diff --git a/node/src/commands/agent/init.ts b/node/src/commands/agent/init.ts
index d19e3414..2873c42e 100644
--- a/node/src/commands/agent/init.ts
+++ b/node/src/commands/agent/init.ts
@@ -7,7 +7,7 @@ import { SkillManager } from "../../utils/skill-manager.js";
 import fs from "fs";
 import path from "path";
 import os from "os";
-import { execSync, spawnSync } from "child_process";
+import { execFileSync, execSync, spawnSync } from "child_process";
 import { fileURLToPath } from "url";
 import { createRequire } from "module";
 import { askYesNo } from "../../utils/prompt.js";
@@ -1184,10 +1184,15 @@ function registerGeminiSkills(skillsDir: string): void {
     const absPath = path.resolve(skillsDir, skill.name);
     if (!fs.existsSync(absPath)) continue;
     try {
-      execSync(`gemini skills link ${JSON.stringify(absPath)}`, {
-        stdio: ["ignore", "pipe", "pipe"],
-        timeout: 10000,
-      });
+      const execOpts = { stdio: ["ignore", "pipe", "pipe"] as any, timeout: 10000 };
+      // No POSIX shell: the path comes from the working directory, whose name
+      // may hold shell syntax. Windows needs cmd.exe to run gemini's .cmd shim,
+      // and cmd.exe treats a double-quoted path literally.
+      if (process.platform === "win32") {
+        execSync(`gemini skills link ${JSON.stringify(absPath)}`, execOpts);
+      } else {
+        execFileSync("gemini", ["skills", "link", absPath], execOpts);
+      }
       console.log(fmt.success(`Registered ${skill.name} with Gemini CLI`));
     } catch (e: any) {
       const msg = (e?.stderr?.toString?.() || e?.message || "").trim();
diff --git a/node/src/commands/agent/install-hook.ts b/node/src/commands/agent/install-hook.ts
index 90a79803..e99bd914 100644
--- a/node/src/commands/agent/install-hook.ts
+++ b/node/src/commands/agent/install-hook.ts
@@ -2,7 +2,7 @@ import { Command } from "commander";
 import fs from "fs";
 import os from "os";
 import path from "path";
-import { execSync } from "child_process";
+import { execFileSync, execSync } from "child_process";
 import { fileURLToPath } from 'url';
 import { fmt } from "../../utils/formatter.js";
 
@@ -115,7 +115,7 @@ async function installGlobalHook(hookName: string, templateName: string): Promis
   fs.chmodSync(hookPath, 0o755);
 
   try {
-    execSync(`git config --global core.hooksPath "${globalHooksDir}"`, { stdio: "pipe" });
+    execFileSync("git", ["config", "--global", "core.hooksPath", globalHooksDir], { stdio: "pipe" });
     console.log(fmt.success(`Installed Rafter ${hookName} hook globally`));
     console.log(`  Location: ${hookPath}`);
     console.log(`  Git config: core.hooksPath = ${globalHooksDir}`);
diff --git a/node/src/commands/agent/status.ts b/node/src/commands/agent/status.ts
index 57bf2638..efcfe16d 100644
--- a/node/src/commands/agent/status.ts
+++ b/node/src/commands/agent/status.ts
@@ -2,7 +2,7 @@ import { Command } from "commander";
 import fs from "fs";
 import path from "path";
 import os from "os";
-import { execSync } from "child_process";
+import { execFileSync, execSync } from "child_process";
 import { fileURLToPath } from "url";
 import { getRafterDir, getAuditLogPath, getBinDir } from "../../core/config-defaults.js";
 import { AuditLogger } from "../../core/audit-logger.js";
@@ -85,7 +85,7 @@ export function createStatusCommand(): Command {
       } catch {
         if (fs.existsSync(localBetterleaks)) {
           try {
-            const ver = execSync(`"${localBetterleaks}" version`, { timeout: 5000, encoding: "utf-8", stdio: ["pipe", "pipe", "ignore"] }).trim();
+            const ver = execFileSync(localBetterleaks, ["version"], { timeout: 5000, encoding: "utf-8", stdio: ["pipe", "pipe", "ignore"] }).trim();
             betterleaksStatus = `${ver} (local)`;
           } catch {
             betterleaksStatus = `${localBetterleaks} (binary error)`;
diff --git a/node/tests/agent-init-gemini-link.test.ts b/node/tests/agent-init-gemini-link.test.ts
new file mode 100644
index 00000000..1952f9e9
--- /dev/null
+++ b/node/tests/agent-init-gemini-link.test.ts
@@ -0,0 +1,56 @@
+/**
+ * `agent init --local --with-gemini` registers skills with `gemini skills link
+ * <path>`, where the path is under the working directory. A directory name may
+ * hold shell syntax, so the path must reach gemini as one literal argument and
+ * never be interpreted by a shell.
+ *
+ * Runs the built CLI with a stub `gemini` on PATH that logs its arguments.
+ */
+import { describe, it, expect, beforeAll } from "vitest";
+import { execSync, spawnSync } from "child_process";
+import fs from "fs";
+import path from "path";
+import os from "os";
+
+const PROJECT_ROOT = path.resolve(__dirname, "..");
+const CLI_DIST = path.join(PROJECT_ROOT, "dist", "index.js");
+
+beforeAll(() => {
+  if (!fs.existsSync(CLI_DIST)) {
+    execSync("pnpm run build", { cwd: PROJECT_ROOT, stdio: "inherit" });
+  }
+});
+
+describe.skipIf(process.platform === "win32")("agent init --local --with-gemini", () => {
+  it("passes a working-directory path with shell syntax to gemini literally", () => {
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), "rafter-gemini-link-"));
+    try {
+      const bin = path.join(root, "bin");
+      const log = path.join(root, "calls.log");
+      fs.mkdirSync(bin);
+      fs.writeFileSync(
+        path.join(bin, "gemini"),
+        `#!/bin/sh\nfor a in "$@"; do printf '%s\\n' "$a" >> '${log}'; done\nexit 0\n`,
+        { mode: 0o755 },
+      );
+      const home = path.join(root, "home");
+      fs.mkdirSync(home);
+      const project = path.join(root, "vendor", "$(touch MARKER)");
+      fs.mkdirSync(project, { recursive: true });
+
+      const r = spawnSync(process.execPath, [CLI_DIST, "agent", "init", "--local", "--with-gemini"], {
+        cwd: project,
+        encoding: "utf-8",
+        timeout: 60_000,
+        env: { ...process.env, HOME: home, XDG_CONFIG_HOME: path.join(home, ".config"), PATH: `${bin}:${process.env.PATH}`, CI: "1" },
+      });
+
+      expect(r.status).toBe(0);
+      expect(fs.existsSync(path.join(project, "MARKER"))).toBe(false);
+      const args = fs.readFileSync(log, "utf-8").split("\n");
+      expect(args).toContain(path.join(project, ".agents", "skills", "rafter"));
+    } finally {
+      fs.rmSync(root, { recursive: true, force: true });
+    }
+  });
+});