@grafema/mcp 0.2.11 → 0.3.0-beta

package/dist/handlers/query-handlers.js

@@ -2,54 +2,153 @@
  * MCP Query Handlers
  */
 import { ensureAnalyzed } from '../analysis.js';
-import { normalizeLimit, formatPaginationInfo, guardResponseSize, serializeBigInt, findSimilarTypes, textResult, errorResult, } from '../utils.js';
+import { normalizeLimit, formatPaginationInfo, guardResponseSize, serializeBigInt, findSimilarTypes, extractQueriedTypes, textResult, errorResult, } from '../utils.js';
 // === QUERY HANDLERS ===
 export async function handleQueryGraph(args) {
     const db = await ensureAnalyzed();
-    const { query, limit: requestedLimit, offset: requestedOffset, format: _format, explain: _explain } = args;
+    const { query, language, limit: requestedLimit, offset: requestedOffset, format: _format, explain, count } = args;
     const limit = normalizeLimit(requestedLimit);
     const offset = Math.max(0, requestedOffset || 0);
     try {
+        // Cypher query path
+        if (language === 'cypher') {
+            if (!('cypherQuery' in db)) {
+                return errorResult('Backend does not support Cypher queries');
+            }
+            const cypherFn = db.cypherQuery;
+            const result = await cypherFn.call(db, query);
+            if (count) {
+                return textResult(`Count: ${result.rowCount}`);
+            }
+            if (result.rowCount === 0) {
+                return textResult('Query returned no results.');
+            }
+            const paginatedRows = result.rows.slice(offset, offset + limit);
+            const hasMore = offset + limit < result.rowCount;
+            const paginationInfo = formatPaginationInfo({
+                limit,
+                offset,
+                returned: paginatedRows.length,
+                total: result.rowCount,
+                hasMore,
+            });
+            // Format as table
+            const lines = [];
+            lines.push(`Found ${result.rowCount} row(s):${paginationInfo}`);
+            lines.push('');
+            // Column widths
+            const colWidths = result.columns.map((col, i) => {
+                let maxWidth = col.length;
+                for (const row of paginatedRows) {
+                    const cellLen = String(row[i] ?? '').length;
+                    if (cellLen > maxWidth)
+                        maxWidth = cellLen;
+                }
+                return Math.min(maxWidth, 60);
+            });
+            lines.push(result.columns.map((col, i) => col.padEnd(colWidths[i])).join('  '));
+            lines.push(colWidths.map(w => '-'.repeat(w)).join('  '));
+            for (const row of paginatedRows) {
+                const line = row.map((cell, i) => {
+                    const s = String(cell ?? '');
+                    return s.length > colWidths[i] ? s.slice(0, colWidths[i] - 1) + '\u2026' : s.padEnd(colWidths[i]);
+                }).join('  ');
+                lines.push(line);
+            }
+            return textResult(guardResponseSize(lines.join('\n')));
+        }
         // Check if backend supports Datalog queries
         if (!('checkGuarantee' in db)) {
             return errorResult('Backend does not support Datalog queries');
         }
+        // Explain mode — separate path with step-by-step trace
+        if (explain) {
+            const checkFn = db.checkGuarantee;
+            const result = await checkFn.call(db, query, true);
+            return textResult(guardResponseSize(formatExplainOutput(result)));
+        }
         const checkFn = db.checkGuarantee;
-        const results = await checkFn(query);
+        const results = await checkFn.call(db, query);
         const total = results.length;
+        if (count) {
+            return textResult(`Count: ${total}`);
+        }
         if (total === 0) {
+            const { nodeTypes, edgeTypes } = extractQueriedTypes(query);
+            const hasQueriedTypes = nodeTypes.length > 0 || edgeTypes.length > 0;
             const nodeCounts = await db.countNodesByType();
-            const totalNodes = Object.values(nodeCounts).reduce((a, b) => a + b, 0);
-            const typeMatch = query.match(/node\([^,]+,\s*"([^"]+)"\)/);
-            const queriedType = typeMatch ? typeMatch[1] : null;
+            const edgeCounts = edgeTypes.length > 0 ? await db.countEdgesByType() : {};
+            const availableNodeTypes = Object.keys(nodeCounts);
+            const availableEdgeTypes = Object.keys(edgeCounts);
             let hint = '';
-            if (queriedType && !nodeCounts[queriedType]) {
-                const availableTypes = Object.keys(nodeCounts);
-                const similar = findSimilarTypes(queriedType, availableTypes);
-                if (similar.length > 0) {
-                    hint = `\n💡 Did you mean: ${similar.join(', ')}?`;
+            if (hasQueriedTypes) {
+                const hintLines = [];
+                if (nodeTypes.length > 0 && availableNodeTypes.length === 0) {
+                    hintLines.push('Graph has no nodes');
+                }
+                else {
+                    for (const queriedType of nodeTypes) {
+                        if (!nodeCounts[queriedType]) {
+                            const similar = findSimilarTypes(queriedType, availableNodeTypes);
+                            if (similar.length > 0) {
+                                hintLines.push(`Did you mean: ${similar.join(', ')}? (node type)`);
+                            }
+                            else {
+                                const typeList = availableNodeTypes.slice(0, 10).join(', ');
+                                const more = availableNodeTypes.length > 10 ? '...' : '';
+                                hintLines.push(`Available node types: ${typeList}${more}`);
+                            }
+                        }
+                    }
+                }
+                if (edgeTypes.length > 0 && availableEdgeTypes.length === 0) {
+                    hintLines.push('Graph has no edges');
                 }
                 else {
-                    hint = `\n💡 Available types: ${availableTypes.slice(0, 10).join(', ')}${availableTypes.length > 10 ? '...' : ''}`;
+                    for (const queriedType of edgeTypes) {
+                        if (!edgeCounts[queriedType]) {
+                            const similar = findSimilarTypes(queriedType, availableEdgeTypes);
+                            if (similar.length > 0) {
+                                hintLines.push(`Did you mean: ${similar.join(', ')}? (edge type)`);
+                            }
+                            else {
+                                const typeList = availableEdgeTypes.slice(0, 10).join(', ');
+                                const more = availableEdgeTypes.length > 10 ? '...' : '';
+                                hintLines.push(`Available edge types: ${typeList}${more}`);
+                            }
+                        }
+                    }
+                }
+                if (hintLines.length > 0) {
+                    hint = '\n' + hintLines.map(l => `Hint: ${l}`).join('\n');
                 }
             }
-            return textResult(`Query returned no results.${hint}\n📊 Graph: ${totalNodes.toLocaleString()} nodes`);
+            const totalNodes = Object.values(nodeCounts).reduce((a, b) => a + b, 0);
+            return textResult(`Query returned no results.${hint}\nGraph: ${totalNodes.toLocaleString()} nodes`);
         }
         const paginatedResults = results.slice(offset, offset + limit);
         const hasMore = offset + limit < total;
         const enrichedResults = [];
         for (const result of paginatedResults) {
-            const nodeId = result.bindings?.find((b) => b.name === 'X')?.value;
-            if (nodeId) {
-                const node = await db.getNode(nodeId);
+            const xBinding = result.bindings?.find((b) => b.name === 'X');
+            if (xBinding) {
+                const node = await db.getNode(xBinding.value);
                 if (node) {
                     enrichedResults.push({
                         ...node,
-                        id: nodeId,
+                        id: xBinding.value,
                         file: node.file,
                         line: node.line,
                     });
                 }
+                else {
+                    // Non-node-ID binding (e.g. attr() string value) — return raw bindings map
+                    const bindingsMap = {};
+                    for (const b of result.bindings) {
+                        bindingsMap[b.name] = b.value;
+                    }
+                    enrichedResults.push(bindingsMap);
+                }
             }
         }
         const paginationInfo = formatPaginationInfo({
@@ -69,16 +168,22 @@ export async function handleQueryGraph(args) {
 }
 export async function handleFindCalls(args) {
     const db = await ensureAnalyzed();
-    const { target: name, limit: requestedLimit, offset: requestedOffset, className } = args;
+    const { name, limit: requestedLimit, offset: requestedOffset, className } = args;
     const limit = normalizeLimit(requestedLimit);
     const offset = Math.max(0, requestedOffset || 0);
     const calls = [];
     let skipped = 0;
     let totalMatched = 0;
     for await (const node of db.queryNodes({ type: 'CALL' })) {
-        if (node.name !== name && node['method'] !== name)
+        const nodeName = node.name ?? '';
+        // Method calls are stored as "receiver.method" (e.g., "kb.queryNodes", "<obj>.load").
+        // Extract the method part so find_calls("queryNodes") matches "kb.queryNodes".
+        const dotIdx = nodeName.lastIndexOf('.');
+        const methodPart = dotIdx >= 0 ? nodeName.slice(dotIdx + 1) : null;
+        const receiverPart = dotIdx >= 0 ? nodeName.slice(0, dotIdx) : null;
+        if (nodeName !== name && methodPart !== name)
             continue;
-        if (className && node['object'] !== className)
+        if (className && receiverPart !== className)
             continue;
         totalMatched++;
         if (skipped < offset) {
@@ -130,6 +235,46 @@ export async function handleFindCalls(args) {
         JSON.stringify(serializeBigInt(calls), null, 2);
     return textResult(guardResponseSize(responseText));
 }
+function formatExplainOutput(result) {
+    const lines = [];
+    lines.push(`Query returned ${result.bindings.length} result(s).\n`);
+    if (result.explainSteps.length > 0) {
+        lines.push('Step-by-step execution:');
+        const maxSteps = 50;
+        const stepsToShow = result.explainSteps.slice(0, maxSteps);
+        for (const step of stepsToShow) {
+            const args = step.args.join(', ');
+            lines.push(`  ${step.step}. [${step.operation}] ${step.predicate}(${args}) \u2192 ${step.resultCount} result(s) (${step.durationUs} \u00b5s)`);
+            if (step.details) {
+                lines.push(`     ${step.details}`);
+            }
+        }
+        if (result.explainSteps.length > maxSteps) {
+            lines.push(`  ... ${result.explainSteps.length - maxSteps} more steps`);
+        }
+        lines.push('');
+    }
+    lines.push('Statistics:');
+    lines.push(`  Nodes visited:    ${result.stats.nodesVisited}`);
+    lines.push(`  Edges traversed:  ${result.stats.edgesTraversed}`);
+    lines.push(`  Rule evaluations: ${result.stats.ruleEvaluations}`);
+    lines.push(`  Total results:    ${result.stats.totalResults}`);
+    lines.push(`  Duration:         ${result.profile.totalDurationUs} \u00b5s`);
+    lines.push('');
+    if (result.bindings.length > 0) {
+        lines.push('Bindings:');
+        const maxBindings = 20;
+        const bindingsToShow = result.bindings.slice(0, maxBindings);
+        for (const row of bindingsToShow) {
+            const pairs = Object.entries(row).map(([k, v]) => `${k}=${v}`).join(', ');
+            lines.push(`  { ${pairs} }`);
+        }
+        if (result.bindings.length > maxBindings) {
+            lines.push(`  ... ${result.bindings.length - maxBindings} more results`);
+        }
+    }
+    return lines.join('\n');
+}
 export async function handleFindNodes(args) {
     const db = await ensureAnalyzed();
     const { type, name, file, limit: requestedLimit, offset: requestedOffset } = args;
@@ -142,6 +287,7 @@ export async function handleFindNodes(args) {
         filter.name = name;
     if (file)
         filter.file = file;
+    filter.substringMatch = true;
     const nodes = [];
     let skipped = 0;
     let totalMatched = 0;

package/dist/handlers/query-handlers.js.map

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package/dist/prompts.js

@@ -2,7 +2,7 @@
  * MCP Prompts handler logic.
  * Extracted for testability — server.ts is a thin wrapper.
  */
-import { getOnboardingInstruction } from '@grafema/core';
+import { getOnboardingInstruction } from '@grafema/util';
 export const PROMPTS = [
     {
         name: 'onboard_project',

package/dist/server.d.ts

@@ -2,7 +2,25 @@
 /**
  * Grafema MCP Server
  *
- * Provides code analysis tools via Model Context Protocol.
+ * Graph-driven code analysis for AI agents. Query the code graph instead of reading files.
+ *
+ * Use Grafema when you need to:
+ * - Navigate code structure (find callers, trace data flow, understand impact)
+ * - Answer "who calls this?", "where is this used?", "what does this affect?"
+ * - Analyze untyped/dynamic codebases where static analysis falls short
+ * - Track relationships across files without manual grep
+ *
+ * Core capabilities:
+ * - Datalog queries for pattern matching (query_graph)
+ * - Call graph navigation (find_calls, get_function_details)
+ * - Data flow tracing (trace_dataflow, trace_alias)
+ * - Graph traversal primitives (get_node, get_neighbors, traverse_graph)
+ * - Code guarantees/invariants (create_guarantee, check_guarantees)
+ *
+ * Workflow:
+ * 1. discover_services — identify project structure
+ * 2. analyze_project — build the graph
+ * 3. Use query tools to explore code relationships
  */
 export {};
 //# sourceMappingURL=server.d.ts.map

package/dist/server.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":";AACA;;;;GAIG"}
+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;;;;;;GAsBG"}

package/dist/server.js

@@ -2,17 +2,41 @@
 /**
  * Grafema MCP Server
  *
- * Provides code analysis tools via Model Context Protocol.
+ * Graph-driven code analysis for AI agents. Query the code graph instead of reading files.
+ *
+ * Use Grafema when you need to:
+ * - Navigate code structure (find callers, trace data flow, understand impact)
+ * - Answer "who calls this?", "where is this used?", "what does this affect?"
+ * - Analyze untyped/dynamic codebases where static analysis falls short
+ * - Track relationships across files without manual grep
+ *
+ * Core capabilities:
+ * - Datalog queries for pattern matching (query_graph)
+ * - Call graph navigation (find_calls, get_function_details)
+ * - Data flow tracing (trace_dataflow, trace_alias)
+ * - Graph traversal primitives (get_node, get_neighbors, traverse_graph)
+ * - Code guarantees/invariants (create_guarantee, check_guarantees)
+ *
+ * Workflow:
+ * 1. discover_services — identify project structure
+ * 2. analyze_project — build the graph
+ * 3. Use query tools to explore code relationships
  */
 import { Server } from '@modelcontextprotocol/sdk/server/index.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import { CallToolRequestSchema, ListToolsRequestSchema, ListPromptsRequestSchema, GetPromptRequestSchema, } from '@modelcontextprotocol/sdk/types.js';
 import { PROMPTS, getPrompt } from './prompts.js';
-import { TOOLS } from './definitions.js';
+import { TOOLS } from './definitions/index.js';
 import { initializeFromArgs, setupLogging, getProjectPath } from './state.js';
 import { textResult, errorResult, log } from './utils.js';
 import { discoverServices } from './analysis.js';
-import { handleQueryGraph, handleFindCalls, handleFindNodes, handleTraceAlias, handleTraceDataFlow, handleCheckInvariant, handleAnalyzeProject, handleGetAnalysisStatus, handleGetStats, handleGetSchema, handleCreateGuarantee, handleListGuarantees, handleCheckGuarantees, handleDeleteGuarantee, handleGetCoverage, handleGetDocumentation, handleFindGuards, handleReportIssue, handleGetFunctionDetails, handleGetContext, handleReadProjectStructure, handleWriteConfig, handleGetFileOverview, } from './handlers/index.js';
+import { handleQueryGraph, handleFindCalls, handleFindNodes, handleTraceAlias, handleTraceDataFlow, handleCheckInvariant, handleAnalyzeProject, handleGetAnalysisStatus, handleGetStats, handleGetSchema, handleCreateGuarantee, handleListGuarantees, handleCheckGuarantees, handleDeleteGuarantee, handleGetCoverage, handleGetDocumentation, handleFindGuards, handleReportIssue, handleGetFunctionDetails, handleGetContext, handleReadProjectStructure, handleWriteConfig, handleGetFileOverview, handleGetNode, handleGetNeighbors, handleTraverseGraph, handleAddKnowledge, handleQueryKnowledge, handleQueryDecisions, handleSupersedeFact, handleGetKnowledgeStats, 
+// Disabled: requires git-ingest (US-17). See US-17 in AI-AGENT-STORIES.md
+// handleGitChurn,
+// handleGitCoChange,
+// handleGitOwnership,
+// handleGitArchaeology,
+handleDescribe, handleGraphQLQuery, } from './handlers/index.js';
 /**
  * Type-safe argument casting helper.
  * MCP SDK provides args as Record<string, unknown>, this helper
@@ -30,11 +54,31 @@ log(`[Grafema MCP] Starting server for project: ${projectPath}`);
 const server = new Server({
     name: 'grafema-mcp',
     version: '0.1.0',
+    description: 'Graph-driven code analysis. Query the code graph instead of reading files. Navigate call graphs, trace data flow, verify guarantees. For AI agents working with untyped/dynamic codebases.',
 }, {
     capabilities: {
         tools: {},
         prompts: {},
     },
+    instructions: `Grafema is a code graph — use it instead of reading files.
+
+START HERE: call get_stats to check if the graph is loaded (nodeCount > 0).
+If nodeCount is 0, call analyze_project first.
+
+EXPLORATION WORKFLOW:
+1. To understand a file → get_file_overview (shows imports, exports, functions, classes with relationships)
+2. To find functions/classes/modules → find_nodes (filter by type, name, or file pattern)
+3. To find who calls a function → find_calls (returns call sites with resolution status)
+4. To understand data flow → trace_dataflow (forward: where does this value go? backward: where does it come from?)
+5. To understand full context of a node → get_context (shows surrounding code, scope chain, relationships)
+6. For complex pattern queries → query_graph with Datalog (call get_documentation topic="queries" for syntax)
+7. To query architectural decisions and facts → query_knowledge, query_decisions, get_knowledge_stats
+8. To get a compact visual summary → describe (renders DSL notation with archetype-grouped operators)
+9. For DSL syntax reference → get_documentation topic="notation"
+
+KEY INSIGHT: find_nodes supports partial matching on name and file fields.
+Example: find_nodes(file="auth/") returns all nodes in files matching "auth/".
+Example: find_nodes(name="redis", type="CALL") finds all calls containing "redis".`,
 });
 // List available tools
 server.setRequestHandler(ListToolsRequestSchema, async (_request, _extra) => {
@@ -131,6 +175,52 @@ server.setRequestHandler(CallToolRequestSchema, async (request, extra) => {
             case 'write_config':
                 result = await handleWriteConfig(asArgs(args));
                 break;
+            case 'get_node':
+                result = await handleGetNode(asArgs(args));
+                break;
+            case 'get_neighbors':
+                result = await handleGetNeighbors(asArgs(args));
+                break;
+            case 'traverse_graph':
+                result = await handleTraverseGraph(asArgs(args));
+                break;
+            case 'add_knowledge':
+                result = await handleAddKnowledge(asArgs(args));
+                break;
+            case 'query_knowledge':
+                result = await handleQueryKnowledge(asArgs(args));
+                break;
+            case 'query_decisions':
+                result = await handleQueryDecisions(asArgs(args));
+                break;
+            case 'supersede_fact':
+                result = await handleSupersedeFact(asArgs(args));
+                break;
+            case 'get_knowledge_stats':
+                result = await handleGetKnowledgeStats();
+                break;
+            // Disabled: requires git-ingest (US-17). See US-17 in AI-AGENT-STORIES.md
+            // case 'git_churn':
+            //   result = await handleGitChurn(asArgs<GitChurnArgs>(args));
+            //   break;
+            //
+            // case 'git_cochange':
+            //   result = await handleGitCoChange(asArgs<GitCoChangeArgs>(args));
+            //   break;
+            //
+            // case 'git_ownership':
+            //   result = await handleGitOwnership(asArgs<GitOwnershipArgs>(args));
+            //   break;
+            //
+            // case 'git_archaeology':
+            //   result = await handleGitArchaeology(asArgs<GitArchaeologyArgs>(args));
+            //   break;
+            case 'describe':
+                result = await handleDescribe(asArgs(args));
+                break;
+            case 'query_graphql':
+                result = await handleGraphQLQuery(asArgs(args));
+                break;
             default:
                 result = errorResult(`Unknown tool: ${name}`);
         }

package/dist/server.js.map

@@ -1 +1 @@
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package/dist/state.d.ts

@@ -1,7 +1,7 @@
 /**
  * MCP Server State Management
  */
-import { GuaranteeManager, GuaranteeAPI } from '@grafema/core';
+import { GuaranteeManager, GuaranteeAPI, KnowledgeBase } from '@grafema/util';
 import type { AnalysisStatus } from './types.js';
 import type { GraphBackend } from '@grafema/types';
 export declare function getProjectPath(): string;
@@ -10,6 +10,7 @@ export declare function getAnalysisStatus(): AnalysisStatus;
 export declare function getBackgroundPid(): number | null;
 export declare function getGuaranteeManager(): GuaranteeManager | null;
 export declare function getGuaranteeAPI(): GuaranteeAPI | null;
+export declare function getKnowledgeBase(): KnowledgeBase | null;
 export declare function setProjectPath(path: string): void;
 export declare function setIsAnalyzed(value: boolean): void;
 export declare function setAnalysisStatus(status: Partial<AnalysisStatus>): void;
@@ -54,9 +55,17 @@ export declare function acquireAnalysisLock(): Promise<() => void>;
  * @returns Promise that resolves when no analysis is running
  */
 export declare function waitForAnalysis(): Promise<void>;
+export declare function resetBackend(): void;
+export declare function resetKnowledgeBase(): void;
 export declare function getOrCreateBackend(): Promise<GraphBackend>;
 export declare function getBackendIfExists(): GraphBackend | null;
 export declare function setupLogging(): void;
+/**
+ * Get or create the KnowledgeBase singleton.
+ * Lazy-initializes from knowledge/ directory on first access.
+ * If a backend is available, wires up the SemanticAddressResolver.
+ */
+export declare function getOrCreateKnowledgeBase(): Promise<KnowledgeBase>;
 export declare function initializeFromArgs(): void;
 export declare function cleanup(): Promise<void>;
 //# sourceMappingURL=state.d.ts.map

package/dist/state.d.ts.map

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