refactor(config): skip agent setup when instruction files exist

Align `vp config` agent setup with `vp create`/`vp migrate`:
- Skip agent setup entirely when agent instruction files already exist
- Skip agent setup in non-interactive mode (no silent writes)
- Use shared multiselect prompt and writeAgentInstructions() flow
- Remove config-specific agent detection, MCP config, and skills linking
- Delete config/agent.ts and its tests (superseded by utils/agent.ts)

Author: fengmk2

packages/cli/src/config/__tests__/agent.spec.ts

@@ -1,25 +1,24 @@
 // Unified `vp config` command — merges the old `vp prepare` (hooks setup) and
 // `vp init` (agent integration) into a single entry point.
 //
-// Interactive mode (TTY, no CI): prompts on first run, updates silently after.
-// Non-interactive mode (scripts.prepare, CI, piped): runs everything by default.
+// Interactive mode (TTY, no CI): prompts on first run; prompts for agent setup
+// only if no agent instruction files exist.
+// Non-interactive mode (scripts.prepare, CI, piped): hooks only, agent setup skipped.
 
 import { existsSync } from 'node:fs';
 import { join } from 'node:path';
 
 import mri from 'mri';
 
 import { vitePlusHeader } from '../../binding/index.js';
+import {
+  detectExistingAgentTargetPaths,
+  selectAgentTargetPaths,
+  writeAgentInstructions,
+} from '../utils/agent.js';
 import { renderCliDoc } from '../utils/help.js';
 import { defaultInteractive, promptGitHooks } from '../utils/prompts.js';
-import { linkSkillsForSpecificAgents } from '../utils/skills.js';
 import { log } from '../utils/terminal.js';
-import {
-  resolveAgentSetup,
-  hasExistingAgentInstructions,
-  injectAgentBlock,
-  setupMcpConfig,
-} from './agent.js';
 import { install } from './hooks.js';
 
 async function main() {
@@ -81,15 +80,26 @@ async function main() {
     }
   }
 
-  // --- Step 2: Agent setup (skipped with --hooks-only or during prepare lifecycle) ---
-  if (!hooksOnly && process.env.npm_lifecycle_event !== 'prepare') {
-    const isFirstAgentRun = !hasExistingAgentInstructions(root);
-    const agentSetup = await resolveAgentSetup(root, interactive && isFirstAgentRun);
+  // --- Step 2: Agent setup (interactive only, skipped if files exist / --hooks-only / prepare) ---
+  if (!hooksOnly && interactive && process.env.npm_lifecycle_event !== 'prepare') {
+    // Skip entirely if any agent instruction files already exist
+    const existingAgentTargetPaths = detectExistingAgentTargetPaths(root);
+    if (existingAgentTargetPaths === undefined) {
+      // No existing agent files — prompt for selection
+      const selectedAgentTargetPaths = await selectAgentTargetPaths({
+        interactive,
+        onCancel: () => {
+          process.exit(0);
+        },
+      });
 
-    injectAgentBlock(root, agentSetup.instructionFilePath);
-    setupMcpConfig(root, agentSetup.agents);
-    if (agentSetup.agents.length > 0) {
-      linkSkillsForSpecificAgents(root, agentSetup.agents);
+      if (selectedAgentTargetPaths && selectedAgentTargetPaths.length > 0) {
+        await writeAgentInstructions({
+          projectRoot: root,
+          targetPaths: selectedAgentTargetPaths,
+          interactive,
+        });
+      }
     }
   }
 }

packages/cli/src/config/agent.ts

@@ -100,14 +100,14 @@ Behavior:
 1. Built-in husky-compatible install logic (reimplementation of husky v9, not a bundled dependency)
 2. Sets `core.hooksPath` to `<hooks-dir>/_` (default: `.vite-hooks/_`)
 3. Creates hook scripts in `<hooks-dir>/_/` that source the user-defined hooks in `<hooks-dir>/`
-4. Agent integration: injects agent instructions and MCP config (skipped during `prepare` lifecycle — see point 9)
+4. Agent integration (interactive only): writes agent instructions to selected instruction files (aligned with `vp create`/`vp migrate`). Skipped entirely if agent instruction files already exist — never modifies user-maintained files.
 5. Safe to run multiple times (idempotent)
 6. Exits 0 and skips hooks if `VITE_GIT_HOOKS=0` or `HUSKY=0` environment variable is set (backwards compatible)
 7. Exits 0 and skips hooks if `.git` directory doesn't exist (safe during `npm install` in consumer projects)
 8. Exits 1 on real errors (git command not found, `git config` failed)
 9. `prepare` lifecycle detection: when `npm_lifecycle_event=prepare`, agent setup is skipped. This ensures `"prepare": "vp config"` only installs hooks during install — agent setup is handled by `vp create`/`vp migrate`
-10. Interactive mode: prompts on first run for hooks and agent setup; updates silently on subsequent runs
-11. Non-interactive mode: runs everything by default
+10. Interactive mode: prompts on first run for hooks; prompts for agent setup only if no agent instruction files exist (multiselect prompt, same as `vp create`/`vp migrate`). Skips agent setup silently if files already exist.
+11. Non-interactive mode: sets up hooks by default; skips agent setup entirely (no silent writes without user consent)
 
 ### `vp staged`