diff --git a/plugins/repo-hygiene/.claude-plugin/plugin.json b/plugins/repo-hygiene/.claude-plugin/plugin.json
index 688b710bc2..f4e117faa3 100644
--- a/plugins/repo-hygiene/.claude-plugin/plugin.json
+++ b/plugins/repo-hygiene/.claude-plugin/plugin.json
@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "repo-hygiene",
-  "version": "0.10.19",
+  "version": "0.10.20",
   "description": "Repo hygiene action-router: /repo-hygiene:clean sweeps reclaimable caches, build artifacts, and stale git metadata, and can realign the working tree to a fresh-pull state — dry-run-first, with destructive tiers gated behind explicit confirmation and a session-scoped destructive-command guard. Ecosystem targets are detected at runtime; secrets, runtime dependencies, and skill data are preserved by default.",
   "author": {
     "name": "Melodic Software",
diff --git a/plugins/repo-hygiene/CHANGELOG.md b/plugins/repo-hygiene/CHANGELOG.md
index 27ba2cdbf6..d72ef61895 100644
--- a/plugins/repo-hygiene/CHANGELOG.md
+++ b/plugins/repo-hygiene/CHANGELOG.md
@@ -3,6 +3,23 @@
 All notable changes to the `repo-hygiene` plugin are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.10.20]
+
+### Fixed
+
+- **`clean`: `batch_read_lines_into` no longer treats a trailing blank line as
+  "file not found".** The helper's exit status is now a source-open verdict: 0
+  once the selected source was opened and consumed to ordinary EOF (empty
+  input, blank lines, a trailing blank line, and a final non-newline-terminated
+  line are all success), and 1 only when a named source is missing, not a
+  regular file, or cannot be opened. An explicit `return 0` after EOF stops the
+  last `[[ -n "$line" ]]` from becoming the function result. Both
+  `clean-batch.sh` and `git-tree-reset-batch.sh` trust that contract, so a
+  `--repos-from` / `--skip-from` file ending `a\n\n` is accepted and a missing
+  file still errors as file-not-found. Named sources open on fixed fd 3 so a
+  `ulimit -n 10` runner can still read the list
+  ([#3482](https://github.com/melodic-software/claude-code-plugins/issues/3482)).
+
 ## [0.10.19]
 
 ### Changed
diff --git a/plugins/repo-hygiene/skills/clean/scripts/clean-batch.test.sh b/plugins/repo-hygiene/skills/clean/scripts/clean-batch.test.sh
index aaf7e42777..08adf08a81 100755
--- a/plugins/repo-hygiene/skills/clean/scripts/clean-batch.test.sh
+++ b/plugins/repo-hygiene/skills/clean/scripts/clean-batch.test.sh
@@ -339,5 +339,67 @@ else
   fail "all tier plan REPO+GITDIR" "both" "$(cat "$APLAN")"
 fi
 
+# --- 9. --repos-from / --skip-from source-open contract (#3482) ---
+# A trailing blank is ordinary EOF success; only a missing/unopenable named
+# source is "file not found". Empty input is success at the helper and surfaces
+# as "no repos given", never as a missing file.
+RF="$(mkrepo rf)"
+printf '%s\n\n' "$RF" >"$TEST_TMPDIR/repos-trail.txt"
+rc=0
+out="$(bash "$BATCH" --tier caches --repos-from "$TEST_TMPDIR/repos-trail.txt" 2>&1)" || rc=$?
+assert_exit "trailing-blank --repos-from is accepted (exit 0)" 0 "$rc"
+assert_not_contains "trailing blank is not reported as file-not-found" "$out" "file not found"
+assert_contains "trailing-blank list enumerates the repo" "$out" "Repos: 1"
+
+: >"$TEST_TMPDIR/repos-empty.txt"
+rc=0
+out="$(bash "$BATCH" --tier caches --repos-from "$TEST_TMPDIR/repos-empty.txt" 2>&1)" || rc=$?
+assert_exit "empty --repos-from is a usage error (exit 2)" 2 "$rc"
+assert_not_contains "empty file is not reported missing" "$out" "file not found"
+assert_contains "empty file reaches no-repos usage" "$out" "no repos given"
+
+printf '%s' "$RF" >"$TEST_TMPDIR/repos-noeol.txt"
+rc=0
+out="$(bash "$BATCH" --tier caches --repos-from "$TEST_TMPDIR/repos-noeol.txt" 2>&1)" || rc=$?
+assert_exit "unterminated --repos-from is accepted (exit 0)" 0 "$rc"
+assert_contains "unterminated list enumerates the repo" "$out" "Repos: 1"
+
+printf '%s\r\n' "$RF" >"$TEST_TMPDIR/repos-cr.txt"
+rc=0
+out="$(bash "$BATCH" --tier caches --repos-from "$TEST_TMPDIR/repos-cr.txt" 2>&1)" || rc=$?
+assert_exit "CR-terminated --repos-from is accepted (exit 0)" 0 "$rc"
+assert_contains "CR-stripped list enumerates the repo" "$out" "Repos: 1"
+
+rc=0
+out="$(bash "$BATCH" --tier caches --repos-from "$TEST_TMPDIR/no-such-repos.txt" 2>&1)" || rc=$?
+assert_exit "missing --repos-from exits 2" 2 "$rc"
+assert_contains "missing file reported not found" "$out" "file not found:"
+
+SKIP_TRAIL="$TEST_TMPDIR/skips-trail.txt"
+printf 'rf\n\n' >"$SKIP_TRAIL"
+rc=0
+out="$(bash "$BATCH" --tier caches --repo "$RF" --skip-from "$SKIP_TRAIL" 2>&1)" || rc=$?
+assert_exit "trailing-blank --skip-from is accepted (exit 0)" 0 "$rc"
+assert_not_contains "trailing-blank skip-from is not file-not-found" "$out" "file not found"
+assert_contains "trailing-blank skip-from still skips" "$out" "skip-list"
+
+rc=0
+out="$(bash "$BATCH" --tier caches --repo "$RF" --skip-from "$TEST_TMPDIR/no-such-skips.txt" 2>&1)" || rc=$?
+assert_exit "missing --skip-from exits 2" 2 "$rc"
+assert_contains "missing skip-from reported not found" "$out" "file not found:"
+
+UNREAD_LIST="$TEST_TMPDIR/unreadable-repos.txt"
+printf '%s\n' "$RF" >"$UNREAD_LIST"
+chmod 000 "$UNREAD_LIST" 2>/dev/null || true
+if [[ -r "$UNREAD_LIST" ]]; then
+  skip_case "unopenable --repos-from: chmod 000 not enforced on this filesystem (CAP_DAC_OVERRIDE)"
+else
+  rc=0
+  out="$(bash "$BATCH" --tier caches --repos-from "$UNREAD_LIST" 2>&1)" || rc=$?
+  assert_exit "unopenable --repos-from exits 2" 2 "$rc"
+  assert_contains "unopenable file reported not found" "$out" "file not found:"
+fi
+chmod 644 "$UNREAD_LIST" 2>/dev/null || true
+
 [[ $FAILED -eq 0 ]] || exit 1
 echo "clean-batch.test.sh: all passed"
diff --git a/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.sh b/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.sh
index 590d54cd0f..20d7363024 100755
--- a/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.sh
+++ b/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.sh
@@ -140,8 +140,7 @@ while [[ $# -gt 0 ]]; do
     ;;
   --repos-from)
     [[ $# -ge 2 ]] || fail_usage "--repos-from requires a file or -"
-    [[ "$2" == "-" || -f "$2" ]] || fail_usage "file not found: $2"
-    batch_read_lines_into REPO_INPUTS "$2"
+    batch_read_lines_into REPO_INPUTS "$2" || fail_usage "file not found: $2"
     shift
     ;;
   --skip)
@@ -151,8 +150,7 @@ while [[ $# -gt 0 ]]; do
     ;;
   --skip-from)
     [[ $# -ge 2 ]] || fail_usage "--skip-from requires a file"
-    [[ -f "$2" ]] || fail_usage "file not found: $2"
-    batch_read_lines_into SKIP_INPUTS "$2"
+    batch_read_lines_into SKIP_INPUTS "$2" || fail_usage "file not found: $2"
     shift
     ;;
   -h | --help)
diff --git a/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.test.sh b/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.test.sh
index f680c01f27..c21880f0c5 100755
--- a/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.test.sh
+++ b/plugins/repo-hygiene/skills/clean/scripts/git-tree-reset-batch.test.sh
@@ -325,6 +325,63 @@ out="$(bash "$BATCH" --dry-run --repos-from "$NOEOL_REPOS" 2>&1)" || true
 assert_contains "unterminated repos-from still enumerates the repo" "$out" "Repos: 1"
 assert_contains "unterminated repos-from repo would reset" "$out" "would-reset"
 
+# --- 22b. source-open contract (#3482): trailing blank / empty / CR / missing ---
+# A file ending `path\n\n` is ordinary EOF success. The sibling clean-batch used
+# to map that helper rc 1 onto "file not found"; tree-batch must keep accepting
+# it after dropping its duplicate `-f` precheck, and a truly missing file must
+# still error as file-not-found.
+TRAIL_REPOS="$TEST_TMPDIR/repos-trail.txt"
+printf '%s\n\n' "$CLEAN_REPO" >"$TRAIL_REPOS"
+rc=0
+out="$(bash "$BATCH" --dry-run --repos-from "$TRAIL_REPOS" 2>&1)" || rc=$?
+assert_exit "trailing-blank --repos-from is accepted (exit 0)" 0 "$rc"
+assert_not_contains "trailing blank is not reported as file-not-found" "$out" "file not found"
+assert_contains "trailing-blank list enumerates the repo" "$out" "Repos: 1"
+
+: >"$TEST_TMPDIR/repos-empty.txt"
+rc=0
+out="$(bash "$BATCH" --dry-run --repos-from "$TEST_TMPDIR/repos-empty.txt" 2>&1)" || rc=$?
+assert_exit "empty --repos-from is a usage error (exit 2)" 2 "$rc"
+assert_not_contains "empty file is not reported missing" "$out" "file not found"
+assert_contains "empty file reaches no-repos usage" "$out" "no repos given"
+
+printf '%s\r\n' "$CLEAN_REPO" >"$TEST_TMPDIR/repos-cr.txt"
+rc=0
+out="$(bash "$BATCH" --dry-run --repos-from "$TEST_TMPDIR/repos-cr.txt" 2>&1)" || rc=$?
+assert_exit "CR-terminated --repos-from is accepted (exit 0)" 0 "$rc"
+assert_contains "CR-stripped list enumerates the repo" "$out" "Repos: 1"
+
+rc=0
+out="$(bash "$BATCH" --dry-run --repos-from "$TEST_TMPDIR/no-such-repos.txt" 2>&1)" || rc=$?
+assert_exit "missing --repos-from exits 2" 2 "$rc"
+assert_contains "missing file reported not found" "$out" "file not found:"
+
+TRAIL_SKIP="$TEST_TMPDIR/skips-trail.txt"
+printf 'keepme\n\n' >"$TRAIL_SKIP"
+rc=0
+out="$(bash "$BATCH" --dry-run --repo "$CLEAN_REPO" --repo "$SKIP_REPO" --skip-from "$TRAIL_SKIP" 2>&1)" || rc=$?
+assert_exit "trailing-blank --skip-from is accepted (exit 0)" 0 "$rc"
+assert_not_contains "trailing-blank skip-from is not file-not-found" "$out" "file not found"
+assert_contains "trailing-blank skip-from still skips" "$out" "skip-list"
+
+rc=0
+out="$(bash "$BATCH" --dry-run --repo "$CLEAN_REPO" --skip-from "$TEST_TMPDIR/no-such-skips.txt" 2>&1)" || rc=$?
+assert_exit "missing --skip-from exits 2" 2 "$rc"
+assert_contains "missing skip-from reported not found" "$out" "file not found:"
+
+UNREAD_LIST="$TEST_TMPDIR/unreadable-repos.txt"
+printf '%s\n' "$CLEAN_REPO" >"$UNREAD_LIST"
+chmod 000 "$UNREAD_LIST" 2>/dev/null || true
+if [[ -r "$UNREAD_LIST" ]]; then
+  skip_case "unopenable --repos-from: chmod 000 not enforced on this filesystem (CAP_DAC_OVERRIDE)"
+else
+  rc=0
+  out="$(bash "$BATCH" --dry-run --repos-from "$UNREAD_LIST" 2>&1)" || rc=$?
+  assert_exit "unopenable --repos-from exits 2" 2 "$rc"
+  assert_contains "unopenable file reported not found" "$out" "file not found:"
+fi
+chmod 644 "$UNREAD_LIST" 2>/dev/null || true
+
 # --- 23. a single --repo consumes consecutive paths (shell-glob-after-expansion) ---
 # `--repo ~/repos/*` reaches the script as ONE --repo flag followed by N positional
 # paths (the shell expanded the glob before exec). A single --repo must ingest every
diff --git a/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.sh b/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.sh
index aec700f2b8..4276d32249 100644
--- a/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.sh
+++ b/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.sh
@@ -28,6 +28,15 @@ batch_normalize_input() {
 # batch_read_lines_into <array-name> <file|-> — append non-empty CR-stripped
 # lines. Raw (unnormalized): repo paths are normalized at resolve time, skip
 # entries are normalized by clean_skip_matches, so neither is pre-mangled here.
+#
+# Exit status is a source-open verdict, not a record-read verdict. Bash `read`
+# returns nonzero at ordinary EOF (help read: "unless end-of-file is
+# encountered"); that is not evidence the containing file operation failed.
+#   0  the selected source was opened/accepted and consumed to ordinary EOF.
+#      Empty input, blank lines, a trailing blank line, and a final
+#      non-newline-terminated line are all success.
+#   1  a named source is missing, not a regular file, or cannot be opened/read.
+#      No input-content shape returns 1. For `-`, ordinary stdin EOF is success.
 batch_read_lines_into() {
   local -n _dest="$1"
   local src="$2" line
@@ -36,13 +45,24 @@ batch_read_lines_into() {
       line="${line%$'\r'}"
       [[ -n "$line" ]] && _dest+=("$line")
     done
-  else
-    [[ -f "$src" ]] || return 1
-    while IFS= read -r line || [[ -n "$line" ]]; do
-      line="${line%$'\r'}"
-      [[ -n "$line" ]] && _dest+=("$line")
-    done <"$src"
+    return 0
   fi
+  # Named source: reject missing/non-regular before open so a directory never
+  # blocks on `read`. Then open explicitly so a permission/open failure is
+  # retained (a `while ... done <"$src"` that never enters the body would
+  # otherwise look like success).
+  [[ -f "$src" ]] || return 1
+  # Fixed fd 3: Bash `{fd}` only allocates from 10 upward, so `ulimit -n 10`
+  # makes that open fail even when the list file is readable.
+  exec 3<"$src" || return 1
+  while IFS= read -r -u 3 line || [[ -n "$line" ]]; do
+    line="${line%$'\r'}"
+    [[ -n "$line" ]] && _dest+=("$line")
+  done
+  exec 3<&-
+  # Explicit success: do not let the last `[[ -n "$line" ]]` (false on a
+  # trailing blank, or on the EOF guard after a delimiter) become the result.
+  return 0
 }
 
 # Resolve-and-dedup accumulators, populated by batch_resolve_repos. Reset per call.
diff --git a/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.test.sh b/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.test.sh
index a5992744d2..5a1433227e 100755
--- a/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.test.sh
+++ b/plugins/repo-hygiene/skills/clean/scripts/lib/batch-common.test.sh
@@ -98,15 +98,92 @@ else
   fail "distinct common dir" 2 "${#BATCH_GITDIR_KEYS[@]}"
 fi
 
-# --- 5. batch_read_lines_into: CR-stripped, non-empty ---
+# --- 5. batch_read_lines_into: CR-stripped, non-empty, rc 0 ---
 printf 'a\r\n\nb\n' >"$TEST_TMPDIR/lines.txt"
 LINES=()
-batch_read_lines_into LINES "$TEST_TMPDIR/lines.txt"
+rc=0
+batch_read_lines_into LINES "$TEST_TMPDIR/lines.txt" || rc=$?
+assert_exit "CR-stripped file is success (rc 0)" 0 "$rc"
 if [[ "${#LINES[@]}" -eq 2 && "${LINES[0]}" == a && "${LINES[1]}" == b ]]; then
   pass "read_lines_into strips CR and empties"
 else
   fail "read_lines_into strips CR and empties" "a,b" "${LINES[*]}"
 fi
 
+# --- 5b. empty file, trailing blank, missing final newline: all rc 0 ---
+: >"$TEST_TMPDIR/empty.txt"
+LINES=()
+rc=0
+batch_read_lines_into LINES "$TEST_TMPDIR/empty.txt" || rc=$?
+assert_exit "empty file is success (rc 0)" 0 "$rc"
+if [[ "${#LINES[@]}" -eq 0 ]]; then
+  pass "empty file appends nothing"
+else
+  fail "empty file appends nothing" 0 "${#LINES[@]}"
+fi
+
+printf 'a\n\n' >"$TEST_TMPDIR/trail.txt"
+LINES=()
+rc=0
+batch_read_lines_into LINES "$TEST_TMPDIR/trail.txt" || rc=$?
+assert_exit "trailing blank line is success (rc 0)" 0 "$rc"
+if [[ "${#LINES[@]}" -eq 1 && "${LINES[0]}" == a ]]; then
+  pass "trailing blank keeps the preceding entry"
+else
+  fail "trailing blank keeps the preceding entry" "a" "${LINES[*]}"
+fi
+
+printf 'a' >"$TEST_TMPDIR/noeol.txt"
+LINES=()
+rc=0
+batch_read_lines_into LINES "$TEST_TMPDIR/noeol.txt" || rc=$?
+assert_exit "unterminated final line is success (rc 0)" 0 "$rc"
+if [[ "${#LINES[@]}" -eq 1 && "${LINES[0]}" == a ]]; then
+  pass "unterminated final line is kept"
+else
+  fail "unterminated final line is kept" "a" "${LINES[*]}"
+fi
+
+# Stdin (`-`): ordinary EOF is success, including a trailing blank.
+LINES=()
+rc=0
+batch_read_lines_into LINES - < <(printf 'a\n\n') || rc=$?
+assert_exit "stdin trailing blank is success (rc 0)" 0 "$rc"
+if [[ "${#LINES[@]}" -eq 1 && "${LINES[0]}" == a ]]; then
+  pass "stdin trailing blank keeps the preceding entry"
+else
+  fail "stdin trailing blank keeps the preceding entry" "a" "${LINES[*]}"
+fi
+
+# --- 5c. missing / non-regular / unopenable named sources return 1 ---
+LINES=()
+rc=0
+batch_read_lines_into LINES "$TEST_TMPDIR/no-such-list.txt" || rc=$?
+assert_exit "missing named source returns 1" 1 "$rc"
+if [[ "${#LINES[@]}" -eq 0 ]]; then
+  pass "missing source appends nothing"
+else
+  fail "missing source appends nothing" 0 "${#LINES[@]}"
+fi
+
+mkdir -p "$TEST_TMPDIR/not-a-file"
+LINES=()
+rc=0
+batch_read_lines_into LINES "$TEST_TMPDIR/not-a-file" || rc=$?
+assert_exit "directory (non-regular) returns 1" 1 "$rc"
+
+UNREAD="$TEST_TMPDIR/unreadable.txt"
+printf 'a\n' >"$UNREAD"
+chmod 000 "$UNREAD" 2>/dev/null || true
+if [[ -r "$UNREAD" ]]; then
+  skip_case "unopenable regular file: chmod 000 not enforced on this filesystem (CAP_DAC_OVERRIDE); missing/non-regular cases already cover rc 1"
+else
+  LINES=()
+  rc=0
+  batch_read_lines_into LINES "$UNREAD" || rc=$?
+  assert_exit "unopenable regular file returns 1" 1 "$rc"
+fi
+chmod 644 "$UNREAD" 2>/dev/null || true
+
 [[ $FAILED -eq 0 ]] || exit 1
 echo "batch-common.test.sh: all passed"