@grainulation/wheat 1.0.9 → 1.0.11

package/README.md

@@ -39,11 +39,13 @@ Works with [Claude Code](https://claude.com/claude-code), [Cursor](https://curso
 For native tool access in Claude Code:
 
 ```bash
-claude mcp add wheat -- npx -y @grainulation/wheat mcp
+claude mcp add wheat -- npx -y @grainulation/wheat-mcp
 ```
 
 This gives Claude direct access to wheat's claims engine — add-claim, compile, search, status — without shelling out.
 
+> **Note:** `wheat mcp` still works as a subcommand, but the dedicated `wheat-mcp` entry point is recommended for MCP integrations — it bypasses CLI dispatch and starts the server directly.
+
 ## See it in 30 seconds
 
 ```bash

package/bin/wheat-mcp.cjs

@@ -0,0 +1,18 @@
+#!/usr/bin/env node
+/**
+ * wheat-mcp (CJS) — Dedicated MCP server entry point
+ *
+ * CJS wrapper that dynamically imports the ESM serve-mcp module.
+ * Claude Code's plugin transport reliably keeps CJS-spawned processes
+ * alive but drops ESM processes. This file bridges the gap.
+ */
+
+const dirIdx = process.argv.indexOf("--dir");
+const dir = dirIdx !== -1 && process.argv[dirIdx + 1]
+  ? process.argv[dirIdx + 1]
+  : process.cwd();
+
+// Dynamic import of ESM module from CJS
+import("../lib/serve-mcp.js").then((mod) => {
+  mod.startServer(dir);
+});

package/compiler/wheat-compiler.js

@@ -836,7 +836,9 @@ function compile(inputPath, outputPath, dir, opts = {}) {
       id: c.id,
       type: c.type,
       topic: c.topic,
+      content: c.content,
       evidence: c.evidence,
+      confidence: c.confidence,
       status: c.status,
       phase_added: c.phase_added,
       source: c.source,

package/lib/init.js

@@ -341,6 +341,11 @@ fi
 // ─── .mcp.json & AGENTS.md ──────────────────────────────────────────────────
 
 function writeMcpJson(dir) {
+  if (process.env.CLAUDE_PLUGIN_ROOT) {
+    console.log("  - .mcp.json              (skipped — plugin provides MCP servers)");
+    return;
+  }
+
   const mcpPath = target(dir, ".mcp.json");
   const wheatEntry = {
     command: "npx",
@@ -577,10 +582,24 @@ export async function run(dir, args) {
   fs.renameSync(tmpClaims, claimsPath);
   console.log("  \x1b[32m+\x1b[0m claims.json");
 
-  // CLAUDE.md
+  // CLAUDE.md (preserve existing content unless --force)
   const claudePath = target(dir, "CLAUDE.md");
-  fs.writeFileSync(claudePath, claudeMd);
-  console.log("  \x1b[32m+\x1b[0m CLAUDE.md");
+  const claudeExists = fs.existsSync(claudePath);
+  if (claudeExists && flags.force) {
+    // --force with existing file: back up before overwriting
+    fs.copyFileSync(claudePath, claudePath + ".bak");
+    fs.writeFileSync(claudePath, claudeMd);
+    console.log("  \x1b[32m+\x1b[0m CLAUDE.md (backed up existing to CLAUDE.md.bak)");
+  } else if (claudeExists) {
+    // Existing file, no --force: append wheat section with separator
+    const existing = fs.readFileSync(claudePath, "utf8");
+    fs.writeFileSync(claudePath, existing + "\n\n---\n\n" + claudeMd);
+    console.log("  \x1b[32m+\x1b[0m CLAUDE.md (appended wheat sprint section)");
+  } else {
+    // No existing file: write normally
+    fs.writeFileSync(claudePath, claudeMd);
+    console.log("  \x1b[32m+\x1b[0m CLAUDE.md");
+  }
 
   // .claude/commands/wheat/
   const copied = copyCommands(dir);

package/lib/serve-mcp.js

@@ -22,7 +22,10 @@
  *
  * Protocol: MCP over stdio (JSON-RPC 2.0, newline-delimited)
  *
- * Install:
+ * Install (recommended):
+ *   claude mcp add wheat -- npx @grainulation/wheat-mcp
+ *
+ * Legacy (still works, but routes through CLI dispatch):
  *   claude mcp add wheat -- npx @grainulation/wheat mcp
  *
  * Zero npm dependencies.
@@ -218,6 +221,15 @@ function toolResolve(dir, args) {
   if (!loserClaim)
     return { status: "error", message: `Claim "${loser}" not found.` };
 
+  const winnerConflicts = winnerClaim.conflicts_with || [];
+  const loserConflicts = loserClaim.conflicts_with || [];
+  if (!winnerConflicts.includes(loser) && !loserConflicts.includes(winner)) {
+    return {
+      status: "error",
+      message: `Cannot resolve: "${winner}" and "${loser}" have no conflicts_with relationship.`,
+    };
+  }
+
   // Clear conflict references
   winnerClaim.conflicts_with = (winnerClaim.conflicts_with || []).filter(
     (cid) => cid !== loser
@@ -850,10 +862,11 @@ export async function run(dir, args) {
     console.log(`wheat mcp -- Local MCP server for Claude Code
 
 Usage:
-  wheat mcp [--dir <path>]
+  wheat-mcp [--dir <path>]      (recommended)
+  wheat mcp [--dir <path>]      (legacy, still works)
 
 Install in Claude Code:
-  claude mcp add wheat -- npx @grainulation/wheat mcp
+  claude mcp add wheat -- npx @grainulation/wheat-mcp
 
 Tools exposed:
   wheat/compile     Run the compiler

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@grainulation/wheat",
-  "version": "1.0.9",
+  "version": "1.0.11",
   "description": "Research-driven development framework — structured claims, compiled evidence, deterministic output",
   "license": "MIT",
   "author": "grainulation contributors",
@@ -47,7 +47,7 @@
     "templates/"
   ],
   "scripts": {
-    "test": "node --test test/cli.test.js test/compiler.test.js test/guard.test.js test/init.test.js test/migration.test.js"
+    "test": "node --test test/cli.test.js test/compiler.test.js test/guard.test.js test/init.test.js test/migration.test.js test/mcp.test.js"
   },
   "engines": {
     "node": ">=20"