diff --git a/.githooks/README.md b/.githooks/README.md
new file mode 100644
index 000000000..5952ca25b
--- /dev/null
+++ b/.githooks/README.md
@@ -0,0 +1,42 @@
+# Native Git hooks
+
+`pnpm install` configures `core.hooksPath=.githooks` via
+`scripts/install-git-hooks.mjs`. Tracked hooks exist in every linked worktree.
+
+## `post-checkout`
+
+### 1. Clear TypeScript project emit (always on branch / worktree checkout)
+
+`pnpm check` is `tsgo --build` with composite + incremental. Package outputs
+(`.tsbuildinfo` + `.d.ts` / `.js`) live under `packages/*/dist` and are
+gitignored.
+
+After a branch switch, **sources** follow HEAD but **dist** can still belong to
+another tree. tsgo may treat projects as up to date and typecheck new sources
+against old declarations → phantom type errors that disappear on
+`pnpm rbuild` (`clean` + check). Same class of failure as
+[scanner#1495](https://github.com/macs-holding/scanner/pull/1495) /
+[scanner#2166](https://github.com/macs-holding/scanner/pull/2166).
+
+On every **branch** checkout (`post-checkout` flag `1`), this hook deletes:
+
+- `packages/*/dist`, `packages/*/build`, root `dist` if present
+- any remaining `*.tsbuildinfo` outside `node_modules` / `repos` / `.git`
+
+File-only checkouts (flag `0`) are left alone.
+
+**This is a workaround.** Root cause belongs in tsgo incremental invalidation
+(e.g. [typescript-go#2666](https://github.com/microsoft/typescript-go/issues/2666),
+[#4664](https://github.com/microsoft/typescript-go/issues/4664),
+[#4262](https://github.com/microsoft/typescript-go/issues/4262)). Remove when
+upstream is reliable. Do not re-enable cross-tree dist reuse without an exact
+source-identity key.
+
+### 2. Reconcile pnpm (when package/lock changed)
+
+Records package/lockfile state under `node_modules` so T3 handoff does not
+repeat an install Git already completed.
+
+## `pre-commit` / `pre-push`
+
+lint-staged on commit; agent ship gate on push (see repo AGENTS.md).
diff --git a/.githooks/post-checkout b/.githooks/post-checkout
new file mode 100755
index 000000000..e1fb69449
--- /dev/null
+++ b/.githooks/post-checkout
@@ -0,0 +1,82 @@
+#!/bin/sh
+# 1) After a branch/worktree checkout: drop TypeScript project-reference emit so
+#    tsgo --build never typechecks against foreign-tree .tsbuildinfo / .d.ts.
+# 2) Reconcile pnpm when package.json / lockfile changed.
+
+PATH="$HOME/.local/bin:$HOME/.local/share/pnpm:$HOME/.local/share/mise/shims:/run/current-system/sw/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:$PATH"
+export PATH
+
+# post-checkout also runs after file-only checkouts; those are not a tree switch.
+[ "${3:-0}" = "1" ] || exit 0
+
+wt_root=$(git rev-parse --show-toplevel 2>/dev/null) || exit 0
+[ -f "$wt_root/package.json" ] || exit 0
+
+# --- TS build-cache wipe (every branch / worktree checkout) -----------------
+#
+# Why: `pnpm check` is `tsgo --build` with composite + incremental. Package
+# outputs live in packages/*/dist (gitignored). After checkout/rebase, sources
+# belong to HEAD but dist may still be from another branch. tsgo can treat
+# projects as up-to-date and typecheck new sources against old .d.ts → phantom
+# errors that vanish on `pnpm rbuild` (clean+check).
+#
+# Same class as macs-holding/scanner#1495 / #2166 and upstream typescript-go
+# incremental gaps (#2666, #4664, #4262, #3787).
+#
+# Workaround only — remove when upstream invalidation is reliable. Do not
+# re-introduce foreign dist reuse without an exact source-identity key.
+#
+clean_ts_project_emit() {
+  root=$1
+  removed=0
+
+  for d in \
+    "$root"/packages/*/dist \
+    "$root"/packages/*/build \
+    "$root"/dist
+  do
+    [ -e "$d" ] || continue
+    rm -rf "$d"
+    removed=1
+  done
+
+  if [ -d "$root" ]; then
+    tsbuild_files=$(
+      find "$root" \
+        \( -path "$root/node_modules" -o -path "$root/repos" -o -path "$root/.git" -o -path "$root/.run" -o -path "$root/build" \) -prune -o \
+        -type f -name '*.tsbuildinfo' -print 2>/dev/null || true
+    )
+    if [ -n "$tsbuild_files" ]; then
+      printf '%s\n' "$tsbuild_files" | while IFS= read -r f; do
+        [ -n "$f" ] || continue
+        rm -f "$f"
+      done
+      removed=1
+    fi
+  fi
+
+  if [ "$removed" = 1 ]; then
+    echo "post-checkout: cleared TypeScript project emit (dist / tsbuildinfo) under $root" >&2
+    echo "post-checkout: workaround for tsgo stale incremental cache after tree switch — see .githooks/README.md (remove when upstream fixed)" >&2
+  fi
+}
+
+clean_ts_project_emit "$wt_root"
+
+# --- pnpm install when lockfile / package.json changed -----------------------
+[ -f "$wt_root/pnpm-lock.yaml" ] || exit 0
+state_file="$wt_root/node_modules/.pnpm-checkout-state"
+state=$(cksum "$wt_root/package.json" "$wt_root/pnpm-lock.yaml" | cksum | awk '{print $1 ":" $2}')
+if [ -f "$wt_root/node_modules/.modules.yaml" ] && [ "$(cat "$state_file" 2>/dev/null)" = "$state" ]; then
+  exit 0
+fi
+command -v pnpm >/dev/null 2>&1 || {
+  echo "post-checkout: pnpm not on PATH; node_modules not installed" >&2
+  exit 1
+}
+
+export CI=1
+echo "post-checkout: pnpm install in $wt_root" >&2
+cd "$wt_root" || exit 1
+pnpm install --frozen-lockfile --prefer-offline --config.confirmModulesPurge=false || exit $?
+printf '%s\n' "$state" >"$state_file"
diff --git a/scripts/hooks/post-checkout.test.sh b/scripts/hooks/post-checkout.test.sh
new file mode 100755
index 000000000..f36f7587d
--- /dev/null
+++ b/scripts/hooks/post-checkout.test.sh
@@ -0,0 +1,64 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+root="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
+hook="$root/.githooks/post-checkout"
+work="$(mktemp -d)"
+trap 'rm -rf "$work"' EXIT
+
+git init -q "$work/idempotent-main"
+cd "$work/idempotent-main"
+git config user.email test@example.com
+git config user.name test
+mkdir -p .githooks "$work/fake-home/.local/bin"
+install -m 0755 "$hook" .githooks/post-checkout
+printf '{}\n' >package.json
+printf 'lockfileVersion: 9\n' >pnpm-lock.yaml
+printf '#!/bin/sh\nroot=$(git rev-parse --show-toplevel)\nmkdir -p "$root/node_modules"\ntouch "$root/node_modules/.modules.yaml"\nprintf x >>"$root/.pnpm-runs"\n' >"$work/fake-home/.local/bin/pnpm"
+chmod +x "$work/fake-home/.local/bin/pnpm"
+git add .githooks package.json pnpm-lock.yaml
+git commit -q -m init
+git config core.hooksPath .githooks
+HOME="$work/fake-home" git worktree add -q "$work/idempotent-linked" -b idempotent
+ref=$(git -C "$work/idempotent-linked" rev-parse HEAD)
+HOME="$work/fake-home" git -C "$work/idempotent-linked" -c core.hooksPath=.githooks \
+  hook run post-checkout -- "$ref" "$ref" 1
+test "$(wc -c <"$work/idempotent-linked/.pnpm-runs")" = 1
+
+# Branch checkout must wipe packages/*/dist.
+git init -q "$work/ts-clean-main"
+cd "$work/ts-clean-main"
+git config user.email test@example.com
+git config user.name test
+mkdir -p .githooks
+install -m 0755 "$hook" .githooks/post-checkout
+printf '{}\n' >package.json
+printf 'lockfileVersion: 9\n' >pnpm-lock.yaml
+mkdir -p node_modules
+touch node_modules/.modules.yaml
+ts_root=$(pwd)
+state=$(cksum "$ts_root/package.json" "$ts_root/pnpm-lock.yaml" | cksum | awk '{print $1 ":" $2}')
+printf '%s\n' "$state" >node_modules/.pnpm-checkout-state
+printf '#!/bin/sh\necho pnpm-should-not-run >>"$(git rev-parse --show-toplevel)/.pnpm-runs"\n' >"$work/fake-home/.local/bin/pnpm"
+chmod +x "$work/fake-home/.local/bin/pnpm"
+git add .githooks package.json pnpm-lock.yaml
+git commit -q -m init
+git config core.hooksPath .githooks
+ref=$(git rev-parse HEAD)
+mkdir -p packages/effect-app/dist packages/vue/dist
+printf 'poison\n' >packages/effect-app/dist/.tsbuildinfo
+printf 'poison\n' >packages/effect-app/dist/foo.d.ts
+printf 'poison\n' >packages/vue/dist/bar.d.ts
+HOME="$work/fake-home" git -c core.hooksPath=.githooks \
+  hook run post-checkout -- "$ref" "$ref" 1
+test ! -e packages/effect-app/dist
+test ! -e packages/vue/dist
+test ! -f .pnpm-runs
+
+mkdir -p packages/effect-app/dist
+printf 'keep\n' >packages/effect-app/dist/keep.d.ts
+HOME="$work/fake-home" git -c core.hooksPath=.githooks \
+  hook run post-checkout -- "$ref" "$ref" 0
+test -f packages/effect-app/dist/keep.d.ts
+
+echo "portable worktree hooks passed"
diff --git a/scripts/install-git-hooks.mjs b/scripts/install-git-hooks.mjs
index 5cb6894e7..de57ede06 100644
--- a/scripts/install-git-hooks.mjs
+++ b/scripts/install-git-hooks.mjs
@@ -47,6 +47,15 @@ try {
   console.error(`install-git-hooks: could not install agent gh shim: ${error?.message ?? error}`)
 }
 
+for (const name of ["post-checkout", "pre-commit", "pre-push"]) {
+  const p = path.join(root, ".githooks", name)
+  try {
+    chmodSync(p, 0o755)
+  } catch {
+    // best-effort when the hook is absent or chmod is unavailable
+  }
+}
+
 try {
   execFileSync("git", ["config", "core.hooksPath", ".githooks"], { cwd: root })
 } catch (error) {