gsd-pi 2.77.0-dev.c9c8932c6 → 2.77.0-dev.eaa4973bc

package/dist/web/standalone/.next/static/chunks/{webpack-1832629448831fdc.js → webpack-2e68521d7c82f7c2.js}

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gsd-pi",
-  "version": "2.77.0-dev.c9c8932c6",
+  "version": "2.77.0-dev.eaa4973bc",
   "description": "GSD — Get Shit Done coding agent",
   "license": "MIT",
   "repository": {
@@ -68,13 +68,13 @@
     "test:coverage": "c8 --reporter=text --reporter=lcov --exclude=\"src/resources/extensions/gsd/tests/**\" --exclude=\"src/tests/**\" --exclude=\"scripts/**\" --exclude=\"native/**\" --exclude=\"node_modules/**\" --check-coverage --statements=40 --lines=40 --branches=20 --functions=20 node --import ./src/resources/extensions/gsd/tests/resolve-ts.mjs --experimental-strip-types --experimental-test-isolation=process --test src/resources/extensions/gsd/tests/*.test.ts src/resources/extensions/gsd/tests/*.test.mjs src/tests/*.test.ts src/resources/extensions/shared/tests/*.test.ts",
     "test:integration": "node --import ./src/resources/extensions/gsd/tests/resolve-ts.mjs --experimental-strip-types --test \"src/tests/integration/*.test.ts\" \"src/resources/extensions/gsd/tests/integration/*.test.ts\" \"src/resources/extensions/async-jobs/*.test.ts\" \"src/resources/extensions/browser-tools/tests/*.test.mjs\"",
     "pretest": "npm run typecheck:extensions",
-    "test": "npm run test:unit && npm run test:integration",
+    "test": "npm run test:unit && npm run test:integration && npm run test:packages",
     "test:smoke": "node --experimental-strip-types tests/smoke/run.ts",
     "test:fixtures": "node --experimental-strip-types tests/fixtures/run.ts",
     "test:fixtures:record": "node scripts/with-env.mjs GSD_FIXTURE_MODE=record -- node --experimental-strip-types tests/fixtures/record.ts",
     "test:live": "node scripts/with-env.mjs GSD_LIVE_TESTS=1 -- node --experimental-strip-types tests/live/run.ts",
     "test:browser-tools": "node --test src/resources/extensions/browser-tools/tests/browser-tools-unit.test.cjs src/resources/extensions/browser-tools/tests/browser-tools-integration.test.mjs",
-    "test:native": "node --test packages/native/src/__tests__/grep.test.mjs",
+    "test:native": "npm run test -w @gsd/native",
     "test:secret-scan": "node --import ./src/resources/extensions/gsd/tests/resolve-ts.mjs --experimental-strip-types --test src/tests/secret-scan.test.ts",
     "secret-scan": "node scripts/secret-scan.mjs",
     "secret-scan:install-hook": "node scripts/install-hooks.mjs",

package/packages/mcp-server/README.md

@@ -113,15 +113,15 @@ These tools use the same GSD workflow handlers as the native in-process tool pat
 
 ### Interactive tools
 
-The packaged server now exposes `ask_user_questions` through MCP form elicitation. This keeps the existing GSD answer payload shape while allowing Claude Code CLI and other elicitation-capable clients to surface structured user choices.
+The packaged server exposes `ask_user_questions` through MCP form elicitation. This keeps the existing GSD answer payload shape while allowing Claude Code CLI and other elicitation-capable clients to surface structured user choices.
 
-`secure_env_collect` is still not exposed by this package. That path needs MCP URL elicitation or an equivalent secure bridge because secrets should not flow through form elicitation.
+The packaged server also exposes `secure_env_collect` through MCP form elicitation. Secret values are written directly to the selected destination and are not included in tool output. For dotenv writes, `envFilePath` must resolve inside the validated project directory; parent traversal and symlink escapes are rejected.
 
 Current support boundary:
 
 - when running inside the GSD monorepo checkout, the MCP server auto-discovers the shared workflow executor module
 - outside the monorepo, set `GSD_WORKFLOW_EXECUTORS_MODULE` to an importable `workflow-tool-executors` module path if you want the mutation tools enabled
-- `ask_user_questions` requires an MCP client that supports form elicitation
+- `ask_user_questions` and `secure_env_collect` require an MCP client that supports form elicitation
 - session/read tools do not depend on this bridge
 
 If the executor bridge cannot be loaded, workflow mutation calls will fail with a precise configuration error instead of silently degrading.

package/packages/mcp-server/dist/env-writer.d.ts

@@ -15,6 +15,7 @@ export declare function detectDestination(basePath: string): "dotenv" | "vercel"
 export declare function writeEnvKey(filePath: string, key: string, value: string): Promise<void>;
 export declare function isSafeEnvVarKey(key: string): boolean;
 export declare function isSupportedDeploymentEnvironment(env: string): boolean;
+export declare function resolveProjectEnvFilePath(projectDir: string, envFilePath?: string): string;
 export declare function shellEscapeSingle(value: string): string;
 interface ApplyResult {
     applied: string[];

package/packages/mcp-server/dist/env-writer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"env-writer.d.ts","sourceRoot":"","sources":["../src/env-writer.ts"],"names":[],"mappings":"AAeA;;;GAGG;AACH,wBAAsB,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAiBjG;AAMD;;;GAGG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,QAAQ,GAAG,QAAQ,GAAG,QAAQ,CAalF;AAMD;;;GAGG;AACH,wBAAsB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAoB7F;AAMD,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAEpD;AAED,wBAAgB,gCAAgC,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAErE;AAMD,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEvD;AAMD,UAAU,WAAW;IACnB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,QAAQ,EAAE,KAAK,CAAC;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,EAC/C,WAAW,EAAE,QAAQ,GAAG,QAAQ,GAAG,QAAQ,EAC3C,IAAI,EAAE;IACJ,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,OAAO,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACrF,GACA,OAAO,CAAC,WAAW,CAAC,CAkDtB"}
+{"version":3,"file":"env-writer.d.ts","sourceRoot":"","sources":["../src/env-writer.ts"],"names":[],"mappings":"AAeA;;;GAGG;AACH,wBAAsB,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAiBjG;AAMD;;;GAGG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,QAAQ,GAAG,QAAQ,GAAG,QAAQ,CAalF;AAMD;;;GAGG;AACH,wBAAsB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAmD7F;AAmBD,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAEpD;AAED,wBAAgB,gCAAgC,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAErE;AAOD,wBAAgB,yBAAyB,CAAC,UAAU,EAAE,MAAM,EAAE,WAAW,SAAS,GAAG,MAAM,CAmB1F;AAMD,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEvD;AAMD,UAAU,WAAW;IACnB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,QAAQ,EAAE,KAAK,CAAC;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,EAC/C,WAAW,EAAE,QAAQ,GAAG,QAAQ,GAAG,QAAQ,EAC3C,IAAI,EAAE;IACJ,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,OAAO,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACrF,GACA,OAAO,CAAC,WAAW,CAAC,CAkDtB"}

package/packages/mcp-server/dist/env-writer.js

@@ -4,9 +4,9 @@
 // Shared helpers for writing env vars to .env files, detecting project
 // destinations, and checking existing keys. Used by secure_env_collect
 // MCP tool. No TUI dependencies — pure filesystem + process.env operations.
-import { readFile, writeFile } from "node:fs/promises";
-import { existsSync, statSync } from "node:fs";
-import { resolve } from "node:path";
+import { open, readFile, rename, rm } from "node:fs/promises";
+import { constants, existsSync, lstatSync, realpathSync, statSync } from "node:fs";
+import { basename, dirname, isAbsolute, join, relative, resolve } from "node:path";
 // ---------------------------------------------------------------------------
 // checkExistingEnvKeys
 // ---------------------------------------------------------------------------
@@ -65,11 +65,21 @@ export async function writeEnvKey(filePath, key, value) {
     if (typeof value !== "string") {
         throw new TypeError(`writeEnvKey expects a string value for key "${key}", got ${typeof value}`);
     }
+    assertWritableEnvFileTarget(filePath);
     let content = "";
     try {
-        content = await readFile(filePath, "utf8");
+        const handle = await open(filePath, constants.O_RDONLY | constants.O_NOFOLLOW);
+        try {
+            content = await handle.readFile("utf8");
+        }
+        finally {
+            await handle.close();
+        }
     }
-    catch {
+    catch (err) {
+        if (err.code !== "ENOENT") {
+            throw err;
+        }
         content = "";
     }
     const escaped = value.replace(/\\/g, "\\\\").replace(/\n/g, "\\n").replace(/\r/g, "");
@@ -83,7 +93,41 @@ export async function writeEnvKey(filePath, key, value) {
             content += "\n";
         content += `${line}\n`;
     }
-    await writeFile(filePath, content, "utf8");
+    const tempPath = join(dirname(filePath), `.${basename(filePath)}.${process.pid}.${Date.now()}.${Math.random().toString(16).slice(2)}.tmp`);
+    let handle;
+    try {
+        handle = await open(tempPath, constants.O_WRONLY | constants.O_CREAT | constants.O_EXCL, 0o600);
+        await handle.writeFile(content, "utf8");
+        await handle.close();
+        handle = undefined;
+        assertWritableEnvFileTarget(filePath);
+        await rename(tempPath, filePath);
+    }
+    catch (err) {
+        if (handle) {
+            try {
+                await handle.close();
+            }
+            catch {
+                // Best-effort cleanup.
+            }
+        }
+        await rm(tempPath, { force: true }).catch(() => undefined);
+        throw err;
+    }
+}
+function assertWritableEnvFileTarget(filePath) {
+    try {
+        if (lstatSync(filePath).isSymbolicLink()) {
+            throw new Error("Refusing to write symlinked env file");
+        }
+    }
+    catch (err) {
+        if (err.code === "ENOENT") {
+            return;
+        }
+        throw err;
+    }
 }
 // ---------------------------------------------------------------------------
 // Validation helpers
@@ -94,6 +138,30 @@ export function isSafeEnvVarKey(key) {
 export function isSupportedDeploymentEnvironment(env) {
     return env === "development" || env === "preview" || env === "production";
 }
+function isWithinProjectRoot(projectRoot, candidatePath) {
+    const rel = relative(projectRoot, candidatePath);
+    return rel === "" || (!rel.startsWith("..") && !isAbsolute(rel));
+}
+export function resolveProjectEnvFilePath(projectDir, envFilePath = ".env") {
+    const projectRoot = realpathSync.native(resolve(projectDir));
+    const candidate = resolve(projectRoot, envFilePath);
+    if (!isWithinProjectRoot(projectRoot, candidate)) {
+        throw new Error("envFilePath must resolve inside the project directory");
+    }
+    if (existsSync(candidate)) {
+        const targetRealPath = realpathSync.native(candidate);
+        if (isWithinProjectRoot(projectRoot, targetRealPath)) {
+            return candidate;
+        }
+        throw new Error("envFilePath must resolve inside the project directory");
+    }
+    const candidateParent = dirname(candidate);
+    const parentRealPath = realpathSync.native(candidateParent);
+    if (isWithinProjectRoot(projectRoot, parentRealPath)) {
+        return candidate;
+    }
+    throw new Error("envFilePath must resolve inside the project directory");
+}
 // ---------------------------------------------------------------------------
 // Shell helpers (for vercel/convex CLI)
 // ---------------------------------------------------------------------------

package/packages/mcp-server/dist/env-writer.js.map

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@gsd-build/mcp-server — Environment variable write utilities\n// Copyright (c) 2026 Jeremy McSpadden <jeremy@fluxlabs.net>\n//\n// Shared helpers for writing env vars to .env files, detecting project\n// destinations, and checking existing keys. Used by secure_env_collect\n// MCP tool. 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key.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n    const regex = new RegExp(`^${escaped}\\\\s*=`, \"m\");\n    if (regex.test(fileContent) || key in process.env) {\n      existing.push(key);\n    }\n  }\n  return existing;\n}\n\n// ---------------------------------------------------------------------------\n// detectDestination\n// ---------------------------------------------------------------------------\n\n/**\n * Detect the write destination based on project files in basePath.\n * Priority: vercel.json → convex/ dir → fallback \"dotenv\".\n */\nexport function detectDestination(basePath: string): \"dotenv\" | \"vercel\" | \"convex\" {\n  if (existsSync(resolve(basePath, \"vercel.json\"))) {\n    return \"vercel\";\n  }\n  const convexPath = resolve(basePath, \"convex\");\n  try {\n    if (existsSync(convexPath) && statSync(convexPath).isDirectory()) {\n      return \"convex\";\n    }\n  } catch {\n    // stat error — treat as not found\n  }\n  return \"dotenv\";\n}\n\n// ---------------------------------------------------------------------------\n// writeEnvKey\n// ---------------------------------------------------------------------------\n\n/**\n * Write a single key=value pair to a .env file.\n * Updates existing keys in-place, appends new ones at the end.\n */\nexport async function writeEnvKey(filePath: string, key: string, value: string): Promise<void> {\n  if (typeof value !== \"string\") {\n    throw new TypeError(`writeEnvKey expects a string value for key \"${key}\", got ${typeof value}`);\n  }\n  assertWritableEnvFileTarget(filePath);\n  let content = \"\";\n  try {\n    const handle = await open(filePath, constants.O_RDONLY | constants.O_NOFOLLOW);\n    try {\n      content = await handle.readFile(\"utf8\");\n    } finally {\n      await handle.close();\n    }\n  } catch (err) {\n    if ((err as NodeJS.ErrnoException).code !== \"ENOENT\") {\n      throw err;\n    }\n    content = \"\";\n  }\n  const escaped = value.replace(/\\\\/g, \"\\\\\\\\\").replace(/\\n/g, \"\\\\n\").replace(/\\r/g, \"\");\n  const line = `${key}=${escaped}`;\n  const regex = new RegExp(`^${key.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\")}\\\\s*=.*$`, \"m\");\n  if (regex.test(content)) {\n    content = content.replace(regex, line);\n  } else {\n    if (content.length > 0 && !content.endsWith(\"\\n\")) content += \"\\n\";\n    content += `${line}\\n`;\n  }\n  const tempPath = join(\n    dirname(filePath),\n    `.${basename(filePath)}.${process.pid}.${Date.now()}.${Math.random().toString(16).slice(2)}.tmp`,\n  );\n  let handle: Awaited<ReturnType<typeof open>> | undefined;\n  try {\n    handle = await open(tempPath, constants.O_WRONLY | constants.O_CREAT | constants.O_EXCL, 0o600);\n    await handle.writeFile(content, \"utf8\");\n    await handle.close();\n    handle = undefined;\n    assertWritableEnvFileTarget(filePath);\n    await rename(tempPath, filePath);\n  } catch (err) {\n    if (handle) {\n      try {\n        await handle.close();\n      } catch {\n        // Best-effort cleanup.\n      }\n    }\n    await rm(tempPath, { force: true }).catch(() => undefined);\n    throw err;\n  }\n}\n\nfunction assertWritableEnvFileTarget(filePath: string): void {\n  try {\n    if (lstatSync(filePath).isSymbolicLink()) {\n      throw new Error(\"Refusing to write symlinked env file\");\n    }\n  } catch (err) {\n    if ((err as NodeJS.ErrnoException).code === \"ENOENT\") {\n      return;\n    }\n    throw err;\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Validation helpers\n// ---------------------------------------------------------------------------\n\nexport function isSafeEnvVarKey(key: string): boolean {\n  return /^[A-Za-z_][A-Za-z0-9_]*$/.test(key);\n}\n\nexport function isSupportedDeploymentEnvironment(env: string): boolean {\n  return env === \"development\" || env === \"preview\" || env === \"production\";\n}\n\nfunction isWithinProjectRoot(projectRoot: string, candidatePath: string): boolean {\n  const rel = relative(projectRoot, candidatePath);\n  return rel === \"\" || (!rel.startsWith(\"..\") && !isAbsolute(rel));\n}\n\nexport function resolveProjectEnvFilePath(projectDir: string, envFilePath = \".env\"): string {\n  const projectRoot = realpathSync.native(resolve(projectDir));\n  const candidate = resolve(projectRoot, envFilePath);\n  if (!isWithinProjectRoot(projectRoot, candidate)) {\n    throw new Error(\"envFilePath must resolve inside the project directory\");\n  }\n  if (existsSync(candidate)) {\n    const targetRealPath = realpathSync.native(candidate);\n    if (isWithinProjectRoot(projectRoot, targetRealPath)) {\n      return candidate;\n    }\n    throw new Error(\"envFilePath must resolve inside the project directory\");\n  }\n  const candidateParent = dirname(candidate);\n  const parentRealPath = realpathSync.native(candidateParent);\n  if (isWithinProjectRoot(projectRoot, parentRealPath)) {\n    return candidate;\n  }\n  throw new Error(\"envFilePath must resolve inside the project directory\");\n}\n\n// ---------------------------------------------------------------------------\n// Shell helpers (for vercel/convex CLI)\n// ---------------------------------------------------------------------------\n\nexport function shellEscapeSingle(value: string): string {\n  return `'${value.replace(/'/g, `'\\\\''`)}'`;\n}\n\n// ---------------------------------------------------------------------------\n// applySecrets\n// ---------------------------------------------------------------------------\n\ninterface ApplyResult {\n  applied: string[];\n  errors: string[];\n}\n\n/**\n * Apply collected secrets to the target destination.\n * Dotenv writes are handled directly; vercel/convex shell out via execFn.\n */\nexport async function applySecrets(\n  provided: Array<{ key: string; value: string }>,\n  destination: \"dotenv\" | \"vercel\" | \"convex\",\n  opts: {\n    envFilePath: string;\n    environment?: string;\n    execFn?: (cmd: string, args: string[]) => Promise<{ code: number; stderr: string }>;\n  },\n): Promise<ApplyResult> {\n  const applied: string[] = [];\n  const errors: string[] = [];\n\n  if (destination === \"dotenv\") {\n    for (const { key, value } of provided) {\n      try {\n        await writeEnvKey(opts.envFilePath, key, value);\n        applied.push(key);\n        // Hydrate process.env so the current session sees the new value\n        process.env[key] = value;\n      } catch (err: unknown) {\n        const msg = err instanceof Error ? err.message : String(err);\n        errors.push(`${key}: ${msg}`);\n      }\n    }\n  }\n\n  if ((destination === \"vercel\" || destination === \"convex\") && opts.execFn) {\n    const env = opts.environment ?? \"development\";\n    if (!isSupportedDeploymentEnvironment(env)) {\n      errors.push(`environment: unsupported target environment \"${env}\"`);\n      return { applied, errors };\n    }\n    for (const { key, value } of provided) {\n      if (!isSafeEnvVarKey(key)) {\n        errors.push(`${key}: invalid environment variable name`);\n        continue;\n      }\n      const cmd = destination === \"vercel\"\n        ? `printf %s ${shellEscapeSingle(value)} | vercel env add ${key} ${env}`\n        : \"\";\n      try {\n        const result = destination === \"vercel\"\n          ? await opts.execFn(\"sh\", [\"-c\", cmd])\n          : await opts.execFn(\"npx\", [\"convex\", \"env\", \"set\", key, value]);\n        if (result.code !== 0) {\n          errors.push(`${key}: ${result.stderr.slice(0, 200)}`);\n        } else {\n          applied.push(key);\n          process.env[key] = value;\n        }\n      } catch (err: unknown) {\n        const msg = err instanceof Error ? err.message : String(err);\n        errors.push(`${key}: ${msg}`);\n      }\n    }\n  }\n\n  return { applied, errors };\n}\n"]}

package/packages/mcp-server/dist/server.d.ts.map

@@ -1 +1 @@
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package/packages/mcp-server/dist/server.js

@@ -12,6 +12,7 @@
  */
 import { readFile, readdir, stat } from 'node:fs/promises';
 import { join, resolve } from 'node:path';
+import { spawn } from 'node:child_process';
 import { z } from 'zod';
 import { isRemoteConfigured, tryRemoteQuestions } from './remote-questions.js';
 import { readProgress } from './readers/state.js';
@@ -23,7 +24,7 @@ import { buildGraph, writeGraph, writeSnapshot, graphStatus, graphQuery, graphDi
 import { resolveGsdRoot } from './readers/paths.js';
 import { runDoctorLite } from './readers/doctor-lite.js';
 import { registerWorkflowTools, validateProjectDir } from './workflow-tools.js';
-import { applySecrets, checkExistingEnvKeys, detectDestination } from './env-writer.js';
+import { applySecrets, checkExistingEnvKeys, detectDestination, resolveProjectEnvFilePath } from './env-writer.js';
 // ---------------------------------------------------------------------------
 // Constants
 // ---------------------------------------------------------------------------
@@ -32,6 +33,27 @@ const SERVER_NAME = 'gsd';
 const SERVER_VERSION = '2.53.0';
 /** User-interaction timeout — generous but bounded so elicitation can't hang indefinitely (#4586). */
 const ELICIT_TIMEOUT_MS = 10 * 60 * 1000; // 10 minutes
+/**
+ * Default child-process runner used by secure_env_collect to push secrets
+ * into `vercel env add` / `npx convex env set`. Previously `applySecrets`
+ * was called without an `execFn`, so vercel/convex destinations silently
+ * dropped every collected key. This restores the write path.
+ */
+function defaultExecFn(cmd, args) {
+    return new Promise((res) => {
+        // stdin: ignore — avoids hanging if the child ever prompts interactively.
+        // stdout: ignore — consumer only cares about stderr + exit code, and an
+        //   un-drained pipe deadlocks once the kernel buffer (~64KB) fills.
+        // stderr: pipe — captured below for error surfacing.
+        const child = spawn(cmd, args, { stdio: ['ignore', 'ignore', 'pipe'] });
+        let stderr = '';
+        child.stderr.on('data', (chunk) => {
+            stderr += chunk.toString('utf8');
+        });
+        child.on('error', (err) => res({ code: 1, stderr: err.message }));
+        child.on('close', (code) => res({ code: code ?? 1, stderr }));
+    });
+}
 /**
  * Race a promise against a timeout. Rejects with a typed error on timeout so
  * callers can return a specific MCP error response rather than hanging.
@@ -470,7 +492,7 @@ export async function createMcpServer(sessionManager) {
         const { projectDir, keys, destination, envFilePath, environment } = args;
         try {
             const resolvedProjectDir = validateProjectDir(projectDir);
-            const resolvedEnvPath = resolve(resolvedProjectDir, envFilePath ?? '.env');
+            const resolvedEnvPath = resolveProjectEnvFilePath(resolvedProjectDir, envFilePath ?? '.env');
             // (1) Check which keys already exist
             const allKeyNames = keys.map((k) => k.key);
             const existingKeys = await checkExistingEnvKeys(allKeyNames, resolvedEnvPath);
@@ -531,6 +553,7 @@ export async function createMcpServer(sessionManager) {
             const { applied, errors } = await applySecrets(provided, resolvedDestination, {
                 envFilePath: resolvedEnvPath,
                 environment,
+                execFn: defaultExecFn,
             });
             // (7) Build result — NEVER include secret values
             const lines = [