@monoes/monomindcli 2.7.3 → 2.7.5

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@monoes/monomindcli",
-  "version": "2.7.3",
+  "version": "2.7.5",
   "type": "module",
   "description": "CLI engine for Monomind — an open-source MCP server that extends Claude Code with a codebase knowledge graph (tree-sitter + SQLite), persistent memory, multi-agent task coordination, and session hooks. MIT licensed, fully local.",
   "main": "dist/src/index.js",

package/.claude/skills/github-toolkit/SKILL.md

@@ -1,60 +0,0 @@
----
-name: github-toolkit
-description: >
-  GitHub workflow guidance for monomind projects — issues, PRs, releases,
-  repo structure, and multi-package sync. Trigger on "open a PR", "manage
-  issues", "cut a release", "sync packages", or any GitHub Actions/repo
-  automation request. All GitHub operations use the `gh` CLI plus monomind's
-  MCP GitHub tools — there is no `monomind github` CLI command group.
----
-
-# GitHub Toolkit
-
-Guidance for GitHub-integrated workflows in monomind projects. All GitHub
-operations go through the `gh` CLI directly (for PRs, issues, releases) or
-through monomind's MCP GitHub tools when running inside a swarm.
-
-## Core operations
-
-- **Issues** — triage, label, and track via `gh issue` or `mcp__monomind__github_issue_track`.
-  See `.claude/commands/github/issue-tracker.md`.
-- **Pull requests** — create, review, and merge via `gh pr` or `mcp__monomind__github_pr_manage`.
-  See `.claude/commands/github/pr-manager.md`.
-- **Releases** — version bump, changelog, tag, and publish coordination.
-  See `.claude/commands/github/release-manager.md`.
-- **Repo structure** — multi-repo layout and package boundary decisions.
-  See `.claude/commands/github/repo-architect.md`.
-- **Multi-package sync** — version alignment and dependency sync across a monorepo.
-  See `.claude/commands/github/sync-coordinator.md`.
-- **Integration modes overview** — which mode to use for which workflow.
-  See `.claude/commands/github/github-modes.md`.
-
-## Quick reference
-
-```bash
-# Issues
-gh issue list --state open
-gh issue create --title "..." --body "..."
-
-# Pull requests
-gh pr create --title "..." --body "..."
-gh pr view <number> --json reviews,statusCheckRollup
-
-# Releases
-gh release create v1.2.3 --generate-notes
-```
-
-## MCP tools (when running inside a swarm)
-
-```javascript
-mcp__monomind__github_pr_manage({ action: "review", pr: 123 })
-mcp__monomind__github_issue_track({ action: "list", state: "open" })
-mcp__monomind__github_metrics({ repo: "owner/repo" })
-```
-
-## When to reach for the full docs
-
-Each linked command file under `.claude/commands/github/` has the complete
-option/flag reference and swarm-coordination patterns for its area — read
-the relevant one before doing multi-step GitHub automation (e.g. spawning
-a `pr-manager` or `release-manager` agent).

package/.claude/skills/memory-toolkit/SKILL.md

@@ -1,75 +0,0 @@
----
-name: memory-toolkit
-description: >
-  Use monomind's persistent memory store (LanceDB + pure-JS HNSW) to save,
-  search, list, and retrieve cross-session knowledge — patterns, solutions,
-  decisions. Trigger on "remember this", "store in memory", "search memory",
-  "have we solved this before", "recall past decisions", or before starting
-  work that benefits from prior context (debugging, refactors, repeated tasks).
----
-
-# Memory Toolkit
-
-Monomind ships a persistent, namespaced memory store backed by LanceDB with
-a pure-JS HNSW index for approximate nearest-neighbor vector search. Use it
-to avoid re-solving the same problem twice across sessions.
-
-## Before starting non-trivial work
-
-Search for prior art first:
-
-```bash
-npx monomind memory search --query "[task keywords]" --namespace patterns
-npx monomind memory search --query "[task keywords]" --namespace solutions
-```
-
-## Store data
-
-```bash
-# REQUIRED: --key and --value. OPTIONAL: --namespace (default: "default"), --ttl, --tags
-npx monomind memory store --key "pattern-auth" --value "JWT with refresh tokens" --namespace patterns
-npx monomind memory store --key "bug-fix-123" --value "Fixed null check in parser" --namespace solutions --tags "bugfix,auth"
-```
-
-## Search data (semantic / keyword / hybrid)
-
-```bash
-# REQUIRED: --query. OPTIONAL: --namespace, --limit, --threshold, --type
-npx monomind memory search --query "authentication patterns"
-npx monomind memory search --query "JWT" --type keyword
-npx monomind memory search --query "error handling" --namespace patterns --limit 5
-```
-
-| Search type | Description                  | Best for                  |
-| ----------- | ----------------------------- | -------------------------- |
-| `semantic`  | Vector similarity search       | Concept / meaning matching |
-| `keyword`   | BM25 full-text search          | Exact term matching        |
-| `hybrid`    | Combined semantic + keyword    | General purpose (default)  |
-
-Use `--build-hnsw` before searching large memory stores (1,000+ entries) —
-it builds a pure-JS HNSW index for O(log n) queries instead of O(n) linear
-scan (one-time build cost).
-
-## List and retrieve
-
-```bash
-npx monomind memory list --namespace patterns --limit 10
-npx monomind memory retrieve --key "pattern-auth" --namespace patterns
-```
-
-## MCP equivalents
-
-```javascript
-mcp__monomind__memory_store({ key: "pattern-auth", value: "...", namespace: "patterns" })
-mcp__monomind__memory_search({ query: "authentication patterns", namespace: "default", limit: 10, threshold: 0.7, type: "hybrid" })
-```
-
-## After completing non-trivial work
-
-Store what worked so the next session (or agent) doesn't start from zero:
-
-```bash
-npx monomind memory store --key "[short-name]" --value "[what worked and why]" --namespace patterns
-```
-
-See also: `.claude/commands/memory/memory-search.md` for the full flag reference.

package/dist/src/mcp-tools/coherence/causal-infer.d.ts

@@ -1,15 +0,0 @@
-/**
- * Causal Graph Analysis Tool - pr_causal_infer
- *
- * Analyzes causal graph structure to assess identifiability.
- * Identifies confounders, finds backdoor paths, and determines
- * whether a causal effect can be identified from the graph.
- * Does NOT estimate causal effect magnitude (that requires data).
- */
-import type { MCPTool } from './types.js';
-/**
- * pr_causal_infer MCP Tool Definition
- */
-export declare const causalInferTool: MCPTool;
-export default causalInferTool;
-//# sourceMappingURL=causal-infer.d.ts.map

package/dist/src/mcp-tools/coherence/causal-infer.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/mcp-tools/coherence/causal-infer.js

@@ -1,333 +0,0 @@
-/**
- * Causal Graph Analysis Tool - pr_causal_infer
- *
- * Analyzes causal graph structure to assess identifiability.
- * Identifies confounders, finds backdoor paths, and determines
- * whether a causal effect can be identified from the graph.
- * Does NOT estimate causal effect magnitude (that requires data).
- */
-import { CausalInputSchema, successResult, errorResult, } from './types.js';
-// Default logger
-const defaultLogger = {
-    debug: (msg, meta) => console.debug(`[pr_causal_infer] ${msg}`, meta),
-    info: (msg, meta) => console.info(`[pr_causal_infer] ${msg}`, meta),
-    warn: (msg, meta) => console.warn(`[pr_causal_infer] ${msg}`, meta),
-    error: (msg, meta) => console.error(`[pr_causal_infer] ${msg}`, meta),
-};
-function buildGraphStructure(graph) {
-    const nodes = new Map();
-    // Initialize nodes
-    for (const nodeId of graph.nodes) {
-        nodes.set(nodeId, {
-            id: nodeId,
-            parents: new Set(),
-            children: new Set(),
-        });
-    }
-    // Add edges
-    for (const [from, to] of graph.edges) {
-        const fromNode = nodes.get(from);
-        const toNode = nodes.get(to);
-        if (fromNode && toNode) {
-            fromNode.children.add(to);
-            toNode.parents.add(from);
-        }
-    }
-    return nodes;
-}
-/**
- * Find all ancestors of a node (including the node itself)
- */
-function findAncestors(nodeId, graph) {
-    const ancestors = new Set();
-    const queue = [nodeId];
-    while (queue.length > 0) {
-        const current = queue.shift();
-        if (ancestors.has(current))
-            continue;
-        ancestors.add(current);
-        const node = graph.get(current);
-        if (node) {
-            for (const parent of node.parents) {
-                queue.push(parent);
-            }
-        }
-    }
-    return ancestors;
-}
-/**
- * Find all descendants of a node (including the node itself)
- */
-function findDescendants(nodeId, graph) {
-    const descendants = new Set();
-    const queue = [nodeId];
-    while (queue.length > 0) {
-        const current = queue.shift();
-        if (descendants.has(current))
-            continue;
-        descendants.add(current);
-        const node = graph.get(current);
-        if (node) {
-            for (const child of node.children) {
-                queue.push(child);
-            }
-        }
-    }
-    return descendants;
-}
-/**
- * Identify confounders (common causes of treatment and outcome)
- */
-function identifyConfounders(treatment, outcome, graph) {
-    const treatmentAncestors = findAncestors(treatment, graph);
-    const outcomeAncestors = findAncestors(outcome, graph);
-    // Confounders are ancestors of both treatment and outcome
-    // that are not the treatment itself
-    const confounders = [];
-    for (const ancestor of treatmentAncestors) {
-        if (ancestor !== treatment && ancestor !== outcome && outcomeAncestors.has(ancestor)) {
-            confounders.push(ancestor);
-        }
-    }
-    return confounders;
-}
-/**
- * Find backdoor paths from treatment to outcome
- * A backdoor path is a path that goes into the treatment node
- */
-function findBackdoorPaths(treatment, outcome, graph, maxPaths = 10) {
-    const backdoorPaths = [];
-    const treatmentNode = graph.get(treatment);
-    if (!treatmentNode)
-        return [];
-    // Start from each parent of treatment (backdoor)
-    for (const parent of treatmentNode.parents) {
-        const paths = findAllPaths(parent, outcome, graph, new Set([treatment]), maxPaths - backdoorPaths.length);
-        for (const path of paths) {
-            backdoorPaths.push([treatment, ...path]);
-            if (backdoorPaths.length >= maxPaths)
-                break;
-        }
-        if (backdoorPaths.length >= maxPaths)
-            break;
-    }
-    return backdoorPaths;
-}
-/**
- * Find all paths from source to target (BFS with path tracking)
- */
-function findAllPaths(source, target, graph, exclude, maxPaths) {
-    const paths = [];
-    const queue = [{ node: source, path: [source] }];
-    while (queue.length > 0 && paths.length < maxPaths) {
-        const { node, path } = queue.shift();
-        if (node === target) {
-            paths.push(path);
-            continue;
-        }
-        const currentNode = graph.get(node);
-        if (!currentNode)
-            continue;
-        // Consider both parents and children for undirected path finding
-        const neighbors = new Set([...currentNode.parents, ...currentNode.children]);
-        for (const neighbor of neighbors) {
-            if (!path.includes(neighbor) && !exclude.has(neighbor)) {
-                queue.push({
-                    node: neighbor,
-                    path: [...path, neighbor],
-                });
-            }
-        }
-    }
-    return paths;
-}
-/**
- * Check if intervention is valid (treatment must exist and have outgoing edges)
- */
-function validateIntervention(treatment, outcome, graph) {
-    const treatmentNode = graph.get(treatment);
-    const outcomeNode = graph.get(outcome);
-    if (!treatmentNode || !outcomeNode) {
-        return false;
-    }
-    // Check if there's any path from treatment to outcome
-    const descendants = findDescendants(treatment, graph);
-    return descendants.has(outcome);
-}
-/**
- * Assess identifiability of the causal effect based on graph structure.
- * Does NOT estimate the causal effect magnitude -- that requires
- * observational or experimental data which this tool does not have.
- * Returns an identifiability score reflecting how cleanly the effect
- * can be estimated if data were available (fewer confounders and
- * unblocked backdoor paths = higher identifiability).
- */
-function assessIdentifiability(confounders, backdoorPaths) {
-    // Identifiability decreases with confounders and unblocked backdoor paths
-    const confounderPenalty = Math.min(confounders.length * 0.1, 0.3);
-    const pathPenalty = Math.min(backdoorPaths.length * 0.05, 0.2);
-    const identifiability = Math.max(0.1, 1 - confounderPenalty - pathPenalty);
-    return { identifiability };
-}
-/**
- * Get interpretation of causal graph analysis results
- */
-function getInterpretation(interventionValid, confounders, backdoorPaths, identifiability) {
-    if (!interventionValid) {
-        return 'Intervention is not valid - no causal path exists from treatment to outcome';
-    }
-    if (confounders.length === 0 && backdoorPaths.length === 0) {
-        return 'Clean causal identification - no confounding detected. Effect is identifiable with data.';
-    }
-    if (identifiability > 0.8) {
-        return 'Strong identifiability - confounders can be adjusted for with observational data';
-    }
-    if (identifiability > 0.5) {
-        return `Moderate identifiability - ${confounders.length} confounder(s) require adjustment`;
-    }
-    return `Weak identifiability - multiple confounders (${confounders.length}) and backdoor paths (${backdoorPaths.length}) detected`;
-}
-/**
- * Handler for pr_causal_infer tool
- */
-async function handler(input, context) {
-    const logger = context?.logger ?? defaultLogger;
-    const startTime = performance.now();
-    try {
-        // Validate input
-        const validationResult = CausalInputSchema.safeParse(input);
-        if (!validationResult.success) {
-            logger.error('Input validation failed', { error: validationResult.error.message });
-            return errorResult(`Invalid input: ${validationResult.error.message}`);
-        }
-        const { graph, intervention, outcome } = validationResult.data;
-        logger.debug('Processing causal inference', {
-            nodes: graph.nodes.length,
-            edges: graph.edges.length,
-            intervention,
-            outcome,
-        });
-        // Validate nodes exist
-        if (!graph.nodes.includes(intervention)) {
-            return errorResult(`Intervention variable "${intervention}" not found in graph nodes`);
-        }
-        if (!graph.nodes.includes(outcome)) {
-            return errorResult(`Outcome variable "${outcome}" not found in graph nodes`);
-        }
-        const maxBackdoorPaths = context?.config?.causal?.maxBackdoorPaths ?? 10;
-        let identifiability;
-        let confounders;
-        let backdoorPaths;
-        let interventionValid;
-        // Try to use WASM bridge if available
-        if (context?.bridge?.initialized) {
-            try {
-                logger.debug('Using WASM bridge for causal inference');
-                const result = await context.bridge.inferCausal(graph, intervention, outcome);
-                confounders = result.confounders;
-                backdoorPaths = result.backdoorPaths;
-                interventionValid = result.interventionValid;
-                identifiability = assessIdentifiability(confounders, backdoorPaths).identifiability;
-            }
-            catch (wasmError) {
-                logger.warn('WASM bridge failed, falling back to JS implementation', {
-                    error: wasmError instanceof Error ? wasmError.message : String(wasmError),
-                });
-                // Use JavaScript implementation
-                const graphStructure = buildGraphStructure(graph);
-                interventionValid = validateIntervention(intervention, outcome, graphStructure);
-                confounders = identifyConfounders(intervention, outcome, graphStructure);
-                backdoorPaths = findBackdoorPaths(intervention, outcome, graphStructure, maxBackdoorPaths);
-                identifiability = assessIdentifiability(confounders, backdoorPaths).identifiability;
-            }
-        }
-        else {
-            // Pure JavaScript fallback
-            logger.debug('Using JavaScript fallback for causal inference');
-            const graphStructure = buildGraphStructure(graph);
-            interventionValid = validateIntervention(intervention, outcome, graphStructure);
-            confounders = identifyConfounders(intervention, outcome, graphStructure);
-            backdoorPaths = findBackdoorPaths(intervention, outcome, graphStructure, maxBackdoorPaths);
-            identifiability = assessIdentifiability(confounders, backdoorPaths).identifiability;
-        }
-        const output = {
-            identifiability,
-            backdoorPaths: backdoorPaths.map(p => p.join(' -> ')),
-            details: {
-                confounders,
-                interventionValid,
-                interpretation: getInterpretation(interventionValid, confounders, backdoorPaths, identifiability),
-                nodeCount: graph.nodes.length,
-                edgeCount: graph.edges.length,
-            },
-        };
-        const duration = performance.now() - startTime;
-        logger.info('Causal graph analysis completed', {
-            identifiability: identifiability.toFixed(4),
-            confounders: confounders.length,
-            backdoorPaths: backdoorPaths.length,
-            interventionValid,
-            durationMs: duration.toFixed(2),
-        });
-        return successResult(output);
-    }
-    catch (error) {
-        const duration = performance.now() - startTime;
-        logger.error('Causal inference failed', {
-            error: error instanceof Error ? error.message : String(error),
-            durationMs: duration.toFixed(2),
-        });
-        return errorResult(error instanceof Error ? error : new Error(String(error)));
-    }
-}
-/**
- * pr_causal_infer MCP Tool Definition
- */
-export const causalInferTool = {
-    name: 'pr_causal_infer',
-    description: 'Analyze causal graph structure for identifiability. Identifies confounders, finds backdoor paths, and assesses whether a causal effect can be identified. Does not estimate effect magnitude (requires observational data).',
-    category: 'causal',
-    version: '0.1.3',
-    tags: ['causal', 'do-calculus', 'confounders', 'backdoor-paths', 'ai-interpretability'],
-    cacheable: true,
-    cacheTTL: 60000,
-    inputSchema: {
-        type: 'object',
-        properties: {
-            graph: {
-                type: 'object',
-                properties: {
-                    nodes: {
-                        type: 'array',
-                        items: { type: 'string' },
-                        description: 'List of variable names',
-                    },
-                    edges: {
-                        type: 'array',
-                        items: {
-                            type: 'array',
-                            items: { type: 'string' },
-                            minItems: 2,
-                            maxItems: 2,
-                        },
-                        description: 'Directed edges as [from, to] pairs',
-                    },
-                },
-                required: ['nodes', 'edges'],
-                description: 'Causal graph with nodes and directed edges',
-            },
-            intervention: {
-                type: 'string',
-                description: 'Treatment/intervention variable',
-            },
-            outcome: {
-                type: 'string',
-                description: 'Outcome variable to measure effect on',
-            },
-        },
-        required: ['graph', 'intervention', 'outcome'],
-    },
-    handler,
-};
-export default causalInferTool;
-//# sourceMappingURL=causal-infer.js.map

package/dist/src/mcp-tools/coherence/causal-infer.js.map

@@ -1 +0,0 @@
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package/dist/src/mcp-tools/coherence/coherence-check.d.ts

@@ -1,15 +0,0 @@
-/**
- * Coherence Check Tool - pr_coherence_check
- *
- * Checks coherence of vectors using Sheaf Laplacian energy.
- * Energy 0 = fully coherent, Energy 1 = contradictory
- *
- * Uses CohomologyEngine from prime-radiant-advanced-wasm
- */
-import type { MCPTool } from './types.js';
-/**
- * pr_coherence_check MCP Tool Definition
- */
-export declare const coherenceCheckTool: MCPTool;
-export default coherenceCheckTool;
-//# sourceMappingURL=coherence-check.d.ts.map

package/dist/src/mcp-tools/coherence/coherence-check.d.ts.map

@@ -1 +0,0 @@
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