomind performance optimize --target memory --apply
-
-# CPU optimization only
-npx monomind performance optimize --target cpu --apply
-
-# Latency optimization (MCP response time)
-npx monomind performance optimize --target latency --apply
-```
-
-## Optimization Targets
-
-| Target | What It Optimizes |
-|---|---|
-| `memory` | Memory backend compression, HNSW rebuild, cache eviction |
-| `cpu` | Agent pool sizing, task batching, concurrency limits |
-| `latency` | MCP response caching, neural model quantization |
-| `all` | All of the above |
-
-## Related Commands
-
-```bash
-# Find bottlenecks before optimizing
-npx monomind performance bottleneck
-
-# Run benchmarks to measure before/after
-npx monomind performance benchmark --suite all
-
-# View current performance metrics
-npx monomind performance metrics
-```
-
-## MCP Tool
-
-```javascript
-mcp__monomind__performance_optimize({
-  target: "all",
-  apply: false
-})
-```
-
-## See Also
-
-- `performance bottleneck` — diagnose what to optimize first
-- `performance benchmark` — measure optimization impact
-- `performance metrics` — track performance over time
-- `neural optimize` — optimize neural model weights

package/.claude/commands/pair/README.md

@@ -1,79 +0,0 @@
----
-name: pair:README
-description: Pair programming with Claude Code — driver/navigator modes, TDD sessions, review sessions, Task tool agent spawning, and hooks integration
----
-
-# Pair Programming with Claude Code
-
-Collaborative development using Claude Code as your AI pair partner. No special CLI needed — Claude Code IS the pair partner.
-
-## How It Works
-
-Pair programming with Claude Code means structuring your conversation to get the most out of the collaboration. Depending on your goal, you drive or Claude drives.
-
-## Quick Start
-
-**You drive, Claude reviews (driver mode):**
-> "I'm going to implement JWT auth. Review my approach and flag issues as we go."
-
-**Claude drives, you guide (navigator mode):**
-> "Implement a JWT auth middleware for Express with refresh token support. I'll review each piece."
-
-**TDD session:**
-> "Let's do TDD for this shopping cart feature. Write the failing tests first, then we'll implement."
-
-**Review session:**
-> "Review all the changes I've made today to `src/auth/`. Focus on security issues."
-
-## Using the Pair Programming Skill
-
-Invoke the `pair-programming` skill for structured collaboration:
-
-```
-/pair-programming
-```
-
-This loads the workflow guide and sets up the session context.
-
-## Spawning a Specialized Agent
-
-For long-running or complex sessions, spawn a dedicated coding agent via the Task tool:
-
-```javascript
-Task({
-  prompt: "Act as a senior developer pair programming partner. The user is implementing JWT auth. Review their code as they write it, suggest improvements, catch issues, and explain patterns. Start by asking what they want to build.",
-  subagent_type: "Senior Developer",
-  run_in_background: false
-})
-```
-
-Or use a specific specialist:
-- `superpowers:test-driven-development` — TDD-focused pairing
-- `superpowers:systematic-debugging` — debugging sessions
-- `superpowers:receiving-code-review` — code review sessions
-
-## Hooks Integration
-
-Use hooks to track pair session quality:
-
-```bash
-# Register session start
-npx monomind hooks pre-task -d "Pair programming: implement JWT auth"
-
-# After session, record outcome
-npx monomind hooks post-task --task-id <id> --success true --quality 0.95
-```
-
-## Files
-
-- [modes.md](./modes.md) — Driver, navigator, TDD, review, debug modes
-- [session.md](./session.md) — Session lifecycle and real monitoring commands
-- [examples.md](./examples.md) — Real-world pair programming scenarios
-
-## See Also
-
-- `superpowers:pair-programming` — structured pair programming skill
-- `superpowers:test-driven-development` — TDD workflow
-- `superpowers:systematic-debugging` — debugging workflow
-- `superpowers:requesting-code-review` — code review workflow
-- `hooks pre-task` — register task start and get recommendations