monomind 1.9.17 → 1.10.1

package/.claude/commands/monitoring/agents.md

@@ -1,71 +0,0 @@
----
-name: monitoring:agents
----
-
-# status agents
-
-Show detailed agent status — ID, type, current task, uptime, and success rate for all running agents.
-
-## Usage
-
-```bash
-npx monomind status agents [options]
-```
-
-## Options
-
-| Flag | Type | Description |
-|---|---|---|
-| `--format` | string | Output format: `json` |
-
-## Examples
-
-```bash
-# Show all agents
-npx monomind status agents
-
-# JSON output
-npx monomind status agents --format json
-```
-
-## Output Columns
-
-| Column | Description |
-|---|---|
-| ID | Agent identifier |
-| Type | Agent type (coder, reviewer, tester, etc.) |
-| Status | `healthy` / `degraded` / `stopped` |
-| Current Task | Task the agent is executing (or `-`) |
-| Uptime | How long the agent has been running |
-| Success | Task success rate (%) |
-
-## Related Commands
-
-```bash
-# Quick agent count overview (in main status)
-npx monomind status
-
-# Agent performance metrics by type
-npx monomind agent metrics
-
-# Agent health check
-npx monomind agent health
-
-# List all agents
-npx monomind agent list
-```
-
-## MCP Tool
-
-```javascript
-mcp__monomind__agent_list({
-  includeMetrics: true,
-  status: "all"
-})
-```
-
-## See Also
-
-- `status` — full system status including agents
-- `agent metrics` — performance metrics over time
-- `agent health` — per-agent health checks

package/.claude/commands/monitoring/status.md

@@ -1,108 +0,0 @@
----
-name: monitoring:status
----
-
-# status
-
-Show system status — swarm health, agents, tasks, memory, and MCP server. The primary monitoring command.
-
-## Usage
-
-```bash
-npx monomind status [options]
-npx monomind status <subcommand>
-```
-
-## Options
-
-| Flag | Short | Type | Default | Description |
-|---|---|---|---|---|
-| `--watch` | `-w` | boolean | `false` | Continuously refresh status (live view) |
-| `--interval` | `-i` | number | `2` | Refresh interval in seconds (watch mode) |
-| `--health-check` | — | boolean | `false` | Run structured health checks and exit |
-| `--format` | — | string | — | Output format: `json` |
-
-## Subcommands
-
-| Subcommand | Description |
-|---|---|
-| `status agents` | Detailed agent status table (ID, type, current task, uptime, success rate) |
-| `status tasks` | Detailed task status table (ID, type, priority, agent, progress) |
-| `status memory` | Memory backend stats (entries, size, HNSW, performance metrics) |
-
-## Examples
-
-```bash
-# One-shot status snapshot
-npx monomind status
-
-# Live watch mode (refreshes every 2s)
-npx monomind status --watch
-
-# Watch with custom interval
-npx monomind status --watch -i 5
-
-# Health checks with pass/warn/fail output
-npx monomind status --health-check
-
-# JSON output for scripting
-npx monomind status --format json
-
-# Detailed agent table
-npx monomind status agents
-
-# Detailed task table
-npx monomind status tasks
-
-# Memory backend details
-npx monomind status memory
-```
-
-## Status Display Sections
-
-- **Swarm** — ID, topology, health (`healthy` / `degraded` / `stopped`), uptime
-- **Agents** — active / idle / total counts
-- **Tasks** — pending / running / completed / failed / total
-- **Memory** — backend, entries, size, search time, cache hit rate
-- **MCP Server** — running state, transport, port
-- **Performance** — CPU usage, memory usage, Flash Attention, vector search speed
-
-## Health Check Mode
-
-`--health-check` runs structured checks and exits with code 0 (all pass) or 1 (any fail):
-
-| Check | Pass Condition |
-|---|---|
-| System Running | MCP/swarm reachable |
-| Swarm Health | status = `healthy` |
-| Agents Available | active > 0 |
-| MCP Server | running |
-| Memory Backend | backend != `none` |
-| Task Success Rate | < 5% failure rate |
-
-## Watch Mode
-
-`--watch` clears the screen and re-renders on each interval. Press `Ctrl+C` to exit.
-
-## MCP Tools (equivalent)
-
-```javascript
-// Swarm status
-mcp__monomind__swarm_status({ includeMetrics: true })
-
-// Memory stats
-mcp__monomind__memory_stats({})
-
-// Task summary
-mcp__monomind__task_summary({})
-
-// Agent list
-mcp__monomind__agent_list({ includeMetrics: true, status: "all" })
-```
-
-## See Also
-
-- `agent metrics` — performance metrics per agent type
-- `agent health` — agent-specific health check
-- `swarm status` — swarm-specific status
-- `doctor` — comprehensive system diagnostics

package/.claude/commands/monograph/README.md

@@ -1,102 +0,0 @@
----
-name: monograph:README
-description: Monograph skills index — build, search, and explore the knowledge graph across code, docs, and PDFs using real CLI subcommands and MCP tools
----
-
-# Monograph Commands
-
-Knowledge graph for code and documents — build, search, and explore relationships across your entire codebase and documentation.
-
-Alias: `monomind kg`
-
-## CLI Subcommands
-
-| Subcommand | Description |
-|---|---|
-| `monograph build` | Build knowledge graph from code + docs + PDFs |
-| `monograph wiki` | Scan all docs and PDFs into a searchable knowledge graph |
-| `monograph search` | Search the graph (BM25 / semantic / hybrid) |
-| `monograph stats` | Show node/edge counts and top concepts |
-| `monograph watch` | Watch for file changes and rebuild incrementally |
-
-## Quick Reference
-
-```bash
-# First-time build (code + all docs)
-npx monomind monograph build
-
-# Doc/wiki-focused build with Claude semantic extraction
-npx monomind monograph wiki --llm
-
-# Search
-npx monomind monograph search -q "authentication flow"
-npx monomind monograph search -q "pipeline" --mode semantic --label Section
-
-# Stats
-npx monomind monograph stats --top 20
-
-# Auto-rebuild on changes
-npx monomind monograph watch
-```
-
-## Files
-
-- [monograph-build.md](./monograph-build.md) — Full build (code + docs + PDFs)
-- [monograph-wiki.md](./monograph-wiki.md) — Doc/PDF-focused wiki build
-- [monograph-search.md](./monograph-search.md) — Search the knowledge graph
-- [monograph-stats.md](./monograph-stats.md) — Graph statistics
-- [monograph-watch.md](./monograph-watch.md) — Watch mode (incremental rebuild)
-
-## MCP Tools
-
-The monograph MCP tools (available in Claude Code via monomind MCP server) provide programmatic access to the graph without invoking the CLI:
-
-| Tool | Use When |
-|---|---|
-| `mcp__monomind__monograph_build` | Build/rebuild the graph |
-| `mcp__monomind__monograph_query` | BM25 keyword search; returns file + line number |
-| `mcp__monomind__monograph_suggest` | Start every task — returns relevant files ranked by task description |
-| `mcp__monomind__monograph_god_nodes` | Find high-centrality internal files |
-| `mcp__monomind__monograph_stats` | Node/edge counts |
-| `mcp__monomind__monograph_report` | Generate GRAPH_REPORT.md |
-| `mcp__monomind__monograph_shortest_path` | How two modules are connected |
-| `mcp__monomind__monograph_community` | Files forming a cohesive cluster |
-| `mcp__monomind__monograph_surprises` | Unexpected cross-community edges |
-| `mcp__monomind__monograph_export` | Export graph in various formats |
-| `mcp__monomind__monograph_watch` | Start watch mode via MCP |
-| `mcp__monomind__monograph_watch_stop` | Stop watch mode |
-| `mcp__monomind__monograph_context` | 360-degree view of a file: importers, imports, siblings |
-| `mcp__monomind__monograph_health` | Index staleness (commits behind HEAD) |
-
-## Node Types
-
-| Type | Description |
-|---|---|
-| `File` | Source code or document file |
-| `Section` | Markdown heading or document section |
-| `Function` | Code function or method |
-| `Class` | Code class or interface |
-| `Concept` | Extracted semantic concept |
-| `PDF` | PDF document chunk |
-
-## Edge Types
-
-| Relation | Meaning |
-|---|---|
-| `IMPORTS` | Code import dependency |
-| `DEFINES` | File defines symbol |
-| `TAGGED_AS` | Section tagged with concept |
-| `CO_OCCURS` | Concepts appear together |
-| `INFERRED` | Claude-extracted semantic relationship |
-| `DESCRIBES` / `CAUSES` / `PART_OF` | LLM-enriched semantic edges |
-
-## When to Use CLI vs MCP
-
-- **CLI** (`npx monomind monograph ...`) — One-time builds, manual searches, watching from terminal
-- **MCP tools** (`mcp__monomind__monograph_*`) — Claude Code integration, programmatic queries during tasks
-
-## See Also
-
-- `memory` — Vector memory storage (separate from graph)
-- `hooks intelligence` — Pattern learning
-- CLAUDE.md Knowledge Graph section — workflow guidance for multi-file tasks

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