codestrate 0.6.2 → 0.6.3

package/dist/index.js

@@ -1,46 +1,29 @@
 #!/usr/bin/env node
 /**
- * Coding Intelligence MCP Server
+ * Coding Intelligence MCP Server (codestrate)
  *
- * An "external fine-tuning" layer for cloud coding models.
- * Provides structural code retrieval, project memory, and executable validation.
+ * External fine-tuning layer for coding agents: structural retrieval,
+ * graph navigation, project memory, and allowlisted validation.
  *
- * Tools:
- *   ci_repo_overview     — Project structure, build system, frameworks
- *   ci_search_code       — Hybrid code search (ripgrep + symbol matching)
- *   ci_inspect_symbol    — Symbol definition, callers, callees, tests
- *   ci_get_context       — [Primary] Context bundle for a task
- *   ci_search_history    — Git commit history search
- *   ci_recall_experience — Retrieve past verified solutions
- *   ci_trace_flow        — Call/import flow graph traversal
- *   ci_status            — Index health and staleness check
- *   ci_run_validation    — Execute build/test/lint (allowlist-gated)
- *   ci_analyze_impact    — Multi-file change impact analysis
- *   ci_reindex           — Full or incremental re-indexing
- *   ci_record_experience — Save verified experience to memory
- *
- * Resources (prompts):
- *   ci://prompts/debug-runtime-error
- *   ci://prompts/implement-feature
- *   ci://prompts/review-code
- *
- * Usage:
- *   node dist/index.js          # stdio mode (default for local use)
+ * Transport: stdio only (Streamable HTTP is intentionally not shipped).
+ * Default profile: `core` (≤7 read-only tools). Set CI_MCP_PROFILE=full
+ * or `"profile": "full"` in .ci-mcp.json for mutations and extras.
  */
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { McpServer, ResourceTemplate } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { readFileSync, existsSync } from "fs";
-import { appendFileSync } from "fs";
 import { join, resolve } from "path";
-import { SERVER_NAME, SERVER_VERSION } from "./constants.js";
-import { loadIndex, setSnapshot, setSymbols, setRelations, resetIndex, saveIndex } from "./store/index.js";
-import { loadMemoryStore } from "./store/memory.js";
-import { loadConfig } from "./constants.js";
+import { SERVER_NAME, SERVER_VERSION, loadConfig } from "./constants.js";
 import { parseRepository } from "./services/repository-parser.js";
 import { indexSymbols } from "./services/symbol-indexer.js";
 import { getStore } from "./store/sqlite.js";
 import { initTreeSitter } from "./services/tree-sitter.js";
-// ─── Import tool registrations ────────────────────────────
+import { markIndexing, markIndexReady, markIndexFailed, markIndexEmpty, getIndexState, isIndexReady, } from "./services/index-state.js";
+import { isToolInProfile, getProfile } from "./profiles.js";
+import { ensureEmbeddingRuntime, shutdownEmbeddingRuntime } from "./services/embedding-runtime.js";
+import { indexVectors } from "./services/vector-indexer.js";
+import { isEmbeddingEnabled } from "./services/embedding.js";
+// ─── Tool registrations ───────────────────────────────────
 import { registerRepoOverview } from "./tools/repo-overview.js";
 import { registerSearchCode } from "./tools/search-code.js";
 import { registerInspectSymbol } from "./tools/inspect-symbol.js";
@@ -59,135 +42,178 @@ import { registerPing } from "./tools/ping.js";
 import { registerSessionHeartbeat } from "./tools/session-heartbeat.js";
 import { registerSessionStatus } from "./tools/session-status.js";
 import { registerDeepExplore } from "./tools/deep-explore.js";
+import { registerProfileTool } from "./tools/profile.js";
+import { registerTraceBfs } from "./tools/trace-bfs.js";
+import { registerGraphStats } from "./tools/graph-stats.js";
+import { registerGraphExplain } from "./tools/graph-explain.js";
+import { registerQueryGraph } from "./tools/query-graph.js";
+import { registerDetectCycles } from "./tools/detect-cycles.js";
+import { registerReflect, registerReflectHistory } from "./tools/reflect.js";
 // ─── Initialize server ────────────────────────────────────
 const server = new McpServer({
     name: SERVER_NAME,
     version: SERVER_VERSION,
 });
-// ─── Load persisted state ─────────────────────────────────
 const config = loadConfig();
+const activeProfile = config.profile ?? "core";
+// Open SQLite store early (single production source of truth)
 if (config.repoPath) {
-    loadIndex(config.storePath);
-    loadMemoryStore(config.storePath);
-}
-// ─── AGENTS.md injection ───────────────────────────────
-// Tự động thêm hướng dẫn sử dụng codestrate tools vào AGENTS.md
-// để Claude Code hiểu cách dùng tool đúng.
-const AGENTS_CONTENT = `
-## Codestrate — MCP Tools
-
-Codestrate cung cấp structural code understanding. Dùng thay grep khi cần tìm symbol, trace call graph, hoặc hiểu architecture.
-
-- **ci_explore** — search symbol bằng FTS5 + camelCase. Gọi đầu tiên khi cần tìm class/function
-- **ci_inspect_symbol** — xem definition + callers/callees của symbol
-- **ci_trace_flow** — BFS trace dependency chain (độ sâu 1-5)
-- **ci_get_context** — context bundle cho task: symbols + files + history
-- **ci_analyze_impact** — file A đổi → ai bị ảnh hưởng
-- **ci_repo_overview** — project structure: build system, frameworks, entry points
-- **ci_recall_experience** — tra cứu bug fix / decision từng làm
-
-Chi tiết: chạy \`ci_status\` hoặc xem tool descriptions trong MCP tool list.
-`;
-function injectAgentsMd() {
-    const repoPath = config.repoPath ?? process.cwd();
-    const agentsPath = join(repoPath, "AGENTS.md");
-    const MARKER = "<!-- codestrate -->";
-    try {
-        if (existsSync(agentsPath)) {
-            const existing = readFileSync(agentsPath, "utf8");
-            if (existing.includes(MARKER))
-                return; // đã inject rồi
-        }
-        appendFileSync(agentsPath, `\n${MARKER}\n${AGENTS_CONTENT}\n`);
-    }
-    catch {
-        console.warn("[index] không ghi được AGENTS.md:", agentsPath);
-        // Không ghi được → bỏ qua, không crash server
-    }
-}
-injectAgentsMd();
-// ─── Auto-index on connect ─────────────────────────────
-// Tự động index repo khi server start nếu có repoPath.
-// Chạy background — không block server startup.
-let _indexReady = false;
-/** True once auto-reindex has completed at least once. */
-export function isIndexReady() {
-    return _indexReady;
+    getStore();
 }
+// ─── Auto-index on connect (SQLite only) ──────────────────
+/** @deprecated Prefer isIndexReady from index-state — kept for external importers. */
+export { isIndexReady };
 async function autoReindex() {
     if (!config.repoPath) {
-        _indexReady = true; // No repo to index — nothing to wait for
+        markIndexEmpty();
         return;
     }
+    markIndexing();
     try {
         await initTreeSitter();
-        resetIndex();
+        const store = getStore();
+        // Clear index tables only — do not wipe experiences/memories
+        store.clearSymbols();
+        store.clearRelations();
         const snapshot = await parseRepository({ path: config.repoPath, depth: 3 });
-        setSnapshot(snapshot);
-        const allFiles = snapshot.files.map(f => ({ path: f.path, language: f.language }));
+        store.setSnapshot(snapshot);
+        store.setIndexedCommit(snapshot.commitSha);
+        store.setIndexedAt(new Date().toISOString());
+        store.setRepoFingerprint(snapshot.repoFingerprint);
+        const allFiles = snapshot.files.map((f) => ({ path: f.path, language: f.language }));
         const { symbols, relations } = await indexSymbols({
             repoPath: config.repoPath,
             files: allFiles,
             commitSha: snapshot.commitSha,
             repoFingerprint: snapshot.repoFingerprint,
         });
-        setSymbols(symbols);
-        setRelations(relations);
-        saveIndex(config.storePath);
+        store.addSymbols(symbols);
+        store.addRelations(relations);
+        let graphOk = true;
+        let graphError;
         try {
-            getStore().populateGraph(symbols, relations);
+            store.populateGraph(symbols, relations);
+        }
+        catch (err) {
+            graphOk = false;
+            graphError = err instanceof Error ? err.message : String(err);
+            console.error("[index] populateGraph failed:", graphError);
         }
-        catch {
-            console.warn("[index] populateGraph thất bại (JSON store fallback)"); /* JSON store */
+        if (symbols.length === 0) {
+            markIndexEmpty(snapshot.repoFingerprint);
+            console.error(`Auto-index: empty (${allFiles.length} files scanned)`);
+            return;
         }
-        _indexReady = true;
+        if (!graphOk) {
+            markIndexFailed(`Graph population failed: ${graphError}`, {
+                partial: true,
+                symbolCount: symbols.length,
+                relationCount: relations.length,
+                snapshotId: snapshot.repoFingerprint,
+            });
+            console.error(`Auto-index partial: ${allFiles.length} files, ${symbols.length} symbols (graph failed)`);
+            return;
+        }
+        markIndexReady({
+            symbolCount: symbols.length,
+            relationCount: relations.length,
+            snapshotId: snapshot.repoFingerprint,
+        });
         console.error(`Auto-index: ${allFiles.length} files, ${symbols.length} symbols`);
+        // Dense vectors: bootstrap runtime (download model + llama-server if needed)
+        if (isEmbeddingEnabled(config)) {
+            try {
+                console.error("[index] bootstrapping embedding runtime (auto)...");
+                const rt = await ensureEmbeddingRuntime(config);
+                if (rt.ready) {
+                    console.error(`[index] embedding runtime: ${rt.message}`);
+                    const v = await indexVectors({
+                        config,
+                        repoPath: config.repoPath,
+                        symbols,
+                        files: allFiles,
+                        repoFingerprint: snapshot.repoFingerprint,
+                        recreate: true,
+                    });
+                    if (v.skipped) {
+                        console.error(`[index] vectors skipped: ${v.reason}`);
+                    }
+                    else {
+                        console.error(`[index] vectors: ${v.chunksEmbedded}/${v.chunksTotal} chunks (${v.backend})`);
+                    }
+                }
+                else {
+                    console.error(`[index] embedding runtime not ready: ${rt.error ?? rt.message}`);
+                }
+            }
+            catch (err) {
+                console.error("[index] vector bootstrap failed (non-fatal):", err instanceof Error ? err.message : String(err));
+            }
+        }
     }
     catch (err) {
-        _indexReady = true; // Mark ready even on failure — tools work with last loaded index
-        console.error("Auto-index failed (non-fatal):", err instanceof Error ? err.message : err);
+        const message = err instanceof Error ? err.message : String(err);
+        markIndexFailed(message);
+        console.error("Auto-index failed:", message);
     }
 }
 autoReindex();
-// ─── Register tools ───────────────────────────────────────
-registerRepoOverview(server);
-registerSearchCode(server);
-registerInspectSymbol(server);
-registerGetContext(server);
-registerSearchHistory(server);
-registerRecallExperience(server);
-registerDetectDeadCode(server);
-registerTraceFlow(server);
-registerStatus(server);
-registerRunValidation(server);
-registerAnalyzeImpact(server);
-registerReindex(server);
-registerSessionHeartbeat(server);
-registerSessionStatus(server);
-registerRecordExperience(server);
-registerDeepExplore(server);
-registerPing(server);
-registerExplore(server);
+process.on("exit", () => {
+    void shutdownEmbeddingRuntime();
+});
+// ─── Profile-gated tool registration ─────────────────────
+// Only tools in the active profile appear in tools/list.
+function registerWhenAllowed(toolName, register) {
+    if (isToolInProfile(toolName, activeProfile)) {
+        register();
+    }
+}
+registerWhenAllowed("ci_reindex", () => registerReindex(server));
+registerWhenAllowed("ci_repo_overview", () => registerRepoOverview(server));
+registerWhenAllowed("ci_search_code", () => registerSearchCode(server));
+registerWhenAllowed("ci_inspect_symbol", () => registerInspectSymbol(server));
+registerWhenAllowed("ci_get_context", () => registerGetContext(server));
+registerWhenAllowed("ci_search_history", () => registerSearchHistory(server));
+registerWhenAllowed("ci_recall_experience", () => registerRecallExperience(server));
+registerWhenAllowed("ci_run_validation", () => registerRunValidation(server));
+registerWhenAllowed("ci_trace_flow", () => registerTraceFlow(server));
+registerWhenAllowed("ci_detect_dead_code", () => registerDetectDeadCode(server));
+registerWhenAllowed("ci_status", () => registerStatus(server));
+registerWhenAllowed("ci_analyze_impact", () => registerAnalyzeImpact(server));
+registerWhenAllowed("ci_session_heartbeat", () => registerSessionHeartbeat(server));
+registerWhenAllowed("ci_session_status", () => registerSessionStatus(server));
+registerWhenAllowed("ci_record_experience", () => registerRecordExperience(server));
+registerWhenAllowed("ci_deep_explore", () => registerDeepExplore(server));
+registerWhenAllowed("ci_ping", () => registerPing(server));
+registerWhenAllowed("ci_graph_stats", () => registerGraphStats(server));
+registerWhenAllowed("ci_graph_explain", () => registerGraphExplain(server));
+registerWhenAllowed("ci_query_graph", () => registerQueryGraph(server));
+registerWhenAllowed("ci_explore", () => registerExplore(server));
+registerWhenAllowed("ci_detect_cycles", () => registerDetectCycles(server));
+registerWhenAllowed("ci_reflect", () => registerReflect(server));
+registerWhenAllowed("ci_reflect_history", () => registerReflectHistory(server));
+registerWhenAllowed("ci_profile", () => registerProfileTool(server));
+registerWhenAllowed("ci_trace_bfs", () => registerTraceBfs(server));
 // ─── Register prompt resources ────────────────────────────
 const PROMPTS_DIR = resolve(import.meta.dirname, "../prompts");
 function registerPromptResource(name, description) {
-    const label = name.replace(/-/g, " ").replace(/\b\w/g, c => c.toUpperCase());
+    const label = name.replace(/-/g, " ").replace(/\b\w/g, (c) => c.toUpperCase());
     const filePath = join(PROMPTS_DIR, `${name}.md`);
-    // Register as a resource
     server.registerResource(label, `ci://prompts/${name}`, { mimeType: "text/markdown", description }, async (uri) => {
         if (!existsSync(filePath)) {
             throw new Error(`Prompt not found: ${name}`);
         }
         const content = readFileSync(filePath, "utf-8");
         return {
-            contents: [{
+            contents: [
+                {
                     uri: uri.toString(),
                     mimeType: "text/markdown",
                     text: content,
-                }],
+                },
+            ],
         };
     });
-    // Register as a prompt template
     server.registerPrompt(name, { description, argsSchema: undefined }, async (args) => {
         if (!existsSync(filePath)) {
             throw new Error(`Prompt not found: ${name}`);
@@ -212,16 +238,69 @@ function registerPromptResource(name, description) {
 registerPromptResource("debug-runtime-error", "10-step workflow for debugging runtime errors");
 registerPromptResource("implement-feature", "8-step workflow for implementing new features");
 registerPromptResource("review-code", "6-step code review checklist with security and testing concerns");
-// ─── Transport setup ──────────────────────────────────────
+// ─── Resource templates ───────────────────────────────────
+server.registerResource("Symbol Source", new ResourceTemplate("code://symbol/{name}", {
+    list: undefined,
+    complete: {
+        name: async (value) => {
+            const matches = getStore().searchSymbolsFTS(value, 10);
+            return matches.map((s) => s.name);
+        },
+    },
+}), { mimeType: "text/plain", description: "Source code context for a named symbol" }, async (uri) => {
+    const name = uri.pathname.replace("/symbol/", "");
+    const symbol = getStore().getSymbol(name);
+    if (!symbol) {
+        throw new Error(`Symbol "${name}" not found`);
+    }
+    return {
+        contents: [
+            {
+                uri: uri.toString(),
+                mimeType: "text/plain",
+                text: `${symbol.kind} ${symbol.name}\nFile: ${symbol.file}:${symbol.line}\n\n${symbol.signature ?? ""}`,
+            },
+        ],
+    };
+});
+server.registerResource("Repository Snapshot", "repo://snapshot", {
+    mimeType: "application/json",
+    description: "Current repository snapshot with symbol and relation counts",
+}, async (uri) => {
+    const snapshot = getStore().getSnapshot();
+    const symbols = getStore().getSymbols();
+    const relations = getStore().getRelations();
+    const idx = getIndexState();
+    const data = {
+        snapshot,
+        symbolCount: symbols.length,
+        relationCount: relations.length,
+        filesByLanguage: getStore().getFilesByLanguage(),
+        indexLifecycle: idx.lifecycle,
+        indexReady: idx.ready,
+        partial: idx.partial,
+    };
+    return {
+        contents: [
+            {
+                uri: uri.toString(),
+                mimeType: "application/json",
+                text: JSON.stringify(data, null, 2),
+            },
+        ],
+    };
+});
+// ─── Transport (stdio only) ───────────────────────────────
 async function runStdio() {
     const transport = new StdioServerTransport();
     await server.connect(transport);
+    const profileDef = getProfile(activeProfile);
     console.error(`${SERVER_NAME} v${SERVER_VERSION} running via stdio`);
-    console.error(`Tools: repo_overview, search_code, inspect_symbol, get_context, search_history, recall_experience, trace_flow, status, run_validation, analyze_impact, reindex, record_experience`);
+    console.error(`Profile: ${activeProfile} (${profileDef.tools.length} tools)`);
+    console.error(`Tools: ${profileDef.tools.map((t) => t.replace(/^ci_/, "")).join(", ")}`);
     console.error(`Prompts: debug-runtime-error, implement-feature, review-code`);
 }
-// ─── Entry point ──────────────────────────────────────────
-runStdio().catch(error => {
+runStdio().catch((error) => {
     console.error("Server error:", error);
     process.exit(1);
 });

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/install.js

@@ -25,8 +25,8 @@ const TOOLS = [
     },
     {
         name: "ci_search_code",
-        description: "Full-text code search via ripgrep + BM25 symbol scoring. Supports language filters and pagination.",
-        usage: "Find code by content or pattern when you need raw text search across files.",
+        description: "Code search: lexical (ripgrep+BM25, default), semantic (LFM2.5+Zvec, opt-in), or hybrid. Language filters and pagination.",
+        usage: "Find code by content/pattern (lexical) or natural-language intent (mode=semantic|hybrid when embeddings enabled).",
     },
     {
         name: "ci_inspect_symbol",

package/dist/install.js.map

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

@@ -0,0 +1,28 @@
+/**
+ * Tool Profile System — controls which tools are registered and callable.
+ *
+ * Profiles reduce the tool surface exposed to coding agents, lowering
+ * context overhead and preventing accidental mutations.
+ *
+ * Built-in profiles:
+ * - `core` (default): ≤7 read-only code-understanding intents
+ * - `full`: all tools including validation, memory, reindex, session
+ *
+ * Set via `.ci-mcp.json` `"profile": "full"` or env `CI_MCP_PROFILE=full`.
+ */
+export type ToolProfile = "core" | "full";
+export interface ProfileDefinition {
+    name: ToolProfile;
+    label: string;
+    description: string;
+    tools: string[];
+    readOnly: boolean;
+}
+/** Mutation / side-effect tools — never in core. */
+export declare const MUTATION_TOOLS: readonly ["ci_run_validation", "ci_record_experience", "ci_reindex", "ci_session_heartbeat", "ci_session_status", "ci_reflect", "ci_reflect_history"];
+export declare function getProfile(name: ToolProfile): ProfileDefinition;
+export declare function getAllProfiles(): ProfileDefinition[];
+export declare function isToolInProfile(toolName: string, profile: ToolProfile): boolean;
+export declare function getCoreToolNames(): readonly string[];
+export declare function isMutationTool(toolName: string): boolean;
+//# sourceMappingURL=profiles.d.ts.map

package/dist/profiles.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"profiles.d.ts","sourceRoot":"","sources":["../src/profiles.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,MAAM,MAAM,WAAW,GAAG,MAAM,GAAG,MAAM,CAAC;AAE1C,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,WAAW,CAAC;IAClB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;IACpB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,QAAQ,EAAE,OAAO,CAAC;CACnB;AAED,oDAAoD;AACpD,eAAO,MAAM,cAAc,uJAQjB,CAAC;AAyDX,wBAAgB,UAAU,CAAC,IAAI,EAAE,WAAW,GAAG,iBAAiB,CAE/D;AAED,wBAAgB,cAAc,IAAI,iBAAiB,EAAE,CAEpD;AAED,wBAAgB,eAAe,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,GAAG,OAAO,CAE/E;AAED,wBAAgB,gBAAgB,IAAI,SAAS,MAAM,EAAE,CAEpD;AAED,wBAAgB,cAAc,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAExD"}

package/dist/profiles.js

@@ -0,0 +1,89 @@
+/**
+ * Tool Profile System — controls which tools are registered and callable.
+ *
+ * Profiles reduce the tool surface exposed to coding agents, lowering
+ * context overhead and preventing accidental mutations.
+ *
+ * Built-in profiles:
+ * - `core` (default): ≤7 read-only code-understanding intents
+ * - `full`: all tools including validation, memory, reindex, session
+ *
+ * Set via `.ci-mcp.json` `"profile": "full"` or env `CI_MCP_PROFILE=full`.
+ */
+/** Mutation / side-effect tools — never in core. */
+export const MUTATION_TOOLS = [
+    "ci_run_validation",
+    "ci_record_experience",
+    "ci_reindex",
+    "ci_session_heartbeat",
+    "ci_session_status",
+    "ci_reflect",
+    "ci_reflect_history",
+];
+/**
+ * Core profile: primary read-safe intents for coding agents.
+ * Keep this list short (≤7) to minimize schema burden.
+ */
+const CORE_TOOLS = [
+    "ci_ping",
+    "ci_status",
+    "ci_repo_overview",
+    "ci_explore",
+    "ci_inspect_symbol",
+    "ci_get_context",
+    "ci_analyze_impact",
+    "ci_trace_flow",
+];
+const FULL_ONLY_TOOLS = [
+    "ci_search_code",
+    "ci_search_history",
+    "ci_deep_explore",
+    "ci_detect_dead_code",
+    "ci_graph_stats",
+    "ci_graph_explain",
+    "ci_query_graph",
+    "ci_detect_cycles",
+    "ci_trace_bfs",
+    "ci_ping",
+    "ci_recall_experience",
+    "ci_record_experience",
+    "ci_run_validation",
+    "ci_reindex",
+    "ci_reflect",
+    "ci_reflect_history",
+    "ci_profile",
+    "ci_session_heartbeat",
+    "ci_session_status",
+];
+const PROFILE_REGISTRY = {
+    core: {
+        name: "core",
+        label: "Core Code Understanding",
+        description: "Read-only tools for code search, symbol navigation, impact analysis, and context retrieval (≤7 tools)",
+        tools: [...CORE_TOOLS],
+        readOnly: true,
+    },
+    full: {
+        name: "full",
+        label: "Full Access",
+        description: "All tools including validation, memory, session management, graph diagnostics, and mutations",
+        tools: [...CORE_TOOLS, ...FULL_ONLY_TOOLS],
+        readOnly: false,
+    },
+};
+export function getProfile(name) {
+    return PROFILE_REGISTRY[name] ?? PROFILE_REGISTRY.core;
+}
+export function getAllProfiles() {
+    return Object.values(PROFILE_REGISTRY);
+}
+export function isToolInProfile(toolName, profile) {
+    return PROFILE_REGISTRY[profile]?.tools.includes(toolName) ?? false;
+}
+export function getCoreToolNames() {
+    return CORE_TOOLS;
+}
+export function isMutationTool(toolName) {
+    return MUTATION_TOOLS.includes(toolName);
+}
+//# sourceMappingURL=profiles.js.map