fix: install() should replace husky hook paths instead of skipping

packages/cli/snap-tests-global/command-config-replace-husky-hookspath/package.json

@@ -0,0 +1,3 @@
+{
+  "name": "command-config-replace-husky-hookspath"
+}

packages/cli/snap-tests-global/command-config-replace-husky-hookspath/snap.txt

@@ -0,0 +1,5 @@
+> git init
+> git config core.hooksPath .husky/_
+> vp config --hooks-only # should replace .husky/_ with .vite-hooks/_
+> git config --local core.hooksPath # should be .vite-hooks/_
+.vite-hooks/_

packages/cli/snap-tests-global/command-config-replace-husky-hookspath/steps.json

@@ -0,0 +1,8 @@
+{
+  "commands": [
+    { "command": "git init", "ignoreOutput": true },
+    { "command": "git config core.hooksPath .husky/_", "ignoreOutput": true },
+    "vp config --hooks-only # should replace .husky/_ with .vite-hooks/_",
+    "git config --local core.hooksPath # should be .vite-hooks/_"
+  ]
+}

packages/cli/src/config/hooks.ts

@@ -87,7 +87,12 @@ export function install(dir = '.vite-hooks'): InstallResult {
   const target = rel ? `${rel}/${dir}/_` : `${dir}/_`;
   const checkResult = spawnSync('git', ['config', '--local', 'core.hooksPath']);
   const existingHooksPath = checkResult.status === 0 ? checkResult.stdout?.toString().trim() : '';
-  if (existingHooksPath && existingHooksPath !== target) {
+  if (
+    existingHooksPath &&
+    existingHooksPath !== target &&
+    existingHooksPath !== '.husky' &&
+    !existingHooksPath.startsWith('.husky/')
+  ) {
     return {
       message: `core.hooksPath is already set to "${existingHooksPath}", skipping`,
       isError: false,

rfcs/lint-staged-pre-commit-hook.md → rfcs/config-and-staged-commands.md

@@ -2,7 +2,7 @@
 
 ## Summary
 
-Add `vp config` and `vp staged` as built-in commands. `vp config` is a unified configuration command that sets up git hooks (husky-compatible reimplementation, not a bundled dependency) and agent integration. `vp staged` bundles lint-staged and reads config from the `staged` key in `vite.config.ts`. Projects get a zero-config pre-commit hook that runs `vp check --fix` on staged files — no extra devDependencies needed.
+Add `vp config` and `vp staged` as built-in commands. `vp config` is a `prepare`-lifecycle command that installs git hook shims (husky-compatible reimplementation, not a bundled dependency). `vp staged` bundles lint-staged and reads config from the `staged` key in `vite.config.ts`. Projects get a zero-config pre-commit hook that runs `vp check --fix` on staged files — no extra devDependencies needed.
 
 ## Motivation
 
@@ -21,50 +21,129 @@ Pain points:
 
 By building these capabilities into vite-plus, projects get pre-commit hooks with zero extra devDependencies. Both `vp create` and `vp migrate` set this up automatically.
 
-## Command Syntax
+## User Workflows
+
+There are three distinct entry points, each with a different responsibility:
+
+### New projects: `vp create`
+
+`vp create` scaffolds a new project and optionally sets up the full hooks pipeline:
+
+1. Prompts "Set up pre-commit hooks?" (default: yes)
+2. If accepted, calls `installGitHooks()` which:
+   - Adds `"prepare": "vp config"` to `package.json`
+   - Adds `staged` config to `vite.config.ts`
+   - Creates `.vite-hooks/pre-commit` containing `vp staged`
+   - Runs `vp config --hooks-only` to install hook shims and set `core.hooksPath`
+
+Flags: `--hooks` (force), `--no-hooks` (skip)
+
+### Existing projects: `vp migrate`
+
+`vp migrate` migrates from husky/lint-staged and sets up the full hooks pipeline:
+
+1. Runs pre-flight checks (husky version, other tools, subdirectory detection)
+2. Prompts "Set up pre-commit hooks?" (default: yes)
+3. If accepted, after migration rewrite, calls `installGitHooks()` which:
+   - Detects old husky directory from `scripts.prepare`
+   - Rewrites `"prepare": "husky"` → `"prepare": "vp config"` via `rewritePrepareScript()`
+   - Migrates `lint-staged` config from `package.json` to `staged` in `vite.config.ts`
+   - Copies `.husky/` hooks to `.vite-hooks/` (or preserves custom dir)
+   - Creates `.vite-hooks/pre-commit` containing `vp staged`
+   - Runs `vp config --hooks-only` to install hook shims and set `core.hooksPath`
+   - Removes husky and lint-staged from `devDependencies`
+
+Flags: `--hooks` (force), `--no-hooks` (skip)
+
+### Ongoing use: `vp config` (prepare lifecycle)
+
+`vp config` is the command that runs on every `npm install` via the `prepare` script. It reinstalls hook shims — it does **not** create the `staged` config or the pre-commit hook file. Those are created by `vp create`/`vp migrate`.
+
+```json
+{ "scripts": { "prepare": "vp config" } }
+```
+
+When `npm_lifecycle_event=prepare` (set by npm/pnpm/yarn during `npm install`), agent setup is skipped automatically — only hooks are reinstalled.
+
+### Manual setup (without `vp create`/`vp migrate`)
+
+For users who want to set up hooks manually, four steps are required:
+
+1. **Add prepare script** to `package.json`:
+   ```json
+   { "scripts": { "prepare": "vp config" } }
+   ```
+2. **Add staged config** to `vite.config.ts`:
+   ```typescript
+   export default defineConfig({
+     staged: { '*': 'vp check --fix' },
+   });
+   ```
+3. **Create pre-commit hook** at `.vite-hooks/pre-commit`:
+   ```sh
+   vp staged
+   ```
+4. **Run `vp config`** to install hook shims and set `core.hooksPath`
+
+## Commands
+
+### `vp config`
 
 ```bash
-# Configure project (hooks + agent integration)
-vp config
+vp config                           # Configure project (hooks + agent integration)
 vp config -h                        # Show help
 vp config --hooks-dir .husky        # Custom hooks directory (default: .vite-hooks)
+```
 
-# Run staged linters on staged files (runs bundled lint-staged with staged config)
-vp staged
+Behavior:
 
-# Control hooks setup during create/migrate
-vp create --hooks           # Force hooks setup
-vp create --no-hooks        # Skip hooks setup
-vp migrate --hooks          # Force hooks setup
-vp migrate --no-hooks       # Skip hooks setup
+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)
+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
+
+### `vp staged`
+
+```bash
+vp staged                           # Run staged linters on staged files
 ```
 
+Behavior:
+
+1. Reads config from `staged` key in `vite.config.ts` via `resolveConfig()`
+2. If `staged` key not found, exits with a warning and setup instructions
+3. Passes config to bundled lint-staged via its programmatic API
+4. Runs configured commands on git-staged files only
+5. Exits with non-zero code if any command fails
+6. Does not support custom config file paths — config must be in `vite.config.ts`
+
 Both commands are listed under "Core Commands" in `vp -h` (global and local CLI).
 
-## User-Facing Configuration
+## Configuration
 
-### vite.config.ts + package.json (zero extra devDependencies)
+### `vite.config.ts`
 
 ```typescript
-// vite.config.ts
 export default defineConfig({
   staged: {
     '*': 'vp check --fix',
   },
 });
 ```
 
-```json
-// package.json (new project)
-{
-  "scripts": {
-    "prepare": "vp config"
-  }
-}
-```
+`vp staged` reads config from the `staged` key via Vite's `resolveConfig()`. If no `staged` key is found, it exits with a warning and instructions to add the config. Standalone config files (`.lintstagedrc.*`, `lint-staged.config.*`) are not supported by the migration — projects using those formats are warned to migrate manually.
+
+### `package.json`
 
 ```json
-// package.json (migrated from husky — default .husky dir migrates to .vite-hooks)
+// New project
 {
   "scripts": {
     "prepare": "vp config"
@@ -73,7 +152,7 @@ export default defineConfig({
 ```
 
 ```json
-// package.json (migrated from husky with custom dir — dir is preserved)
+// Migrated from husky with custom dir — dir is preserved
 {
   "scripts": {
     "prepare": "vp config --hooks-dir .config/husky"
@@ -91,7 +170,7 @@ If the project already has a prepare script, `vp config` is prepended:
 }
 ```
 
-### .vite-hooks/pre-commit (or custom dir for projects with non-default husky dir)
+### `.vite-hooks/pre-commit`
 
 ```
 vp staged
@@ -101,36 +180,7 @@ vp staged
 
 `vp check --fix` already handles unsupported file types gracefully (it only processes files that match known extensions). Using `*` simplifies the configuration — no need to maintain a list of extensions.
 
-### Config Discovery
-
-`vp staged` reads config from the `staged` key in `vite.config.ts` via Vite's `resolveConfig()`. If no `staged` key is found, it exits with a warning and instructions to add the config. Standalone config files (`.lintstagedrc.*`, `lint-staged.config.*`) are not supported by the migration — projects using those formats are warned to migrate manually.
-
-## Behavior
-
-### `vp config`
-
-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 11)
-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. Interactive mode: prompts on first run for hooks and agent setup; updates silently on subsequent runs
-10. Non-interactive mode: runs everything by default
-11. `prepare` lifecycle detection: when `npm_lifecycle_event=prepare` (set by npm/pnpm/yarn during `npm install`), agent setup is skipped automatically. This ensures `"prepare": "vp config"` only installs hooks during install — agent setup is a one-time operation handled by `vp create`/`vp migrate`, not repeated on every `npm install`
-
-### `vp staged`
-
-1. Reads config from `staged` key in `vite.config.ts` via `resolveConfig()`
-2. If `staged` key not found, exits with a warning and setup instructions
-3. Passes config to bundled lint-staged via its programmatic API
-4. Runs configured commands on git-staged files only
-5. Exits with non-zero code if any command fails
-6. Does not support custom config file paths — config must be in vite.config.ts
-
-### Automatic Setup
+## Automatic Setup
 
 Both `vp create` and `vp migrate` prompt the user before setting up pre-commit hooks:
 
@@ -139,14 +189,21 @@ Both `vp create` and `vp migrate` prompt the user before setting up pre-commit h
 - **`--hooks` flag**: Force hooks setup (no prompt)
 - **`--no-hooks` flag**: Skip hooks setup entirely (no prompt)
 
-#### `vp create`
+```bash
+vp create --hooks           # Force hooks setup
+vp create --no-hooks        # Skip hooks setup
+vp migrate --hooks          # Force hooks setup
+vp migrate --no-hooks       # Skip hooks setup
+```
+
+### `vp create`
 
 - After project creation and migration rewrite, prompts for hooks setup
 - If accepted, calls `rewritePrepareScript()` then `setupGitHooks()` — same as `vp migrate`
 - `rewritePrepareScript()` rewrites any template-provided `"prepare": "husky"` to `"prepare": "vp config"` before `setupGitHooks()` runs
 - Creates `.vite-hooks/pre-commit` with `vp staged`
 
-#### `vp migrate`
+### `vp migrate`
 
 Migration rewrite (`rewritePackageJson`) uses `vite-tools.yml` rules to rewrite tool commands (vite, oxlint, vitest, etc.) in all scripts. Crucially, the husky rule is **not** in `vite-tools.yml` — it lives in a separate `vite-prepare.yml` and is only applied to `scripts.prepare` via `rewritePrepareScript()`. This ensures husky is never accidentally rewritten in non-prepare scripts.
 
@@ -163,10 +220,14 @@ Hook setup behavior:
 - **Has `husky install`** — `rewritePrepareScript()` collapses `"husky install"` → `"husky"` before applying the ast-grep rule, so `"husky install .hooks"` becomes `"vp config --hooks-dir .hooks"` (custom dir preserved)
 - **Has existing prepare script** (e.g. `"npm run build"`) — composes as `"vp config && npm run build"` (prepend so hooks are active before other prepare tasks; idempotent if already contains `vp config`)
 - **Has lint-staged** — migrates `"lint-staged"` key to `staged` in vite.config.ts, keeps existing config (already rewritten by migration rules), removes lint-staged from devDeps
+
+## Migration Edge Cases
+
 - **Has husky <9.0.0** — detected **before** migration rewrite. Warns "please upgrade to husky v9+ first", skips hooks setup, and also skips lint-staged migration (`skipStagedMigration` flag). This preserves the `lint-staged` config in package.json and standalone config files, since `.husky/pre-commit` still references `npx lint-staged`.
 - **Has other tool (simple-git-hooks, lefthook, yorkie)** — warns and skips
 - **Subdirectory project** (e.g. `vp migrate foo`) — if the project path differs from the git root, warns "Subdirectory project detected" and skips hooks setup entirely. This prevents `vp config` from setting `core.hooksPath` to a subdirectory path, which would hijack the repo-wide hooks.
 - **No .git directory** — adds package.json config and creates hook pre-commit file, but skips `vp config` hook install (no `core.hooksPath` to set)
+- **Standalone lint-staged config** (`.lintstagedrc.*`, `lint-staged.config.*`) — not supported by auto-migration. Projects using those formats are warned to migrate manually.
 - After creating the pre-commit hook, runs `vp config` directly to install hook shims (does not rely on npm install lifecycle, which may not run in CI or snap test contexts)
 
 ## Implementation Architecture
@@ -218,7 +279,7 @@ Husky <9.0.0 is not supported by auto migration — `vp migrate` detects unsuppo
 | ---------------- | -------------------------------------- | --------------------------- |
 | `vp check`       | Format + lint + type check             | Manual or CI                |
 | `vp check --fix` | Auto-fix format + lint issues          | Manual or pre-commit        |
-| **`vp config`**  | **Configure project (hooks + agent)**  | **npm `prepare` lifecycle** |
+| **`vp config`**  | **Reinstall hook shims + agent setup** | **npm `prepare` lifecycle** |
 | **`vp staged`**  | **Run staged linters on staged files** | **Pre-commit hook**         |
 
 ## Comparison with Other Tools