@grafema/mcp 0.3.24 → 0.3.28

package/README.md

@@ -1,134 +1,147 @@
 # @grafema/mcp
 
-> MCP server for Grafema code analysis toolkit
+> Model Context Protocol server exposing the Grafema code graph to AI
+> agents (Claude, Cursor, Copilot, Continue, …).
 
-**Warning: This package is in beta stage and the API may change between minor versions.**
+Once wired up, your agent can ask **structural** questions about your
+codebase that grep can't answer: "where is the CLASS named UserService",
+"who calls this function", "where does this value flow next". The agent
+gets back semantic IDs and graph neighborhoods, not text matches.
+
+---
 
 ## Installation
 
 ```bash
-npm install @grafema/mcp
+npm install --save-dev @grafema/mcp
 ```
 
-## Overview
-
-Model Context Protocol (MCP) server that exposes Grafema's code analysis capabilities to AI assistants like Claude. Enables AI agents to query code graphs, trace data flow, and check invariants — without reading source code.
+`@grafema/cli` is required as a peer (it builds the graph the MCP server
+queries).
 
-## Quick Start
+---
 
-### Claude Code configuration
+## Quick start
 
-Add to your project's `.mcp.json`:
+### Claude Code
 
-```json
+```jsonc
+// ~/.claude.json or project .claude.json
 {
   "mcpServers": {
     "grafema": {
       "command": "npx",
-      "args": ["@grafema/mcp", "--project", "."]
+      "args": ["-y", "@grafema/mcp"]
     }
   }
 }
 ```
 
-The RFDB graph database server is auto-started on first query. No manual setup needed.
-
-### Claude Desktop configuration
+### Claude Desktop
 
-Add to `~/.config/claude/claude_desktop_config.json`:
-
-```json
+```jsonc
+// ~/Library/Application Support/Claude/claude_desktop_config.json
 {
   "mcpServers": {
     "grafema": {
       "command": "npx",
-      "args": ["@grafema/mcp", "--project", "/path/to/project"]
+      "args": ["-y", "@grafema/mcp"]
     }
   }
 }
 ```
 
-## Available Tools (24)
-
-### Graph Queries
-| Tool | Description |
-|------|-------------|
-| `query_graph` | Execute Datalog queries on the code graph |
-| `find_nodes` | Find nodes by type, name, or file |
-| `find_calls` | Find all calls to a function or method |
-| `get_stats` | Get graph statistics (node/edge counts by type) |
-| `get_schema` | Get available node and edge types |
-
-### Navigation
-| Tool | Description |
-|------|-------------|
-| `get_function_details` | Comprehensive function details (calls, calledBy, parameters) |
-| `get_file_overview` | Structured overview of all entities in a file |
-| `get_context` | Deep context for a node (source code + graph neighborhood) |
-| `find_guards` | Find conditional guards protecting a node |
-| `read_project_structure` | Directory structure of the project |
-
-### Data Flow
-| Tool | Description |
-|------|-------------|
-| `trace_alias` | Trace alias chains to the original source |
-| `trace_dataflow` | Trace data flow from/to a variable or expression |
-
-### Analysis
-| Tool | Description |
-|------|-------------|
-| `analyze_project` | Run full or incremental analysis |
-| `get_analysis_status` | Current analysis status and progress |
-| `get_coverage` | Analysis coverage for a path |
-| `discover_services` | Discover services without full analysis |
-
-### Guarantees
-| Tool | Description |
-|------|-------------|
-| `check_invariant` | Check a code invariant via Datalog rule |
-| `create_guarantee` | Create a Datalog-based or contract-based guarantee |
-| `list_guarantees` | List all defined guarantees |
-| `check_guarantees` | Run all or specific guarantees |
-| `delete_guarantee` | Delete a guarantee by name |
-
-### Utilities
-| Tool | Description |
-|------|-------------|
-| `get_documentation` | Documentation about Grafema usage |
-| `report_issue` | Report a bug to GitHub (requires GITHUB_TOKEN) |
-| `write_config` | Write or update .grafema/config.yaml |
-
-## Example Queries
+After restart, the agent gains 44 tools grouped into:
+
+- **Graph queries** — find_nodes, find_calls, get_neighbors, query_graph, query_graphql, get_stats, get_schema
+- **Navigation** — get_context, get_file_overview, get_function_details, find_guards, read_project_structure
+- **Data flow** — trace_alias, trace_dataflow, trace_calls, trace_effects, traverse_graph
+- **Analysis** — analyze_project, get_analysis_status, get_coverage, discover_services, get_shape
+- **Knowledge base** — add_knowledge, query_knowledge, query_decisions, get_knowledge_stats, supersede_fact
+- **Git history** — git_archaeology, git_churn, git_cochange, git_ownership
+- **Guarantees** — check_invariant, check_guarantees, create_guarantee, list_guarantees, delete_guarantee
+- **Cross-modality** — find_shared_behaviors
+- **Utilities** — get_documentation, report_issue, write_config, query_registry, describe, explain
+
+---
+
+## Common agent workflows
+
+### "Where is this defined?"
+```
+find_nodes(name="UserService", type="CLASS")
+  → returns semantic ID
+get_context(nodeId="…")
+  → source snippet + neighborhood
+```
+
+### "Who calls this function?"
+```
+find_calls(name="handleRequest")
+  → file:line for every resolved caller
+```
+
+### "Where does data come from / go?"
+```
+trace_dataflow(source="userInput", file="src/api.ts", direction="forward")
+trace_dataflow(source="response",  file="src/api.ts", direction="backward")
+```
+
+### "What's in this file?"
+```
+get_file_overview(file="packages/cli/src/cli.ts")
+  → all exports / classes / functions / constants
+```
 
+### "What architectural rules apply here?"
 ```
-// Find all database queries
-query_graph("node(X, 'db:query')")
+list_guarantees()
+check_guarantees(category="dataflow")
+```
+
+---
+
+## All tools
 
-// Trace where user input flows
-trace_dataflow({ from: "req.body", file: "api/users.js" })
+The full per-tool catalogue with input schemas, descriptions, examples,
+and "when to use" guidance lives in **[docs/mcp-reference.md](../../docs/mcp-reference.md)**.
 
-// Check for eval usage
-check_invariant("violation(X) :- node(X, 'CALL'), attr(X, 'name', 'eval')")
+Regenerated from the live graph on each release:
+
+```bash
+grafema export --feature 'mcp:tool' --as docs-md   --output docs/mcp-reference.md
+grafema export --feature 'mcp:tool' --as mcp-schema --output docs/mcp-schema.json
 ```
 
+`mcp-schema` is the canonical JSON-RPC tools array — directly servable
+by any MCP runtime.
+
+---
+
 ## Configuration
 
-### GitHub Token (for bug reporting)
+### GitHub token (for `report_issue`)
 
-```json
-{
-  "mcpServers": {
-    "grafema": {
-      "command": "npx",
-      "args": ["@grafema/mcp", "--project", "."],
-      "env": {
-        "GITHUB_TOKEN": "ghp_your_token_here"
-      }
-    }
-  }
-}
+Set `GITHUB_TOKEN` to a PAT with `issues:write` on the target repo for
+`report_issue` to file bugs from inside the agent.
+
+```bash
+export GITHUB_TOKEN=ghp_…
 ```
 
-## License
+### Project root
+
+The MCP server reads from `.grafema/rfdb.sock` in the current working
+directory. Run `grafema analyze` first to populate the graph.
+
+---
+
+## Notes
 
-Apache-2.0
+- Tool count stays in sync with code — no hand-maintained lists.
+  Add a new MCP tool definition under `packages/mcp/src/definitions/`
+  and it appears in the next reference regen.
+- 4 setRequestHandler entry points (`CallToolRequestSchema`, etc.) are
+  protocol plumbing, not user-facing tools — they don't appear in the
+  reference.
+- For CLI usage, see [@grafema/cli](../cli/README.md).

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package/dist/definitions/query-tools.js

@@ -249,6 +249,44 @@ Returns: Indented call tree showing each hop with file:line location.`,
             required: ['source'],
         },
     },
+    {
+        name: 'trace_effects',
+        description: `Trace transitive side effects of a function through its call graph.
+
+For any function, traverses CALLS edges (DFS) and collects effects from leaf nodes
+using the effects-db (Node.js builtins, npm packages).
+
+Use this when you need to:
+- "What side effects does this function have?" → direct + transitive effects
+- "Does this handler do IO?" → trace shows IO:FILE:READ from fs.readFileSync at depth 3
+- "Where does the fetch() call come from?" → leaf_sources shows the origin at depth N
+- "What crosses module boundaries?" → boundary_crossings shows file-to-file effect flow
+
+Effect types: PURE, MUTATION, IO (with subtypes like IO:FILE:READ, IO:HTTP:REQUEST),
+THROW, ASYNC, NONDETERMINISTIC, UNKNOWN.
+
+UNKNOWN means: unresolved call, external package not in effects-db, or depth limit reached.
+
+Returns: direct effects, transitive effects, boundary crossings, leaf sources.`,
+        inputSchema: {
+            type: 'object',
+            properties: {
+                node: {
+                    type: 'string',
+                    description: 'Function/method name or semantic ID',
+                },
+                file: {
+                    type: 'string',
+                    description: 'File path to disambiguate (optional)',
+                },
+                max_depth: {
+                    type: 'number',
+                    description: 'Maximum call graph traversal depth (default: 10)',
+                },
+            },
+            required: ['node'],
+        },
+    },
     {
         name: 'get_shape',
         description: `Get the shape (methods + properties) of a CLASS, INTERFACE, or typed variable.
@@ -348,5 +386,38 @@ Returns: List of nodes violating the rule, with file and line info.`,
             required: ['rule'],
         },
     },
+    {
+        name: 'find_shared_behaviors',
+        description: `List clusters of FEATUREs whose entry-points share an identical BEHAVIOR (same forward-slice hash).
+
+Surfaces cross-modality duplication — e.g. "this CLI command is a thin wrapper around the
+same library function as that HTTP endpoint" or "this MCP tool and that VS Code command
+delegate to identical logic".
+
+Each cluster contains:
+  - hash:           sha256 of the shared transitive call set (BEHAVIOR.metadata.hash)
+  - effects:        transitive effects (IO, MUTATION, …) attributed to the shared behavior
+  - coreNodeCount:  size of the shared forward slice
+  - features:       array of { id, type, name, file } — the FEATUREs that share this behavior
+
+Cluster types are FEATURE node types: cli:command, mcp:tool, vscode:command (and any future
+domain types created by enrichers).
+
+Returns clusters ordered by size (largest first), then hash (deterministic tie-break).
+Empty result means every FEATURE has a unique implementation.`,
+        inputSchema: {
+            type: 'object',
+            properties: {
+                minClusterSize: {
+                    type: 'number',
+                    description: 'Minimum FEATUREs per cluster (default: 2). Values below 2 are clamped to 2.',
+                },
+                limit: {
+                    type: 'number',
+                    description: 'Maximum clusters to return (default: 100).',
+                },
+            },
+        },
+    },
 ];
 //# sourceMappingURL=query-tools.js.map

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package/dist/handlers/analysis-handlers.d.ts

@@ -2,6 +2,7 @@
  * MCP Analysis Handlers
  */
 import type { ToolResult, AnalyzeProjectArgs, GetSchemaArgs } from '../types.js';
+export declare function handleDiscoverServices(): Promise<ToolResult>;
 export declare function handleAnalyzeProject(args: AnalyzeProjectArgs): Promise<ToolResult>;
 export declare function handleGetAnalysisStatus(): Promise<ToolResult>;
 export declare function handleGetStats(): Promise<ToolResult>;

package/dist/handlers/analysis-handlers.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"analysis-handlers.d.ts","sourceRoot":"","sources":["../../src/handlers/analysis-handlers.ts"],"names":[],"mappings":"AAAA;;GAEG;AAQH,OAAO,KAAK,EACV,UAAU,EACV,kBAAkB,EAClB,aAAa,EACd,MAAM,aAAa,CAAC;AAKrB,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,UAAU,CAAC,CAGlE;AAED,wBAAsB,oBAAoB,CAAC,IAAI,EAAE,kBAAkB,GAAG,OAAO,CAAC,UAAU,CAAC,CA6BxF;AAED,wBAAsB,uBAAuB,IAAI,OAAO,CAAC,UAAU,CAAC,CAYnE;AAED,wBAAsB,cAAc,IAAI,OAAO,CAAC,UAAU,CAAC,CAmD1D;AAED,wBAAsB,eAAe,CAAC,IAAI,EAAE,aAAa,GAAG,OAAO,CAAC,UAAU,CAAC,CAwB9E"}

package/dist/handlers/analysis-handlers.js

@@ -1,10 +1,14 @@
 /**
  * MCP Analysis Handlers
  */
-import { ensureAnalyzed } from '../analysis.js';
+import { ensureAnalyzed, discoverServices } from '../analysis.js';
 import { getAnalysisStatus, isAnalysisRunning } from '../state.js';
 import { textResult, errorResult, } from '../utils.js';
 // === ANALYSIS HANDLERS ===
+export async function handleDiscoverServices() {
+    const services = await discoverServices();
+    return textResult(`Found ${services.length} service(s):\n${JSON.stringify(services, null, 2)}`);
+}
 export async function handleAnalyzeProject(args) {
     const { service, force } = args;
     // Early check: return error for force=true if analysis is already running

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

@@ -1 +1 @@
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package/dist/handlers/behavior-handlers.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Behavior handlers — surface cross-modality FEATURE duplication.
+ *
+ * `find_shared_behaviors` lists clusters of FEATUREs (cli:command, mcp:tool,
+ * vscode:command, …) whose entry-point forward-slice hashes match. Mirrors the
+ * `grafema features --duplicates` CLI subcommand — same algorithm, same
+ * cluster shape — so the two channels return symmetric data.
+ *
+ * REG-1119.
+ */
+import type { ToolResult, FindSharedBehaviorsArgs } from '../types.js';
+import type { EdgeType, EdgeRecord } from '@grafema/types';
+/**
+ * Minimal backend interface used by the logic function. Allows testing with
+ * a simple mock without importing the full GraphBackend. Matches the subset
+ * of RFDBServerBackend that we need.
+ */
+interface BehaviorBackendLike {
+    getNode(id: string): Promise<Record<string, unknown> | null>;
+    queryNodes(query: {
+        type?: string;
+        nodeType?: string;
+    }): AsyncIterable<Record<string, unknown>>;
+    getIncomingEdges(nodeId: string, edgeTypes?: EdgeType[] | null): Promise<EdgeRecord[]>;
+}
+export declare function findSharedBehaviorsLogic(db: BehaviorBackendLike, args: FindSharedBehaviorsArgs): Promise<ToolResult>;
+export declare function handleFindSharedBehaviors(args: FindSharedBehaviorsArgs): Promise<ToolResult>;
+export {};
+//# sourceMappingURL=behavior-handlers.d.ts.map

package/dist/handlers/behavior-handlers.d.ts.map

@@ -0,0 +1 @@
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package/dist/handlers/behavior-handlers.js

@@ -0,0 +1,127 @@
+/**
+ * Behavior handlers — surface cross-modality FEATURE duplication.
+ *
+ * `find_shared_behaviors` lists clusters of FEATUREs (cli:command, mcp:tool,
+ * vscode:command, …) whose entry-point forward-slice hashes match. Mirrors the
+ * `grafema features --duplicates` CLI subcommand — same algorithm, same
+ * cluster shape — so the two channels return symmetric data.
+ *
+ * REG-1119.
+ */
+import { ensureAnalyzed } from '../analysis.js';
+import { textResult, errorResult } from '../utils.js';
+const DEFAULT_MIN_CLUSTER_SIZE = 2;
+const DEFAULT_LIMIT = 100;
+const MAX_LIMIT = 10_000;
+// === Logic function (testable, accepts backend directly) ===
+export async function findSharedBehaviorsLogic(db, args) {
+    const { minClusterSize: rawMin, limit: rawLimit } = args ?? {};
+    if (rawMin !== undefined && (!Number.isFinite(rawMin) || rawMin < 0)) {
+        return errorResult('minClusterSize must be a non-negative number');
+    }
+    if (rawLimit !== undefined && (!Number.isFinite(rawLimit) || rawLimit <= 0)) {
+        return errorResult('limit must be a positive number');
+    }
+    if (rawLimit !== undefined && rawLimit > MAX_LIMIT) {
+        return errorResult(`limit must be <= ${MAX_LIMIT}`);
+    }
+    const minClusterSize = Math.max(2, rawMin ?? DEFAULT_MIN_CLUSTER_SIZE);
+    const limit = rawLimit ?? DEFAULT_LIMIT;
+    const behaviors = [];
+    for await (const node of db.queryNodes({ type: 'BEHAVIOR' })) {
+        const id = String(node.id ?? '');
+        if (!id)
+            continue;
+        const hash = readString(node.hash);
+        if (!hash)
+            continue;
+        behaviors.push({
+            id,
+            hash,
+            effects: readStringArray(node.effects),
+            coreNodeCount: readNumber(node.coreNodeCount) ?? 0,
+        });
+    }
+    // 2. Bucket by hash.
+    const byHash = new Map();
+    for (const b of behaviors) {
+        let bucket = byHash.get(b.hash);
+        if (!bucket) {
+            bucket = [];
+            byHash.set(b.hash, bucket);
+        }
+        bucket.push(b);
+    }
+    // 3. Resolve features (incoming IMPLEMENTED_BY) for clusters.
+    const clusters = [];
+    for (const [hash, bucket] of byHash) {
+        if (bucket.length < minClusterSize)
+            continue;
+        const features = [];
+        const seen = new Set();
+        for (const beh of bucket) {
+            const edges = await db.getIncomingEdges(beh.id, ['IMPLEMENTED_BY']);
+            for (const edge of edges) {
+                const featureId = String(edge.src);
+                if (!featureId || seen.has(featureId))
+                    continue;
+                seen.add(featureId);
+                const node = await db.getNode(featureId);
+                if (!node)
+                    continue;
+                features.push({
+                    id: featureId,
+                    type: readString(node.type) ?? 'UNKNOWN',
+                    name: readString(node.name) ?? '',
+                    file: readString(node.file) ?? '',
+                });
+            }
+        }
+        if (features.length < minClusterSize)
+            continue;
+        features.sort((a, b) => (a.type === b.type ? a.name.localeCompare(b.name) : a.type.localeCompare(b.type)));
+        clusters.push({
+            hash,
+            effects: bucket[0].effects,
+            coreNodeCount: bucket[0].coreNodeCount,
+            features,
+        });
+    }
+    clusters.sort((a, b) => (b.features.length - a.features.length) || a.hash.localeCompare(b.hash));
+    const truncated = clusters.length > limit;
+    const limited = clusters.slice(0, limit);
+    return textResult(JSON.stringify({
+        count: limited.length,
+        truncated,
+        minClusterSize,
+        clusters: limited,
+    }, null, 2));
+}
+// === Public handler (calls ensureAnalyzed, used by MCP routing) ===
+export async function handleFindSharedBehaviors(args) {
+    const db = await ensureAnalyzed();
+    return findSharedBehaviorsLogic(db, args);
+}
+// === Internal helpers ===
+function readString(v) {
+    return typeof v === 'string' ? v : undefined;
+}
+function readNumber(v) {
+    return typeof v === 'number' && Number.isFinite(v) ? v : undefined;
+}
+function readStringArray(v) {
+    if (Array.isArray(v))
+        return v.filter((x) => typeof x === 'string');
+    if (typeof v === 'string') {
+        try {
+            const parsed = JSON.parse(v);
+            if (Array.isArray(parsed))
+                return parsed.filter((x) => typeof x === 'string');
+        }
+        catch {
+            // not JSON
+        }
+    }
+    return [];
+}
+//# sourceMappingURL=behavior-handlers.js.map

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

@@ -0,0 +1 @@
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package/dist/handlers/dataflow-handlers.d.ts

@@ -3,10 +3,10 @@
  *
  * Delegates BFS tracing to @grafema/util's shared traceDataflow module.
  */
-import type { ToolResult, TraceAliasArgs, TraceDataFlowArgs, TraceCallChainArgs, CheckInvariantArgs } from '../types.js';
+import type { ToolResult, TraceAliasArgs, TraceDataFlowArgs, TraceCallChainArgs, TraceEffectsArgs, CheckInvariantArgs } from '../types.js';
 export declare function handleTraceAlias(args: TraceAliasArgs): Promise<ToolResult>;
-export declare function handleTraceDataFlow(args: TraceDataFlowArgs): Promise<ToolResult>;
-export declare function handleTraceCallChain(args: TraceCallChainArgs): Promise<ToolResult>;
+export declare function handleTraceDataflow(args: TraceDataFlowArgs): Promise<ToolResult>;
+export declare function handleTraceCalls(args: TraceCallChainArgs): Promise<ToolResult>;
 export interface ExplainArgs {
     target: string;
     file?: string;
@@ -14,4 +14,5 @@ export interface ExplainArgs {
 }
 export declare function handleExplain(args: ExplainArgs): Promise<ToolResult>;
 export declare function handleCheckInvariant(args: CheckInvariantArgs): Promise<ToolResult>;
+export declare function handleTraceEffects(args: TraceEffectsArgs): Promise<ToolResult>;
 //# sourceMappingURL=dataflow-handlers.d.ts.map

package/dist/handlers/dataflow-handlers.d.ts.map

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