setup-isolated-setup-install

This skill is the on-ramp for adopters who do not yet have the secure setup running. It is a thin walkthrough wrapper around the canonical install path documented in docs/setup/secure-agent-setup.md. The authoritative content lives there; this skill exists so an adopter can say "set up the secure agent setup" in a fresh session and land in the right step-by-step flow without first reading the document.

Adopter overrides

Before running the default behaviour documented below, this skill consults .apache-magpie-local/setup-isolated-setup-install.md (personal, gitignored) and .apache-magpie-overrides/setup-isolated-setup-install.md (committed, project-wide) in the adopter repo if it exists, and applies any agent-readable overrides it finds. See docs/setup/agentic-overrides.md for the contract — what overrides may contain, hard rules, the reconciliation flow on framework upgrade, upstreaming guidance.

Hard rule: agents NEVER modify the snapshot under <adopter-repo>/.apache-magpie/. Local modifications go in the override file. Framework changes go via PR to apache/magpie.

Snapshot drift

Also at the top of every run, this skill compares the gitignored .apache-magpie.local.lock (per-machine fetch) against the committed .apache-magpie.lock (the project pin). On mismatch the skill surfaces the gap and proposes /magpie-setup upgrade. The proposal is non-blocking — the user may defer if they want to run with the local snapshot for now. See docs/setup/install-recipes.md § Subsequent runs and drift detection for the full flow.

Drift severity:

• method or URL differ → ✗ full re-install needed.
• ref differs (project bumped tag, or git-branch local is behind upstream tip) → ⚠ sync needed.
• svn-zip SHA-512 mismatches the committed anchor → ✗ security-flagged; investigate before upgrading.

Golden rules

• Do not auto-run privilege-elevating commands. Anything that needs sudo (apt / dnf installs, system-wide writes) is printed for the user to copy-paste into their own terminal. The skill never invokes sudo itself.
• Do not edit shell rc files without approval. ~/.bashrc / ~/.zshrc modifications (sourcing agent-iso.sh, the optional alias claude='claude-iso') are surfaced as the exact line to add; the user pastes it themselves. The skill confirms the rc file path with the user first; it does not assume.
• Do not overwrite an existing settings file silently. If the user already has a project .claude/settings.json or a user-scope ~/.claude/settings.json, the skill diffs the desired merge against the existing file and asks for explicit approval before writing. Re-installs / partial-state recoveries are common — the skill must not blow away an unrelated pre-existing hook or permissions.ask rule. The desired merge includes the agent-guard hooks.PreToolUse entry (matcher Bash, command running the user-scope ~/.claude/scripts/agent-guard.py) — the deterministic guard from tools/agent-guard. Install the script as ~/.claude/scripts/agent-guard.py and populate ~/.claude/scripts/guards.d/ from both the engine's bundled guards.d/*.py and every skill-owned skills/*/guards/*.py (so skill-owned guards like mention / mark-ready are active), alongside the other user-scope scripts (Step P); wire the PreToolUse entry once, and preserve any pre-existing hooks entries.
• Stop on the first failure. If a step fails (manifest read fails, framework path wrong, an existing file conflicts in a way the user has not yet decided about), stop and report. Do not push past a failure to the next step.

Up-front confirmations

Before walking any install step, confirm with the user:

1. OS / distro. macOS, Ubuntu / Debian (apt), Fedora / RHEL (dnf), or Arch / NixOS / other. macOS skips bubblewrap + socat (Seatbelt is built-in); Linux installs both per the distro shortcut.
2. Framework checkout path. The path to the user's local magpie clone. Required to read tools/agent-isolation/pinned-versions.toml, .claude/settings.json, and the tools/agent-isolation/*.sh scripts. If the user does not have a clone, walk them through git clone first.
3. Fresh install or re-install. For a re-install on a partial existing state, the skill must enumerate the existing wiring (project settings.json, user settings.json, hooks dir, the agent-guard hooks.PreToolUse entry + ~/.claude/scripts/agent-guard.py, shell rc) before any merge so the user knows what is being preserved vs replaced.
4. Sync repo (optional). Whether the user maintains a private dotfile-style ~/.claude-config repo per Syncing user-scope config across machines. If yes, the skill installs user-scope scripts as symlinks into ~/.claude-config/scripts/ rather than cp-ing into ~/.claude/scripts/ — the symlink approach is what makes sync push the upgrades to other machines automatically.

Walk-through

Follow the canonical step list at docs/setup/secure-agent-setup.md → Adopter setup → Via a Claude Code prompt. Each step in that list maps 1:1 to a step in this skill. Do not re-write the list here — read the doc, follow it, and surface each sub-step with the user. The doc names are the source of truth; the skill is the runner.

For the verification step at the end, hand off to the setup-isolated-setup-verify skill rather than re-walking the checklist inline.

Agent runtime — install @latest, enforce the floor

claude-code is not pinned to an exact version. Install it with npm install -g --no-save @anthropic-ai/claude-code@latest (the command in the doc's install list) — latest always carries the newest permission-rule / sandbox / prompt-injection fixes. The manifest's [tools.claude-code] table in pinned-versions.toml declares a min_version floor, not a pin. Because this install is driven from Claude Code, apply the same hard gate setup-isolated-setup-verify check 5 applies: read the running version (claude --version) and, if it is below min_version, hard-fail — stop the install, tell the operator to upgrade to @latest, and have them re-run. The secure setup must not be stood up on a below-floor runtime.

Step P — Project-root coverage in the sandbox allowlists

Per docs/setup/secure-agent-setup.md → Project-root coverage in the sandbox allowlists and issue #197, the harness pre-resolves sandbox.filesystem.allowRead: ["."] at session start in a way that silently drops the literal . from the resolved set, so a session in a freshly-cloned adopter repo can write to CWD but cannot read from it under the sandbox.

The defensive measure is to add the project root as an explicit absolute path to sandbox.filesystem.allowRead and allowWrite in the adopter's project-local settings file (<repo>/.claude/settings.local.json) — gitignored, per-machine, per-project, merged on top of the committed project-scope and user-scope by the harness. Worktrees handle themselves: each worktree has its own <worktree>/.claude/settings.local.json, and each gets its own root added.

Step P.0 — Ask the user: per-project or whole-user scope?

Before installing anything, ask the operator which scope they want — see docs/setup/secure-agent-setup.md → Per-project vs whole-user scope for the full rationale + trade-offs:

• Per-project. The skill runs the helper for the current project only. Future projects on this host need the skill re-run in each, OR the operator can pick whole-user later. No global git config changes.
• Whole-user (global). The skill walks the operator's existing local git checkouts and populates their settings.local.json files, then sets git config --global core.hooksPath so every future git checkout / git clone / git worktree add on the host picks up the framework's universal post-checkout hook.

Detect whether whole-user (global) scope is already active first. Read git config --global --get core.hooksPath:

• If it is unset (or does not point at the framework's shared hook dir), whole-user isolation is not yet set up on this host. In that case propose whole-user (global) as the default — it is the recommended baseline because it covers every current and future repo on the host in one pass, so the operator does not have to re-run this skill per project. Present per-project as the narrower alternative for operators who deliberately want to keep their per-repo git hooks (see the Step P.0a caveats).
• If it is already set to the framework's shared hook dir, whole-user isolation is already in place; default to per-project for this specific project (the global hook already covers the host, so only this project's settings.local.json needs the local pass).

Prefer structured Q&A. When the agent harness offers a structured-question tool (e.g. Claude Code's AskUserQuestion), use a single-select prompt whose default is chosen by the detection above — Whole-user (global, recommended) when whole-user is not yet set up, otherwise Per-project. Free-form chat is the fallback.

If the user picks per-project, skip to Step P.1 — Install the helper script and Step P.2 — Run the helper for this project, then move on to the next step in the canonical install list.

If the user picks whole-user, follow Step P.0a's loud disclosure first, then Step P.0b (pick the whole-user flavour — simple vs dispatcher), then Step P.1, then Steps P.2-whole-user (walk existing checkouts) and P.3-whole-user (install the global hook + set core.hooksPath). If they chose the dispatcher flavour, also run Step P.3b-whole-user (install the dispatcher + prek shim).

Step P.0a — Loud disclosure before setting whole-user scope

If the operator picked whole-user, surface this disclosure before any global config write. The operator must acknowledge it explicitly; no silent proceed:

!!! WHOLE-USER SCOPE — core.hooksPath GLOBAL OVERRIDE !!!

Setting git config --global core.hooksPath makes git look up hooks in one shared directory for every repo on this host. Every .git/hooks/* in every existing repo on this machine becomes inert — git will no longer fire your per-repo pre-commit, commit-msg, pre-push, or any other hook unless the shared dir chains back to them.

There are two whole-user flavours (you choose next, Step P.0b):

• Simple — the framework installs only the post-checkout hook in the shared dir. Every other per-repo hook stays inert until you migrate it into ~/.claude/git-hooks/ yourself. Pick this only if you don't rely on per-repo hooks.
• With per-repo dispatcher (recommended if you use prek / pre-commit / husky / any per-repo hook) — the framework installs a dispatcher for each hook type. Each dispatcher runs the framework's own logic (the post-checkout sandbox-allowlist sync) and then chains through to that repo's own .git/hooks/<name>. Your per-repo hooks keep firing, and a repo with no hook is a clean no-op. A bundled prek PATH shim makes prek install write its shim into the repo-local .git/hooks/ (via --git-dir) so the dispatcher can find it.

Either way, whole-user scope is reversible: git config --global --unset core.hooksPath restores per-repo hook lookup, and (dispatcher flavour) removing ~/.claude/bin from PATH restores the stock prek.

Confirm the operator wants to proceed with whole-user scope after reading the disclosure. If they hesitate or pick per-project, fall back to the per-project path.

Step P.0b — Choose the whole-user flavour: simple or dispatcher

If the operator confirmed whole-user, ask which flavour (see the disclosure above for the trade-off). Default to the dispatcher flavour — it is a strict superset of simple (it still runs the post-checkout sync everywhere) and it avoids silently shadowing per-repo hooks, which is the most common whole-user surprise. Pick simple only if the operator explicitly wants the minimal footprint and confirms they run no per-repo hooks.

Prefer structured Q&A here too: a single-select with With per-repo dispatcher (recommended) as the default and Simple (post-checkout only) as the alternative.

• Simple → Step P.3-whole-user installs git-global-post-checkout.sh only.
• Dispatcher → Step P.3-whole-user still runs, and Step P.3b-whole-user additionally installs git-hook-dispatcher.sh (symlinked to each hook name, including post-checkout — which in this flavour supersedes the standalone git-global-post-checkout.sh) and the prek PATH shim.

Step P.1 — Install the helper script

(Both scopes.)

Copy tools/agent-isolation/sandbox-add-project-root.sh into ~/.claude/scripts/sandbox-add-project-root.sh (or symlink it from ~/.claude-config/scripts/ if the operator uses the private sync repo), mode 0755. The script file lives user-scope so a single install covers every adopter project on the host; what it writes is project-local. The same install mechanism the sandbox-bypass-warn.sh and sandbox-status-line.sh helpers use (see the Sandbox-bypass visibility hook and Sandbox-state status line sections of the doc).

Step P.2 — Run the helper for this project (per-project scope)

Skip if the operator picked whole-user scope (Step P.2-whole-user below covers the equivalent).

Run the helper once with --all-worktrees in the adopter repo's main checkout. The helper enumerates git worktree list --porcelain and, for each worktree, writes that worktree's absolute path into that worktree's own <worktree>/.claude/settings.local.json (creating the file if it does not yet exist). Idempotent, atomic, tolerant of missing prereqs (see the script's header comment for the full failure-mode list). On success, surface the diff so the operator sees which entries landed; on no-op (paths already present), surface a one-line "already covered" confirmation.

Sandbox-bypass requirement when invoked from inside an agent session. .claude/settings.local.json is in Claude Code's built-in sandbox denyWithinAllow set (verified empirically — see docs/setup/secure-agent-setup.md → Security rationale), so the helper's Bash write is blocked when invoked through the agent's Bash tool. If this skill is being walked from inside a sandboxed session, invoke the helper with dangerouslyDisableSandbox: true and the reason "writing project-local sandbox-allowlist entries (issue #197 fix)". The bypass triggers sandbox-bypass-warn.sh's loud-red banner so the operator sees and approves the single write. When the operator runs setup-isolated-setup-install directly from a terminal (the typical first-time-install path), no bypass is needed — the script runs outside the agent sandbox.

Step P.2-whole-user — Walk existing checkouts (whole-user scope)

Skip if the operator picked per-project scope.

Walk the operator's existing git checkouts and populate each one's .claude/settings.local.json. This pass is settings-only by default — it does NOT install per-repo post-checkout hooks (the global hook installed in Step P.3-whole-user covers that for both existing and future repos via core.hooksPath).

1. Prompt the operator for root directories to scan. Default suggestions: ~/code/, ~/projects/, ~/dev/, ~/work/. Show the operator the list, let them edit it. Empty list → skip the walk; the operator can re-run this skill later when they want existing repos covered.
2. Walk each root dir. Use a depth-limited find with reasonable exclusions:

   find "<root>" -maxdepth 5 -type d -name .git \
       -not -path '*/node_modules/*' \
       -not -path '*/.venv/*' \
       -not -path '*/__pycache__/*' \
       -not -path '*/build/*' \
       -not -path '*/dist/*' \
       -not -path '*/.cache/*' \
       -prune
   

   
   For each .git/ found, the parent dir is a working tree. De-duplicate by canonical path.
3. For each working tree found, run the helper with --all-worktrees. Same invocation as the per-project variant — the helper itself handles git worktree list so linked worktrees of the same repo get processed. The helper's built-in git check-ignore guard skips repos whose .claude/settings.local.json is not gitignored (defense in depth — the operator should fix the .gitignore first).
4. Tabulate the result for the operator: how many checkouts were scanned, how many had .claude/ (so the helper wrote), how many were skipped (no .claude/ directory, or .claude/settings.local.json not gitignored).
5. Do not install per-repo post-checkout hooks during this pass. The next sub-step covers future and existing repos uniformly via the global hook.

Step P.3-whole-user — Install the global post-checkout hook (whole-user scope)

Skip if the operator picked per-project scope. Dispatcher flavour (Step P.0b): skip step 1 below — Step P.3b-whole-user installs the dispatcher as post-checkout instead, superseding the standalone git-global-post-checkout.sh. Still run step 2 (set core.hooksPath) here.

1. (Simple flavour only) Install the universal post-checkout hook. Copy tools/agent-isolation/git-global-post-checkout.sh into ~/.claude/git-hooks/post-checkout (or symlink it from ~/.claude-config/git-hooks/post-checkout if the operator uses the private sync repo), mode 0755. The hook content is in tools/agent-isolation/git-global-post-checkout.sh — it calls the sandbox-allowlist helper for Claude-Code-aware worktrees.
2. Set core.hooksPath globally so every git operation across every repo on the host uses the shared hook dir:

   git config --global core.hooksPath "$HOME/.claude/git-hooks"
   

   
   Surface the resulting git config --global --get core.hooksPath value to the operator to confirm the write.
3. Reiterate the implication from Step P.0a's disclosure: per-repo .git/hooks/* are now inert across the entire host. The operator must migrate any per-repo hooks they want to keep. git config --global --unset core.hooksPath is the reversal.

After this step, future git clone, git worktree add, and git checkout operations anywhere on the host invoke the framework's universal post-checkout, which keeps each Claude-Code-aware project's .claude/settings.local.json in sync without any further operator action.

Step P.3b-whole-user — Install the per-repo dispatcher + prek shim (dispatcher flavour only)

Skip unless the operator picked the dispatcher flavour in Step P.0b. This is what keeps the operator's per-repo hooks (prek, pre-commit, husky, hand-written) firing under global core.hooksPath — the shared dir runs the framework's logic and then chains through to each repo's own .git/hooks/<name>. See docs/setup/secure-agent-setup.md → Whole-user with the per-repo dispatcher for the full rationale + the validated behaviour matrix.

1. Install the dispatcher for each hook type. Copy tools/agent-isolation/git-hook-dispatcher.sh into ~/.claude/git-hooks/git-hook-dispatcher.sh (or symlink from ~/.claude-config/git-hooks/ under the private sync repo), mode 0755, then create one symlink per hook name pointing at it — including post-checkout, which replaces the standalone file from Step P.3 (the dispatcher runs the same sandbox sync, then chains to any repo-local post-checkout):

   cd ~/.claude/git-hooks
   for h in post-checkout pre-commit prepare-commit-msg commit-msg \
            post-commit pre-push post-merge post-rewrite \
            pre-rebase pre-merge-commit; do
     ln -sf git-hook-dispatcher.sh "$h"
   done
   

   
   The dispatcher is basename-keyed, so one file serves every hook type. It resolves the repo-local hook via git rev-parse --git-common-dir (worktree-safe) and execs it with the original argv + inherited stdin, so a failing local pre-commit / pre-push still aborts the git operation.
2. Install the prek PATH shim so prek install writes its shim into the repo-local .git/hooks/ (where the dispatcher chains) instead of the shared dir. Copy tools/agent-isolation/prek-shim.sh into ~/.claude/bin/prek (or symlink from ~/.claude-config/bin/prek), mode 0755. The shim rewrites only prek install (injecting --git-dir "$(git rev-parse --git-common-dir)" unless the caller already passed --git-dir, asked for --help, or is outside a git work tree); every other prek invocation passes through unchanged. It is a no-op on hosts with no global core.hooksPath.
3. Surface the PATH line for the operator to add to their ~/.bashrc / ~/.zshrc (per the golden rules — never edit the rc file directly):

   export PATH="$HOME/.claude/bin:$PATH"
   

   
   Confirm the rc path with the operator; print the line for them to paste. Until it is on PATH ahead of the real prek, the shim is inert and prek install reverts to writing into the shared dir.
4. Tell the operator how their existing prek repos are picked up. Repos that already ran prek install before this setup have their shim in .git/hooks/pre-commit already (that is where a pre-core.hooksPath prek install put it), so the dispatcher finds them with no further action. Repos where they run prek install after the global switch will now install locally via the shim. Only repos where the shim already landed in the shared dir (from a prek install run whilecore.hooksPath was set but before this dispatcher setup) need a one-time prek install re-run through the shim.

The . entry stays in the committed project-scope allowRead regardless — the explicit absolute path in settings.local.json is belt-and-braces, not a replacement. If the harness ever stops resolving ., the explicit path still covers the project; if . works correctly, the explicit entry is redundant but harmless. The committed project-scope file is never modified by the helper (machine-specific absolute paths have no business in a file shared across contributors).

The helper is also invoked by /magpie-setup adopt, /magpie-setup upgrade, and /magpie-setup worktree-init for the same reason. The post-checkout git hook installed by /magpie-setup adopt chains into the helper too, so new worktrees added via git worktree add after this install pass inherit access automatically — no operator action needed.

After the install lands

Suggest two follow-up routines the user can wire later:

• setup-isolated-setup-verify — re-run after every Claude Code upgrade or settings-file edit, to confirm denials still fire as expected. The "did a denial silently turn into an allow?" signal is exactly what this skill exists for.
• setup-isolated-setup-update — periodic check for framework updates, pinned-tool upgrade candidates, and drift between the installed user-scope copies and the framework's source-of-truth. Recommend a per-Claude-Code-upgrade or monthly cadence, whichever comes first.

Always propose shared-config sync once the install lands. Regardless of whether the operator already maintains the ~/.claude-config sync repo, proactively offer to run setup-shared-config-sync as a follow-up:

• If the ~/.claude-config sync repo is already in place, the skill commits + pushes the local modifications (the user-scope scripts, hooks, and settings this install just wired up) so the other machines pick them up.
• If the operator does not yet have ~/.claude-config, the setup-shared-config-sync skill bootstraps it (clones the default private remote if it exists, or creates a fresh private remote and scaffolds the layout). Mention this so a first-time operator knows the follow-up will set sync up from scratch — the point of proposing it is precisely so the just-installed config does not stay machine-local.

Surface it as an offer for the operator to accept, not an auto-run — the sync skill has its own confirmation gates before it commits or pushes anything.