fix(deps): run package managers through mise exec

.github/workflows/ci.yml

@@ -15,6 +15,27 @@ permissions:
   issues: read
 
 jobs:
+  test-deps:
+    # Unit tests for lib/deps.sh. No network and no clone, so they run on both
+    # platforms cheaply.
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+        with:
+          submodules: true
+          persist-credentials: false
+      - name: Install modern Bash (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install bash
+          echo "$(brew --prefix)/bin" >> "$GITHUB_PATH"
+      - name: Run deps unit tests
+        run: ./test/bats/bin/bats test/deps.bats
+
   test-single-repo:
     # Run on both Linux and macOS: macOS ships BSD userland (e.g. readlink
     # without -f), so it guards against Linux-only assumptions in the scripts.
@@ -27,6 +48,7 @@ jobs:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           submodules: true
+          persist-credentials: false
       - name: Install modern Bash (macOS)
         if: runner.os == 'macOS'
         run: |
@@ -45,6 +67,7 @@ jobs:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           submodules: true
+          persist-credentials: false
       - name: Install modern Bash (macOS)
         if: runner.os == 'macOS'
         run: |
@@ -63,5 +86,6 @@ jobs:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           submodules: true
+          persist-credentials: false
       - name: Run self-repo smoke tests
         run: ./test/bats/bin/bats test/self_repo_smoke.bats

CLAUDE.md

@@ -126,6 +126,17 @@ create / checkout 時に Worktree Context（タスク名、作業ディレクト
 
 実装は `lib/deps.sh` の `detect_deps_types` (検出) と `install_deps` (実行) に集約されている。
 
+### mise 管理ツールチェーンの解決 (`mise exec`)
+
+worktree は別プロセスが作るディレクトリなので、`mise activate` のシェルフックが発火せず **mise 管理のツール (dotnet / node / php 等) が PATH に載らない**。そのまま `dotnet restore` を呼ぶと `command not found` で install が失敗していた。
+
+- worktree に効く mise 設定ファイルが見つかった場合、パッケージマネージャは `mise exec -- <cmd>` 経由で実行する (`run_deps_cmd` の第 1 引数以降にプレフィックスとして差し込む)。見つからない、あるいは `mise` が PATH に無い場合は従来どおり直接実行。
+- 実行前に **`mise trust <config>` を実行する**。worktree は新しい絶対パスなのでプロジェクトルートで信頼済みの設定でも untrusted 扱いになり、`mise exec` は非対話環境ではプロンプトを出さず **エラー終了する** ため。`[env]` やテンプレートを含む設定で必須。`.tool-versions` はコード実行要素が無いので trust 対象外。
+- **設定探索は `find_mise_configs <dir> [boundary]`** が担当し、`<dir>` から `<boundary>` (= task ディレクトリ) まで遡って探す。マルチリポでは mise.toml が task ディレクトリ側 (プロジェクトルートからの symlink) にあり、install はサブリポ内で走るため。boundary を超えて `/` まで遡らないので、ホーム配下の無関係な設定を拾わない。
+- `install_deps <dir> [config-root]` の第 2 引数が boundary。`cmd_create.sh` / `cmd_checkout.sh` は `$task_dir` を渡す。
+- **`WORKTREE_NO_MISE=1` で mise 連携全体を無効化**できる (常に PATH から直接実行)。
+- セキュリティ上の注意: `worktree checkout <PR URL>` では **PR ブランチ側の mise 設定を trust する**ことになる。`npm install` / `composer install` 自体が既に任意コード実行なので相対的なリスク増は小さいが、信頼できない PR を扱う場合は `WORKTREE_NO_MISE=1` か `--no-install` を使う。
+
 ## mise 設定の引き継ぎ
 
 `worktree create` は、ソース側に `mise.toml` / `mise.local.toml` が存在する場合、それらを新しい worktree にコピーする。gitignored なローカル上書き (`mise.local.toml` など) でも、mise のバージョン固定を引き継げる。

README.md

@@ -342,6 +342,21 @@ mutually exclusive and resolved with priority `npm > pnpm > yarn`.
 
 Skip with `--no-install`.
 
+### mise-managed Toolchains
+
+If a mise config (`mise.toml`, `mise.local.toml`, `.tool-versions`, ...) applies to the
+worktree, the install commands run through `mise exec --`. A worktree is created by a
+separate process, so the shell hook that puts mise-managed tools on `PATH` never fires
+there and commands such as `dotnet restore` would otherwise fail with
+`command not found`.
+
+The config is also passed to `mise trust` first: a worktree is a brand new absolute path,
+so a config trusted in the project root is untrusted there, and `mise exec` aborts on an
+untrusted config instead of prompting. Note that this trusts the config as checked out —
+including on a contributor's branch via `worktree checkout <PR URL>`. Set
+`WORKTREE_NO_MISE=1` to skip mise entirely and run the package managers straight from
+`PATH`.
+
 ## mise Version Inheritance
 
 If `mise.toml` or `mise.local.toml` exists in the source (project root for single-repo, each sub-repo root for multi-repo), `worktree create` copies it into the new worktree. This keeps mise-managed tool versions consistent even when the config is gitignored.

lib/cmd_checkout.sh

@@ -362,7 +362,7 @@ cmd_checkout_pr() {
             echo ""
             log_info "Installing dependencies..."
             log_info "${matching_repo_display} (${deps_types_csv}):"
-            install_deps "$worktree_path" || true
+            install_deps "$worktree_path" "$task_dir" || true
         fi
     else
         echo ""

lib/cmd_create.sh

@@ -283,7 +283,7 @@ cmd_create() {
             deps_types_csv="$(detect_deps_types "$worktree_path" | paste -sd, -)"
             if [ -n "$deps_types_csv" ]; then
                 log_info "${repo} (${deps_types_csv}):"
-                install_deps "$worktree_path" || true
+                install_deps "$worktree_path" "$task_dir" || true
             fi
         done
     elif [ "$no_install" = true ]; then

lib/deps.sh

@@ -29,12 +29,109 @@ detect_deps_types() {
     fi
 }
 
+# File names mise recognises as config files, looked up in every candidate
+# directory when deciding whether package managers should run through mise.
+MISE_CONFIG_NAMES=(
+    mise.toml
+    mise.local.toml
+    .mise.toml
+    .mise.local.toml
+    mise/config.toml
+    .mise/config.toml
+    .config/mise.toml
+    .config/mise/config.toml
+    .tool-versions
+)
+
+# True when mise integration is available and not disabled.
+# Set WORKTREE_NO_MISE=1 to always run package managers straight from PATH.
+mise_enabled() {
+    if [ "${WORKTREE_NO_MISE:-0}" = "1" ]; then
+        return 1
+    fi
+    command -v mise >/dev/null 2>&1
+}
+
+# Emit the mise config files that apply to <dir>, walking up from <dir> to
+# <boundary> (inclusive). <boundary> defaults to <dir> and is ignored when it
+# is not an ancestor of <dir>; the walk always stops at "/".
+# The boundary keeps the search inside the worktree: in a multi-repo layout the
+# config often lives in the task directory (symlinked from the project root)
+# rather than in the sub-repo that is being installed.
+# Usage: find_mise_configs <dir> [boundary]
+find_mise_configs() {
+    local dir boundary
+    dir="$(cd "$1" 2>/dev/null && pwd)" || return 0
+
+    boundary="$dir"
+    if [ -n "${2:-}" ]; then
+        local candidate
+        if candidate="$(cd "$2" 2>/dev/null && pwd)"; then
+            case "${dir}/" in
+                "${candidate}"/*) boundary="$candidate" ;;
+            esac
+        fi
+    fi
+
+    local current="$dir"
+    while :; do
+        local name
+        for name in "${MISE_CONFIG_NAMES[@]}"; do
+            if [ -f "${current}/${name}" ]; then
+                echo "${current}/${name}"
+            fi
+        done
+        if [ "$current" = "$boundary" ] || [ "$current" = "/" ]; then
+            break
+        fi
+        current="$(dirname "$current")"
+    done
+
+    return 0
+}
+
+# Mark mise config files as trusted so `mise exec` can parse the ones that may
+# execute code (templates, [env], tool options). A worktree is a brand new
+# absolute path, so configs trusted in the project root are untrusted here and
+# mise would abort instead of prompting in this non-interactive context.
+# `.tool-versions` carries no executable content and needs no trust.
+# Usage: trust_mise_configs <config-file>...
+trust_mise_configs() {
+    local config
+    for config in "$@"; do
+        case "$config" in
+            *.toml) ;;
+            *) continue ;;
+        esac
+        if ! mise trust "$config" >/dev/null 2>&1; then
+            log_warn "  mise trust failed for ${config} (continuing)"
+        fi
+    done
+}
+
+# Run a package manager inside <dir>, keeping only the last line of its output.
+# The entrypoint runs under `set -o pipefail`, so the reported status is the
+# package manager's, not tail's.
+# Usage: run_deps_cmd <dir> <command> [args...]
+run_deps_cmd() {
+    local dir="$1"
+    shift
+    (cd "$dir" && "$@" 2>&1 | tail -1)
+}
+
 # Install dependencies for every detected package manager.
 # Returns 0 if at least one install succeeded, 1 otherwise (including no
 # managers detected). Callers typically swallow the failure with `|| true`.
-# Usage: install_deps <directory>
+# When a mise config applies to the worktree, commands run through
+# `mise exec --` so mise-managed toolchains (dotnet, node, php, ...) are on
+# PATH: the shell hook that normally sets them up never fires for a directory
+# created by another process, which otherwise fails with "command not found".
+# <config-root> bounds the upward search for mise configs (see
+# find_mise_configs); pass the task directory.
+# Usage: install_deps <directory> [config-root]
 install_deps() {
     local dir="$1"
+    local config_root="${2:-$1}"
 
     if [ ! -d "$dir" ]; then
         return 0
@@ -49,45 +146,61 @@ install_deps() {
         return 1
     fi
 
+    # Resolve the command prefix: `mise exec --` when mise governs this
+    # worktree, empty otherwise.
+    local runner=()
+    if mise_enabled; then
+        local mise_configs=()
+        while IFS= read -r line; do
+            [ -n "$line" ] && mise_configs+=("$line")
+        done < <(find_mise_configs "$dir" "$config_root")
+
+        if [ ${#mise_configs[@]} -gt 0 ]; then
+            trust_mise_configs "${mise_configs[@]}"
+            runner=(mise exec --)
+            log_info "  Using mise (${mise_configs[0]})"
+        fi
+    fi
+
     local installed=false
     local type
     for type in "${types[@]}"; do
         case "$type" in
             npm)
                 log_info "  Running npm install..."
-                if (cd "$dir" && npm install --no-audit --no-fund 2>&1 | tail -1); then
+                if run_deps_cmd "$dir" ${runner[@]+"${runner[@]}"} npm install --no-audit --no-fund; then
                     installed=true
                 else
                     log_warn "  npm install failed"
                 fi
                 ;;
             pnpm)
                 log_info "  Running pnpm install..."
-                if (cd "$dir" && pnpm install --frozen-lockfile 2>&1 | tail -1); then
+                if run_deps_cmd "$dir" ${runner[@]+"${runner[@]}"} pnpm install --frozen-lockfile; then
                     installed=true
                 else
                     log_warn "  pnpm install failed"
                 fi
                 ;;
             yarn)
                 log_info "  Running yarn install..."
-                if (cd "$dir" && yarn install --frozen-lockfile 2>&1 | tail -1); then
+                if run_deps_cmd "$dir" ${runner[@]+"${runner[@]}"} yarn install --frozen-lockfile; then
                     installed=true
                 else
                     log_warn "  yarn install failed"
                 fi
                 ;;
             composer)
                 log_info "  Running composer install..."
-                if (cd "$dir" && composer install --no-interaction 2>&1 | tail -1); then
+                if run_deps_cmd "$dir" ${runner[@]+"${runner[@]}"} composer install --no-interaction; then
                     installed=true
                 else
                     log_warn "  composer install failed"
                 fi
                 ;;
             dotnet)
                 log_info "  Running dotnet restore..."
-                if (cd "$dir" && dotnet restore 2>&1 | tail -1); then
+                if run_deps_cmd "$dir" ${runner[@]+"${runner[@]}"} dotnet restore; then
                     installed=true
                 else
                     log_warn "  dotnet restore failed"

skills/worktree-checkout/SKILL.md

@@ -52,6 +52,11 @@ worktree checkout https://github.com/owner/repo/pull/123 --no-cd
 | `--no-install` | Skip automatic dependency installation |
 | `--no-cd` | Do not auto-cd into the new worktree (interactive shells with `worktree shell-init` only) |
 
+> **Note (mise):** When a mise config applies to the new worktree, the dependency
+> install runs through `mise exec --` (after `mise trust`) so mise-managed
+> toolchains are on `PATH`. This trusts the config as checked out on the PR
+> branch; use `WORKTREE_NO_MISE=1` or `--no-install` for untrusted PRs.
+>
 > **Note (subagents):** In URL mode, `checkout` auto-cds into the new worktree
 > only in an interactive shell that has `eval "$(worktree shell-init)"` installed.
 > From a subagent's `Bash` call there is no directory change, so `--no-cd` has no

skills/worktree-create/SKILL.md

@@ -23,7 +23,7 @@ worktree create $ARGUMENTS
 5. Symlinks non-git items into the task directory (multi-repo only)
 6. Copies `mise.toml` / `mise.local.toml` into each worktree (inherits mise version pinning even when gitignored)
 7. Executes `.worktreerc` `post_create()` hook if present
-8. Auto-installs dependencies based on lock files (unless `--no-install`)
+8. Auto-installs dependencies based on lock files (unless `--no-install`). When a mise config applies to the worktree it is passed to `mise trust` and the install runs through `mise exec --`, so mise-managed toolchains resolve; `WORKTREE_NO_MISE=1` disables this
 
 ## Worktree layout