diff --git a/.claude/hooks/check-affected-pre-push.sh b/.claude/hooks/check-affected-pre-push.sh
index 1684408402..c7b2435424 100755
--- a/.claude/hooks/check-affected-pre-push.sh
+++ b/.claude/hooks/check-affected-pre-push.sh
@@ -177,7 +177,7 @@ segment_push_dir() {
     w="$1"
     shift
     case "$w" in
-    --delete | --dry-run | -[nd]* | -[!-]*[nd]*) return 1 ;;
+    --delete | --dry-run | -[dn]* | -[!-]*[dn]*) return 1 ;;
     --tags) tags=1 ;;
     -o | --push-option | --repo | --receive-pack | --exec) shift ;;
     -*) ;;
@@ -287,7 +287,7 @@ run_checks() (
     extract_tools "$top" "$mb" "$tmp/tools" || exit 2
   fi
   [[ -x "$script" ]] || exit 2
-  (cd "$data" && bash "$script" 2>&1) || rc=$?
+  (cd "$data" && CHECK_DATA_ROOT="$data" bash "$script" 2>&1) || rc=$?
   exit "$rc"
 )
 
diff --git a/scripts/check-affected.sh b/scripts/check-affected.sh
index 84ed4b8b91..f94893feb0 100755
--- a/scripts/check-affected.sh
+++ b/scripts/check-affected.sh
@@ -50,10 +50,11 @@
 # is covered, and scripts/check-affected-gates.test.sh fails when a gate in
 # the workflow's hygiene jobs is in neither column.
 #
-# Code runs from the tree holding this script; the files checked are those of
-# the current directory's repository. The pre-push hook runs a merge-base copy
-# of this script against a branch, so the two differ: then every check script
-# runs from the copy with CHECK_DATA_ROOT naming the branch tree, markdownlint
+# Code runs from the tree holding this script, and the files checked are that
+# tree's too, whatever the working directory, unless CHECK_DATA_ROOT names
+# another tree. The pre-push hook runs a merge-base copy of this script with
+# CHECK_DATA_ROOT naming the branch tree, so the two differ: then every check
+# script runs from the copy with CHECK_DATA_ROOT passed on, markdownlint
 # reads only the copy's configs (a branch config can load a custom rule, which
 # is code), and checks that run the branch's own code skip: --tests, changed-skills, and the
 # validate-plugins steps that report `SKIP` themselves.
@@ -66,7 +67,8 @@
 # A missing tool, a failed fetch, or a check that exits 2 (could not run) is a
 # SKIP with its reason, never a failure. Exit 0 every check passed or skipped;
 # 1 a check failed, with each failure and its reproduce command on stderr; 2
-# usage or a git state the changed set cannot be read from. That is the
+# usage or a git state the changed set cannot be read from, an empty changed
+# set while HEAD is not the base among them. That is the
 # check-script family contract stated in README.md.
 set -uo pipefail
 
@@ -96,11 +98,11 @@ while (($#)); do
 done
 
 tools="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd -P)" || exit 2
-if ! git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-  echo "check-affected: not inside a git work tree" >&2
+top="$(git -C "${CHECK_DATA_ROOT:-$tools}" rev-parse --show-toplevel 2>/dev/null)" || {
+  echo "check-affected: ${CHECK_DATA_ROOT:-$tools} is not inside a git work tree" >&2
   exit 2
-fi
-cd "$(git rev-parse --show-toplevel)" || exit 2
+}
+cd "$top" || exit 2
 
 if ((uncommitted)); then
   # The scratch repository has no remote, so the base is fetched and resolved
@@ -144,8 +146,13 @@ if ((uncommitted)); then
     fi
   fi
   tree="$(git write-tree)" || exit 2
-  commit="$(git -c user.name=check-affected -c user.email=check-affected@localhost \
-    commit-tree "$tree" -p HEAD -m 'check-affected: uncommitted work')" || exit 2
+  # No edits: the snapshot is HEAD itself, so a clean tree is HEAD at its base.
+  if [[ "$tree" == "$(git rev-parse "HEAD^{tree}")" ]]; then
+    commit="$(git rev-parse HEAD)" || exit 2
+  else
+    commit="$(git -c user.name=check-affected -c user.email=check-affected@localhost \
+      commit-tree "$tree" -p HEAD -m 'check-affected: uncommitted work')" || exit 2
+  fi
   unset GIT_INDEX_FILE GIT_OBJECT_DIRECTORY GIT_ALTERNATE_OBJECT_DIRECTORIES
   git -c init.defaultBranch=snapshot init --quiet --template= "$snap/tree" || exit 2
   printf '%s\n' "$snap/objects" "$objects" >"$snap/tree/.git/objects/info/alternates" || exit 2
@@ -155,7 +162,7 @@ if ((uncommitted)); then
   args=(--base "$base" --no-fetch)
   ((run_tests)) && args+=(--tests)
   rc=0
-  (cd "$snap/tree" && bash "$tools/scripts/check-affected.sh" "${args[@]}") || rc=$?
+  CHECK_DATA_ROOT="$snap/tree" bash "$tools/scripts/check-affected.sh" "${args[@]}" || rc=$?
   exit "$rc"
 fi
 base="${base:-origin/main}"
@@ -219,6 +226,12 @@ if ! all_raw="$(git diff --name-only "$merge_base" HEAD)" ||
 fi
 mapfile -t changed <<<"$changed_raw"
 [[ -n "${changed[0]-}" ]] || changed=()
+# Nothing changed is a pass only when HEAD is the base; otherwise the run read
+# the wrong tree or range, and passing would check nothing.
+if [[ -z "$all_raw" && "$(git rev-list --count "$base...HEAD")" != 0 ]]; then
+  echo "check-affected: no changed files in $top since $merge_base, yet HEAD is not $base, so nothing would be checked. Run the check-affected.sh inside the tree you mean to check, or name that tree in CHECK_DATA_ROOT." >&2
+  exit 2
+fi
 
 if ((${#changed[@]})) && ! git diff --quiet HEAD -- "${changed[@]}"; then
   echo "check-affected: SKIP every check (uncommitted edits to changed files; the checks read the working tree, a push sends HEAD, and CI checks the pushed commit). Commit or stash them, then rerun." >&2
diff --git a/scripts/check-affected.test.sh b/scripts/check-affected.test.sh
index 00104036ff..30708b93dc 100755
--- a/scripts/check-affected.test.sh
+++ b/scripts/check-affected.test.sh
@@ -84,6 +84,45 @@ check "every hygiene gate the runner does not run is named CI only" \
 check "a gate the runner runs is not named CI only" \
   '[[ $ERR != *"CI only: markdown "* && $ERR != *"CI only: spoke-plugin-root "* && $ERR != *"CI only: typos "* ]]'
 
+# The tree checked is the one holding the script, whatever the working
+# directory: run by path from another checkout whose HEAD is at its base (a main
+# checkout beside a worktree), it still lists the branch's one change, notes.txt.
+other="$tmp/other"
+git_test_config "$tmp" clone -q --branch base "$repo" "$other"
+git_test_config "$other" update-ref refs/remotes/origin/main "$(git_test_config "$repo" rev-parse HEAD)"
+# run_from <dir> <args...>: runs the fixture repo's script from <dir>; sets RC, OUT, ERR.
+run_from() {
+  local dir="$1"
+  shift
+  RC=0
+  OUT="$(cd "$dir" && bash "$repo/scripts/check-affected.sh" "$@" 2>"$tmp/err")" || RC=$?
+  ERR="$(cat "$tmp/err")"
+}
+run_from "$other" --base base --tests
+check "run from another checkout, it lists the script's own branch's change" \
+  '[[ $RC == 0 && $OUT == *"over 1 changed files"* && $ERR != *"SKIP tests"* ]]'
+git_test_config "$repo" update-ref refs/remotes/origin/main "$(git_test_config "$repo" rev-parse base)"
+run_from "$other" --base origin/main --no-fetch
+check "an explicit --base run from another checkout still lists the change" \
+  '[[ $RC == 0 && $OUT == *"over 1 changed files"* ]]'
+git_test_config "$repo" update-ref -d refs/remotes/origin/main
+
+# An empty changed set while HEAD is not the base means the wrong tree or range
+# was read, never a pass: HEAD behind the base, and commits that change nothing.
+RC=0
+ERR="$(cd "$other" && bash scripts/check-affected.sh --base origin/main --no-fetch 2>&1)" || RC=$?
+check "HEAD behind its base with no changed files exits non-zero with a message" \
+  '[[ $RC != 0 && $ERR == *"no changed files"* && $ERR != *"passed"* ]]'
+git_test_config "$other" commit -q --allow-empty -m empty
+RC=0
+ERR="$(cd "$other" && bash scripts/check-affected.sh --base origin/base --no-fetch 2>&1)" || RC=$?
+check "commits beyond the base that change no file exit non-zero with a message" \
+  '[[ $RC != 0 && $ERR == *"no changed files"* && $ERR != *"passed"* ]]'
+git_test_config "$other" reset -q --hard origin/base
+RC=0
+OUT="$(cd "$other" && bash scripts/check-affected.sh --base base --no-fetch 2>/dev/null)" || RC=$?
+check "HEAD at its base passes with nothing to check" '[[ $RC == 0 && $OUT == *"over 0 changed files"* ]]'
+
 run STUB_TYPOS=2 -- --base base
 check "a typos exit of 2 is a finding, not a check that could not run" \
   '[[ $RC == 1 && $ERR == *"FAIL typos"* && $ERR != *"SKIP typos"* ]]'
@@ -168,9 +207,10 @@ run PATH="$tmp/bin:$PATH" --
 check "a failed fetch skips the stale-base check only" \
   '[[ $RC == 0 && $ERR == *"SKIP stale-base-overlap (git fetch of origin/main failed)"* && $OUT$ERR == *"validate-plugins (no plugin changed)"* ]]'
 
-# Run from another tree (the pre-push hook's merge-base copy), every check
-# script comes from that tree and is told which tree to read; the checked
-# tree's own scripts and its test code never run.
+# A copy outside the checked tree (the pre-push hook's merge-base copy) checks
+# the tree CHECK_DATA_ROOT names: every check script comes from the copy and is
+# told which tree to read; the checked tree's own scripts and its test code
+# never run.
 tools="$tmp/tools"
 mkdir -p "$tools/scripts"
 cp "$SELF_DIR/check-affected.sh" "$tools/scripts/"
@@ -183,7 +223,7 @@ printf 'import os, sys\nsys.stderr.write("copy of sync-plugin-options-docs read
 cp "$SELF_DIR/check-affected-gates.txt" "$tools/scripts/"
 chmod +x "$tools"/scripts/*.sh
 RC=0
-ERR="$(cd "$repo" && bash "$tools/scripts/check-affected.sh" --base base --tests 2>&1)" || RC=$?
+ERR="$(cd "$tmp" && CHECK_DATA_ROOT="$repo" bash "$tools/scripts/check-affected.sh" --base base --tests 2>&1)" || RC=$?
 check "a copy run elsewhere runs its own check scripts against the checked tree" \
   '[[ $RC == 1 && $ERR == *"copy of check-shell-portability read $repo"* ]]'
 check "a copy run elsewhere points the spoke, options-docs and changelog-parity checks at the checked tree" \
@@ -196,7 +236,7 @@ printf 'x\n' >"$repo/plugins/demo/skills/s/notes.txt"
 git_test_config "$repo" add -A
 git_test_config "$repo" commit -q -m skill
 RC=0
-ERR="$(cd "$repo" && bash "$tools/scripts/check-affected.sh" --base base 2>&1)" || RC=$?
+ERR="$(cd "$tmp" && CHECK_DATA_ROOT="$repo" bash "$tools/scripts/check-affected.sh" --base base 2>&1)" || RC=$?
 check "a copy run elsewhere skips changed-skills, which runs the checked tree's skill-quality code" \
   '[[ $ERR == *"SKIP changed-skills (runs the checked tree"* && $ERR != *"copy of check-changed-skills"* ]]'
 git_test_config "$repo" reset -q --hard HEAD~1
@@ -210,13 +250,13 @@ if command -v markdownlint-cli2 >/dev/null 2>&1; then
   git_test_config "$repo" add -A
   git_test_config "$repo" commit -q -m docs
   RC=0
-  ERR="$(cd "$repo" && bash "$tools/scripts/check-affected.sh" --base base 2>&1)" || RC=$?
+  ERR="$(cd "$tmp" && CHECK_DATA_ROOT="$repo" bash "$tools/scripts/check-affected.sh" --base base 2>&1)" || RC=$?
   check "a copy run elsewhere never loads the checked tree's markdownlint config" \
     '[[ ! -e $tmp/md-payload && $ERR != *"SKIP markdown"* ]]'
   printf '# Title\nText.\n' >"$repo/docs/a.md"
   git_test_config "$repo" commit -q -am bad-md
   RC=0
-  ERR="$(cd "$repo" && bash "$tools/scripts/check-affected.sh" --base base 2>&1)" || RC=$?
+  ERR="$(cd "$tmp" && CHECK_DATA_ROOT="$repo" bash "$tools/scripts/check-affected.sh" --base base 2>&1)" || RC=$?
   check "a copy run elsewhere still lints the checked tree's markdown" \
     '[[ $RC == 1 && $ERR == *"FAIL markdown"* && $ERR == *"MD022"* ]]'
 else
@@ -237,6 +277,11 @@ printf '#!/usr/bin/env bash\necho hi\n' >"$repo/new-tool"
 run -- --uncommitted
 check "--uncommitted checks an untracked #! file's mode on disk" \
   '[[ $RC == 1 && $ERR == *"FAIL exec-bit"* && $ERR == *"new-tool starts with #!"* ]]'
+# The issue lane's wrapper sets CHECK_DATA_ROOT to the checkout; the snapshot,
+# not the checkout's committed state, is still what gets checked.
+run CHECK_DATA_ROOT="$repo" -- --uncommitted
+check "--uncommitted under the lane's CHECK_DATA_ROOT still checks the work tree" \
+  '[[ $RC == 1 && $ERR == *"new-tool starts with #!"* ]]'
 run CHECK_AFFECTED_SCRIPT_EXEC_BIT=1 -- --uncommitted
 check "--uncommitted with CHECK_AFFECTED_SCRIPT_EXEC_BIT judges a new #! file as executable, as apply-patch commits it" \
   '[[ $RC == 0 && $OUT == *"over 1 changed files"* && ! -x $repo/new-tool ]]'
@@ -289,6 +334,8 @@ else
   ok "SKIP --uncommitted shellcheck case (no shellcheck with --rcfile here)"
 fi
 check "--uncommitted leaves HEAD, the index and the worktree list as they were" '[[ $(state) == "$before" ]]'
+run -- --uncommitted
+check "--uncommitted with no edits passes with nothing to check" '[[ $RC == 0 && $OUT == *"over 0 changed files"* ]]'
 
 run -- --bogus
 check "an unknown flag is a usage error" '[[ $RC == 2 ]]'