diff --git a/.mise/tasks/lint/mise-run-quiet b/.mise/tasks/lint/mise-run-quiet
new file mode 100644
index 0000000..f3018cc
--- /dev/null
+++ b/.mise/tasks/lint/mise-run-quiet
@@ -0,0 +1,227 @@
+#!/usr/bin/env bash
+#MISE description="Flag mise run without -q in clean-output contexts"
+#USAGE arg "<targets>…" help="Paths to codebases to check (one or more)"
+#USAGE example "codebase lint:mise-run-quiet ." header="Flag mise run calls missing -q"
+#USAGE example "codebase lint:mise-run-quiet /path/to/repo"
+
+set -euo pipefail
+
+# shellcheck source=../../../lib/shell-files.sh
+source "$MISE_CONFIG_ROOT/lib/shell-files.sh"
+
+# Rationale: 'mise run' without -q prints task runner headers such as
+# '[shell] $ ...' to stderr. That is useful for debugging, but harmful
+# when the command output is being eval'd, piped, embedded in generated
+# output, or used in shell startup.
+#
+# Example failure mode: eval "$(shiv shell)" visibly printed the task
+# header in the terminal on every shell startup.
+#
+# Contexts flagged:
+#   - command substitution: $(mise run ...) — header goes into captured output
+#   - eval: eval "$(mise run ...)" — header pollutes the eval'd string
+#   - pipeline: mise run ... | consumer — header goes into the pipe
+#
+# Safe contexts (not flagged):
+#   - mise run -q ... — already quiet
+#   - mise run ... 2>/dev/null — stderr explicitly discarded
+#   - bare mise run at line start (interactive/debug) — no capture
+#   - mise run in comments or string literals
+
+IFS=' ' read -ra TARGETS <<< "${usage_targets}"
+
+if [[ ${#TARGETS[@]} -eq 0 ]]; then
+  echo "ERROR: at least one target is required" >&2
+  exit 1
+fi
+
+# Resolve relative paths against CALLER_PWD (see lib/shell-files.sh).
+for i in "${!TARGETS[@]}"; do
+  TARGETS[i]=$(resolve_target "${TARGETS[i]}")
+done
+
+# ── Helpers ──────────────────────────────────────────────────────────────
+
+# has_stderr_redirect <line>
+# Returns 0 if the line redirects stderr (2>...).
+has_stderr_redirect() {
+  local line="$1"
+  echo "$line" | grep -qE '2>[>&]?[^&[:space:]]' 2>/dev/null
+}
+
+# is_pattern_match <line>
+# Returns 0 if 'mise run' appears inside a grep/sed/awk pattern or string
+# literal rather than as an actual command invocation.
+is_pattern_match() {
+  local line="$1"
+  # grep/sed/awk with 'mise run' in the pattern (single or double quoted)
+  echo "$line" | grep -qE "(grep|sed|awk)[[:space:]].*['\"].*mise run" 2>/dev/null && return 0
+  # echo with 'mise run' in a string
+  echo "$line" | grep -qE "echo[[:space:]].*['\"].*mise run" 2>/dev/null && return 0
+  # printf with 'mise run' in a format string
+  echo "$line" | grep -qE "printf[[:space:]].*['\"].*mise run" 2>/dev/null && return 0
+  return 1
+}
+
+# classify_context <line>
+# Emit the context classification for a mise run invocation.
+classify_context() {
+  local line="$1"
+
+  # Skip if mise run is inside a grep/sed pattern or string literal
+  is_pattern_match "$line" && echo "pattern" && return
+
+  # Already quiet — skip
+  if echo "$line" | grep -qE 'mise run\s+-q'; then
+    echo "quiet"
+    return
+  fi
+
+  # eval context: eval "$(mise run ...)"
+  if echo "$line" | grep -qE 'eval\s+"\$\([^)]*mise run'; then
+    echo "eval"
+    return
+  fi
+
+  # Command substitution context: $(mise run ...)
+  if echo "$line" | grep -qE '\$\([^)]*mise run'; then
+    echo "command-sub"
+    return
+  fi
+
+  # Pipeline context: mise run ... | consumer
+  if echo "$line" | grep -qE 'mise run[^|]*\|'; then
+    echo "pipeline"
+    return
+  fi
+
+  # Has stderr redirect — safe
+  if has_stderr_redirect "$line"; then
+    echo "stderr-redirect"
+    return
+  fi
+
+  # Bare mise run (interactive/debug) — safe
+  echo "bare"
+}
+
+# has_line_ignore <line>
+# Returns 0 if the line has a rule-specific inline ignore.
+has_line_ignore() {
+  local line="$1"
+  echo "$line" | grep -qE 'codebase:ignore[[:space:]]+mise-run-quiet' 2>/dev/null
+}
+
+# scan_file <file>
+# Emit flagged line numbers and context for mise run calls without -q.
+scan_file() {
+  local file="$1"
+  local lineno=0
+  local line
+
+  while IFS= read -r line || [[ -n "$line" ]]; do
+    lineno=$((lineno + 1))
+
+    # Skip full-line comments.
+    [[ "$line" =~ ^[[:space:]]*# ]] && continue
+
+    # Skip lines without mise run.
+    [[ "$line" != *"mise run"* ]] && continue
+
+    # Rule-specific inline ignore with reason is accepted.
+    has_line_ignore "$line" && continue
+
+    # Classify the context.
+    local context
+    context=$(classify_context "$line")
+
+    case "$context" in
+      quiet|stderr-redirect|bare|pattern)
+        # Safe contexts — skip
+        ;;
+      command-sub)
+        local trimmed
+        trimmed="${line#"${line%%[![:space:]]*}"}"
+        echo "[command-sub] $lineno: $trimmed"
+        ;;
+      eval)
+        local trimmed
+        trimmed="${line#"${line%%[![:space:]]*}"}"
+        echo "[eval] $lineno: $trimmed"
+        ;;
+      pipeline)
+        local trimmed
+        trimmed="${line#"${line%%[![:space:]]*}"}"
+        echo "[pipeline] $lineno: $trimmed"
+        ;;
+    esac
+  done < "$file"
+}
+
+# ── Main ──────────────────────────────────────────────────────────────────
+
+failures=0
+
+for target in "${TARGETS[@]}"; do
+  if [[ ! -e "$target" ]]; then
+    echo "ERROR: target does not exist: $target" >&2
+    exit 1
+  fi
+
+  name=$(basename "$target")
+
+  # File-level ignore via mise.toml
+  toml="$target/mise.toml"
+  if [[ -f "$toml" ]] && grep -m1 -q 'codebase:ignore mise-run-quiet' "$toml"; then
+    echo "SKIP  $name (codebase:ignore)"
+    continue
+  fi
+
+  # Collect shell files
+  files=()
+  while IFS= read -r f; do
+    [[ -n "$f" ]] && files+=("$f")
+  done < <(discover_shell_files "$target")
+
+  if [[ ${#files[@]} -eq 0 ]]; then
+    echo "OK    $name (no shell files found)"
+    continue
+  fi
+
+  # Scan each file; collect hits
+  hit_count=0
+  warn_count=0
+  target_output=""
+  for file in "${files[@]}"; do
+    rel="${file#"$target"/}"
+    while IFS= read -r hit; do
+      [[ -z "$hit" ]] && continue
+      target_output+="  $rel:$hit"$'\n'
+      if [[ "$hit" == \[command-sub\]* ]] || [[ "$hit" == \[eval\]* ]]; then
+        hit_count=$((hit_count + 1))
+      elif [[ "$hit" == \[pipeline\]* ]]; then
+        warn_count=$((warn_count + 1))
+      fi
+    done < <(scan_file "$file")
+  done
+
+  if [[ "$hit_count" -gt 0 ]] || [[ "$warn_count" -gt 0 ]]; then
+    detail=""
+    [[ "$hit_count" -gt 0 ]] && detail+="$hit_count mise run call(s) without -q in capture context(s)"
+    [[ "$hit_count" -gt 0 && "$warn_count" -gt 0 ]] && detail+=", "
+    [[ "$warn_count" -gt 0 ]] && detail+="$warn_count pipeline(s) without -q"
+    echo "FAIL  $name: $detail"
+    printf '%s' "$target_output"
+    cat <<'HINT'
+  hint: Add -q to mise run calls in capture contexts: mise run -q <task>
+        For pipelines: mise run -q <task> | consumer
+        For eval: eval "$(mise run -q <task>)"
+        For command substitution: $(mise run -q <task>)
+HINT
+    failures=$((failures + 1))
+  else
+    echo "OK    $name (${#files[@]} file(s) clean)"
+  fi
+done
+
+exit "$failures"
diff --git a/test/lib/shell-files.bats b/test/lib/shell-files.bats
index a462482..5d6ed6e 100644
--- a/test/lib/shell-files.bats
+++ b/test/lib/shell-files.bats
@@ -7,9 +7,7 @@ setup() {
   source "$REPO_DIR/lib/shell-files.sh"
 }
 
-# ============================================================================
 # resolve_target
-# ============================================================================
 
 @test "resolve_target: absolute path passes through unchanged" {
   result=$(resolve_target "/some/absolute/path")
diff --git a/test/lint/bats-test-helper/bats-test-helper.bats b/test/lint/bats-test-helper/bats-test-helper.bats
index 27ebba4..f4b0e76 100644
--- a/test/lint/bats-test-helper/bats-test-helper.bats
+++ b/test/lint/bats-test-helper/bats-test-helper.bats
@@ -7,9 +7,7 @@ setup() {
   FIXTURES="$BATS_TEST_DIRNAME/fixtures"
 }
 
-# ============================================================================
 # Pass paths
-# ============================================================================
 
 @test "bats-test-helper: passes on clean wrapper-based tests" {
   run codebase lint:bats-test-helper "$FIXTURES/clean"
@@ -24,9 +22,7 @@ setup() {
   [[ "$output" == *"no test/ files found"* ]]
 }
 
-# ============================================================================
 # Invocation signatures — each form fails
-# ============================================================================
 
 @test "bats-test-helper: flags 'bash \$TASK' (var whose name contains TASK)" {
   run codebase lint:bats-test-helper "$FIXTURES/dirty-task-var"
@@ -84,9 +80,7 @@ setup() {
   [[ "$output" == *"bash \$REPO_DIR/.mise/tasks/lint/check"* ]]
 }
 
-# ============================================================================
 # False positives — none of these are actual invocations
-# ============================================================================
 
 @test "bats-test-helper: does NOT flag reading a task file as data (grep/cat)" {
   # Regression guard: 'grep "$MCR/.mise/tasks/foo"' reads the script, doesn't
@@ -97,9 +91,7 @@ setup() {
   [[ "$output" == *"OK"* ]]
 }
 
-# ============================================================================
 # Ignore directives
-# ============================================================================
 
 @test "bats-test-helper: inline '# codebase:ignore' suppresses a single line" {
   run codebase lint:bats-test-helper "$FIXTURES/ignored-inline"
@@ -113,9 +105,7 @@ setup() {
   [[ "$output" == *"SKIP"*"ignored-file"* ]]
 }
 
-# ============================================================================
 # Output details
-# ============================================================================
 
 @test "bats-test-helper: fail output includes file:line citations" {
   run codebase lint:bats-test-helper "$FIXTURES/dirty-task-var"
@@ -130,9 +120,7 @@ setup() {
   [[ "$output" == *"Call the Tool"* ]]
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "bats-test-helper: fails when no targets given" {
   run codebase lint:bats-test-helper
@@ -146,9 +134,7 @@ setup() {
   [[ "$output" == *"does not exist"* ]]
 }
 
-# ============================================================================
 # Multi-target
-# ============================================================================
 
 @test "bats-test-helper: accepts multiple targets and reports each" {
   run codebase lint:bats-test-helper "$FIXTURES/clean" "$FIXTURES/dirty-task-var"
diff --git a/test/lint/bats-test-task/bats-test-task.bats b/test/lint/bats-test-task/bats-test-task.bats
index 295d92f..f761f2b 100644
--- a/test/lint/bats-test-task/bats-test-task.bats
+++ b/test/lint/bats-test-task/bats-test-task.bats
@@ -7,9 +7,7 @@ setup() {
   FIXTURES="$BATS_TEST_DIRNAME/fixtures"
 }
 
-# ============================================================================
 # Pass paths
-# ============================================================================
 
 @test "bats-test-task: passes on the canonical pattern" {
   run codebase lint:bats-test-task "$FIXTURES/clean"
@@ -33,9 +31,7 @@ setup() {
   [[ "$output" == *"OK"*"shimmer-variant"* ]]
 }
 
-# ============================================================================
 # Failure modes
-# ============================================================================
 
 @test "bats-test-task: flags missing USAGE arg spec" {
   run codebase lint:bats-test-task "$FIXTURES/missing-usage-arg"
@@ -80,9 +76,7 @@ setup() {
   [[ "$output" != *"invocations found"* ]]
 }
 
-# ============================================================================
 # Ignore directive
-# ============================================================================
 
 @test "bats-test-task: 'codebase:ignore bats-test-task' in mise.toml skips the target" {
   run codebase lint:bats-test-task "$FIXTURES/ignored-file"
@@ -90,9 +84,7 @@ setup() {
   [[ "$output" == *"SKIP"*"ignored-file"* ]]
 }
 
-# ============================================================================
 # Output details
-# ============================================================================
 
 @test "bats-test-task: fail output includes the remediation hint" {
   run codebase lint:bats-test-task "$FIXTURES/missing-usage-arg"
@@ -109,9 +101,7 @@ setup() {
   [[ "$output" == *"invocations"* ]]
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "bats-test-task: fails when no targets given" {
   run codebase lint:bats-test-task
@@ -125,9 +115,7 @@ setup() {
   [[ "$output" == *"does not exist"* ]]
 }
 
-# ============================================================================
 # Multi-target
-# ============================================================================
 
 @test "bats-test-task: accepts multiple targets and reports each" {
   run codebase lint:bats-test-task "$FIXTURES/clean" "$FIXTURES/missing-examples"
diff --git a/test/lint/gum-table/gum-table.bats b/test/lint/gum-table/gum-table.bats
index 2dfddaa..809b670 100644
--- a/test/lint/gum-table/gum-table.bats
+++ b/test/lint/gum-table/gum-table.bats
@@ -7,9 +7,7 @@ setup() {
   FIXTURES="$BATS_TEST_DIRNAME/fixtures"
 }
 
-# ============================================================================
 # High confidence: column -t (always a true positive)
-# ============================================================================
 
 @test "column-t: detects piping to column -t" {
   run codebase lint:gum-table "$FIXTURES/manual-padding/task-c"
@@ -18,9 +16,7 @@ setup() {
   [[ "$output" == *"WARN"* ]]
 }
 
-# ============================================================================
 # High confidence: printf padding inside a loop
-# ============================================================================
 
 @test "loop-table: detects printf %-Ns inside while-read" {
   run codebase lint:gum-table "$FIXTURES/manual-padding/task-b"
@@ -45,9 +41,7 @@ setup() {
   echo "$output" | grep "padding" | grep -q "INFO"
 }
 
-# ============================================================================
 # Low confidence: printf padding outside loops (INFO only, not a failure)
-# ============================================================================
 
 @test "padding: printf %-Ns outside loop is INFO, not a failure" {
   run codebase lint:gum-table "$FIXTURES/manual-padding/task-a"
@@ -69,9 +63,7 @@ setup() {
   [[ "$output" == *"INFO"* ]]
 }
 
-# ============================================================================
 # True negatives — no output at all
-# ============================================================================
 
 @test "clean: already using gum table" {
   run codebase lint:gum-table "$FIXTURES/clean/task-gum"
@@ -103,9 +95,7 @@ setup() {
   [[ "$output" == *"OK"* ]]
 }
 
-# ============================================================================
 # Multi-file scanning
-# ============================================================================
 
 @test "directory scan finds high-confidence hits" {
   run codebase lint:gum-table "$FIXTURES/manual-padding"
@@ -121,9 +111,7 @@ setup() {
   [ "$status" -eq 0 ]
 }
 
-# ============================================================================
 # Output format
-# ============================================================================
 
 @test "WARN output includes file path, category, and line number" {
   run codebase lint:gum-table "$FIXTURES/manual-padding/task-b"
@@ -136,9 +124,7 @@ setup() {
   [[ "$output" =~ INFO.*task-a:\[padding\].*[0-9]+: ]]
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "fails when target does not exist" {
   run codebase lint:gum-table /nonexistent
@@ -146,9 +132,7 @@ setup() {
   [[ "$output" == *"ERROR"* ]]
 }
 
-# ============================================================================
 # Relative path resolution (regression: codebase#24)
-# ============================================================================
 
 @test "relative path resolves against CODEBASE_CALLER_PWD (dirty fixture)" {
   # Regression: relative targets resolved against codebase's install
diff --git a/test/lint/mcr-scope/mcr-scope.bats b/test/lint/mcr-scope/mcr-scope.bats
index 3ae6215..49869b4 100644
--- a/test/lint/mcr-scope/mcr-scope.bats
+++ b/test/lint/mcr-scope/mcr-scope.bats
@@ -7,9 +7,7 @@ setup() {
   FIXTURES="$BATS_TEST_DIRNAME/fixtures"
 }
 
-# ============================================================================
 # Detection
-# ============================================================================
 
 @test "mcr-scope: passes on a clean codebase" {
   run codebase lint:mcr-scope "$FIXTURES/clean"
@@ -102,9 +100,7 @@ setup() {
   [[ "$output" == *"no test/ or lib/ files found"* ]]
 }
 
-# ============================================================================
 # Ignore directives
-# ============================================================================
 
 @test "mcr-scope: inline '# codebase:ignore' suppresses a single line" {
   run codebase lint:mcr-scope "$FIXTURES/ignored-inline"
@@ -118,9 +114,7 @@ setup() {
   [[ "$output" == *"SKIP"*"ignored-file"* ]]
 }
 
-# ============================================================================
 # Output details
-# ============================================================================
 
 @test "mcr-scope: fail output includes file:line citations" {
   run codebase lint:mcr-scope "$FIXTURES/dirty-lib"
@@ -136,9 +130,7 @@ setup() {
   [[ "$output" == *"BASH_SOURCE"* ]]
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "mcr-scope: fails when no targets given" {
   run codebase lint:mcr-scope
@@ -153,9 +145,7 @@ setup() {
   [[ "$output" == *"does not exist"* ]]
 }
 
-# ============================================================================
 # Multi-target
-# ============================================================================
 
 @test "mcr-scope: accepts multiple targets and reports each" {
   run codebase lint:mcr-scope "$FIXTURES/clean" "$FIXTURES/dirty-test"
diff --git a/test/lint/mise-run-quiet/fixtures/clean-already-quiet/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/clean-already-quiet/.mise/tasks/t
new file mode 100644
index 0000000..cfee627
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/clean-already-quiet/.mise/tasks/t
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Already using -q — should be fine
+mise run -q build
+mise run -q test -- --filter unit
+result=$(mise run -q status)
diff --git a/test/lint/mise-run-quiet/fixtures/clean-already-quiet/mise.toml b/test/lint/mise-run-quiet/fixtures/clean-already-quiet/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/clean-already-quiet/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/clean/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/clean/.mise/tasks/t
new file mode 100644
index 0000000..559debd
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/clean/.mise/tasks/t
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+# No mise run calls here — just regular shell commands
+echo "hello world"
+ls -la
+git status
diff --git a/test/lint/mise-run-quiet/fixtures/clean/mise.toml b/test/lint/mise-run-quiet/fixtures/clean/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/clean/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-command-sub/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/dirty-command-sub/.mise/tasks/t
new file mode 100644
index 0000000..493ccb8
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-command-sub/.mise/tasks/t
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Command substitution — header goes into captured output
+result=$(mise run build)
+echo "$result"
+
+# Also in a more complex expression
+count=$(mise run count --all)
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-command-sub/mise.toml b/test/lint/mise-run-quiet/fixtures/dirty-command-sub/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-command-sub/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-eval/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/dirty-eval/.mise/tasks/t
new file mode 100644
index 0000000..4deeb26
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-eval/.mise/tasks/t
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# eval — header pollutes the eval'd string
+eval "$(mise run env)"
+
+# Also with additional flags
+eval "$(mise run shell --init)"
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-eval/mise.toml b/test/lint/mise-run-quiet/fixtures/dirty-eval/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-eval/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-mixed/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/dirty-mixed/.mise/tasks/t
new file mode 100644
index 0000000..9a3a05b
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-mixed/.mise/tasks/t
@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Command substitution
+result=$(mise run build)
+
+# eval
+eval "$(mise run env)"
+
+# Pipeline
+mise run check | grep error
+
+# Bare invocation (interactive) — should be fine
+mise run status
+
+# Already quiet — should be fine
+mise run -q deploy
+
+# Stderr redirect — should be fine
+mise run lint 2>/dev/null
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-mixed/mise.toml b/test/lint/mise-run-quiet/fixtures/dirty-mixed/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-mixed/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-pipe/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/dirty-pipe/.mise/tasks/t
new file mode 100644
index 0000000..3ed5dfe
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-pipe/.mise/tasks/t
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Pipeline — header goes into the pipe
+mise run check | grep error
+
+# Also with multiple pipes
+mise run list | sort | uniq
diff --git a/test/lint/mise-run-quiet/fixtures/dirty-pipe/mise.toml b/test/lint/mise-run-quiet/fixtures/dirty-pipe/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/dirty-pipe/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/ignored-file/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/ignored-file/.mise/tasks/t
new file mode 100644
index 0000000..33859ff
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/ignored-file/.mise/tasks/t
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# This file has repo-level ignore, so violations are skipped
+result=$(mise run build)
+eval "$(mise run env)"
+mise run check | grep error
diff --git a/test/lint/mise-run-quiet/fixtures/ignored-file/mise.toml b/test/lint/mise-run-quiet/fixtures/ignored-file/mise.toml
new file mode 100644
index 0000000..f8a0eb4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/ignored-file/mise.toml
@@ -0,0 +1,3 @@
+codebase:ignore mise-run-quiet
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/ignored-inline/.mise/tasks/t b/test/lint/mise-run-quiet/fixtures/ignored-inline/.mise/tasks/t
new file mode 100644
index 0000000..bd59f9b
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/ignored-inline/.mise/tasks/t
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Inline ignore with reason — accepted
+result=$(mise run build)  # codebase:ignore mise-run-quiet — intentional, header is part of UX
+
+# No ignore — should be flagged
+eval "$(mise run env)"
diff --git a/test/lint/mise-run-quiet/fixtures/ignored-inline/mise.toml b/test/lint/mise-run-quiet/fixtures/ignored-inline/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/ignored-inline/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/fixtures/no-shell-files/mise.toml b/test/lint/mise-run-quiet/fixtures/no-shell-files/mise.toml
new file mode 100644
index 0000000..8a0a5a4
--- /dev/null
+++ b/test/lint/mise-run-quiet/fixtures/no-shell-files/mise.toml
@@ -0,0 +1,2 @@
+[settings]
+quiet = true
diff --git a/test/lint/mise-run-quiet/mise-run-quiet.bats b/test/lint/mise-run-quiet/mise-run-quiet.bats
new file mode 100644
index 0000000..7919f1f
--- /dev/null
+++ b/test/lint/mise-run-quiet/mise-run-quiet.bats
@@ -0,0 +1,143 @@
+#!/usr/bin/env bats
+# Tests for lint:mise-run-quiet rule
+
+load ../../test_helper
+
+setup() {
+  FIXTURES="$BATS_TEST_DIRNAME/fixtures"
+}
+
+# Detection
+
+@test "mise-run-quiet: passes on a clean codebase (no mise run calls)" {
+  run codebase lint:mise-run-quiet "$FIXTURES/clean"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"OK"* ]]
+}
+
+@test "mise-run-quiet: passes when -q is already used" {
+  run codebase lint:mise-run-quiet "$FIXTURES/clean-already-quiet"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"OK"* ]]
+}
+
+@test "mise-run-quiet: flags mise run in command substitution" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-command-sub"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"FAIL"*"dirty-command-sub"* ]]
+  [[ "$output" == *"[command-sub]"* ]]
+  [[ "$output" == *'$(mise run build)'* ]]
+}
+
+@test "mise-run-quiet: flags mise run in eval" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-eval"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"FAIL"*"dirty-eval"* ]]
+  [[ "$output" == *"[eval]"* ]]
+  [[ "$output" == *'eval "$(mise run env)"'* ]]
+}
+
+@test "mise-run-quiet: warns on mise run in pipeline" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-pipe"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"FAIL"*"dirty-pipe"* ]]
+  [[ "$output" == *"[pipeline]"* ]]
+  [[ "$output" == *'mise run check | grep error'* ]]
+}
+
+@test "mise-run-quiet: flags multiple violations in one file" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-mixed"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"FAIL"*"dirty-mixed"* ]]
+  [[ "$output" == *"[command-sub]"* ]]
+  [[ "$output" == *"[eval]"* ]]
+  [[ "$output" == *"[pipeline]"* ]]
+}
+
+@test "mise-run-quiet: fail output includes the violating file path" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-command-sub"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *".mise/tasks/t"* ]]
+}
+
+@test "mise-run-quiet: fail output suggests adding -q" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-command-sub"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"mise run -q"* ]]
+}
+
+# Safe contexts
+
+@test "mise-run-quiet: does not flag bare mise run (interactive)" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-mixed"
+  [ "$status" -ne 0 ]
+  # Should flag the violations but NOT the bare 'mise run status' line
+  [[ "$output" == *"FAIL"* ]]
+  # The bare line should not appear in the output
+  local bare_count
+  bare_count=$(echo "$output" | grep -c "mise run status" || true)
+  # It may appear in the hint text, but should not be flagged as a violation
+  [[ "$output" != *"[command-sub]".*"mise run status"* ]]
+  [[ "$output" != *"[eval]".*"mise run status"* ]]
+  [[ "$output" != *"[pipeline]".*"mise run status"* ]]
+}
+
+@test "mise-run-quiet: does not flag mise run with stderr redirect" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-mixed"
+  [ "$status" -ne 0 ]
+  # The stderr redirect line should not appear as a violation
+  [[ "$output" != *"mise run lint 2>/dev/null"* ]]
+}
+
+@test "mise-run-quiet: does not flag mise run -q in command substitution" {
+  run codebase lint:mise-run-quiet "$FIXTURES/clean-already-quiet"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"OK"* ]]
+}
+
+# Ignore mechanisms
+
+@test "mise-run-quiet: respects file-level codebase:ignore" {
+  run codebase lint:mise-run-quiet "$FIXTURES/ignored-file"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"SKIP"*"ignored-file"* ]]
+}
+
+@test "mise-run-quiet: respects inline codebase:ignore with reason" {
+  run codebase lint:mise-run-quiet "$FIXTURES/ignored-inline"
+  [ "$status" -ne 0 ]
+  # Should flag the eval line (no ignore) but not the command sub line (has ignore)
+  [[ "$output" == *"[eval]"* ]]
+  # The ignored line should not appear as a violation
+  [[ "$output" != *"codebase:ignore mise-run-quiet"* ]]
+}
+
+# Edge cases
+
+@test "mise-run-quiet: skips directories with no shell files" {
+  run codebase lint:mise-run-quiet "$FIXTURES/no-shell-files"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"OK"*"no shell files"* ]]
+}
+
+@test "mise-run-quiet: handles multiple targets" {
+  run codebase lint:mise-run-quiet "$FIXTURES/clean" "$FIXTURES/dirty-command-sub"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"OK"*"clean"* ]]
+  [[ "$output" == *"FAIL"*"dirty-command-sub"* ]]
+}
+
+@test "mise-run-quiet: does not flag 'mise run' in comments" {
+  run codebase lint:mise-run-quiet "$FIXTURES/clean"
+  [ "$status" -eq 0 ]
+  # The clean fixture has no mise run calls at all
+  [[ "$output" == *"OK"* ]]
+}
+
+@test "mise-run-quiet: does not flag mise run with flags (not just bare)" {
+  run codebase lint:mise-run-quiet "$FIXTURES/dirty-command-sub"
+  [ "$status" -ne 0 ]
+  # Should flag both $(mise run build) and $(mise run count --all)
+  [[ "$output" == *"mise run build"* ]]
+  [[ "$output" == *"mise run count"* ]]
+}
diff --git a/test/lint/mise-settings/mise-settings.bats b/test/lint/mise-settings/mise-settings.bats
index 565be0a..d925495 100644
--- a/test/lint/mise-settings/mise-settings.bats
+++ b/test/lint/mise-settings/mise-settings.bats
@@ -7,9 +7,7 @@ setup() {
   FIXTURES="$BATS_TEST_DIRNAME/fixtures"
 }
 
-# ============================================================================
 # Detection
-# ============================================================================
 
 @test "lint: passes when all settings present" {
   run codebase lint:mise-settings "$FIXTURES/complete"
@@ -54,9 +52,7 @@ setup() {
   [[ "$output" == *"FAIL"*"missing-both"* ]]
 }
 
-# ============================================================================
 # Fix mode
-# ============================================================================
 
 @test "fix: adds missing settings" {
   WORK_DIR="$BATS_TEST_TMPDIR/fix-test"
@@ -96,9 +92,7 @@ setup() {
   [[ "$output" == *"OK"* ]]
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "lint: fails when target does not exist" {
   run codebase lint:mise-settings /nonexistent
diff --git a/test/lint/or-true/or-true.bats b/test/lint/or-true/or-true.bats
index 31d7776..68cfaca 100644
--- a/test/lint/or-true/or-true.bats
+++ b/test/lint/or-true/or-true.bats
@@ -7,9 +7,7 @@ setup() {
   FIXTURES="$BATS_TEST_DIRNAME/fixtures"
 }
 
-# ============================================================================
 # Detection
-# ============================================================================
 
 @test "or-true: passes on a clean codebase" {
   run codebase lint:or-true "$FIXTURES/clean"
@@ -76,9 +74,7 @@ setup() {
   [[ "$output" == *"if !"* ]]
 }
 
-# ============================================================================
 # Corpus-calibrated diagnostics
-# ============================================================================
 
 @test "or-true: arithmetic increments get a safer arithmetic suggestion" {
   local tmp
@@ -173,9 +169,7 @@ EOF
   [[ "$output" == *"Intentional cases need a rule-specific reason"* ]]
 }
 
-# ============================================================================
 # Ignore directives
-# ============================================================================
 
 @test "or-true: inline '# codebase:ignore or-true — reason' skips the line" {
   run codebase lint:or-true "$FIXTURES/ignored-inline"
@@ -189,9 +183,7 @@ EOF
   [[ "$output" == *"SKIP"*"ignored-file"* ]]
 }
 
-# ============================================================================
 # Scope / discovery
-# ============================================================================
 
 @test "or-true: walks the whole target — finds hits outside .mise/tasks and lib/" {
   run codebase lint:or-true "$FIXTURES/broad-walk"
@@ -213,9 +205,7 @@ EOF
   [[ "$output" == *"no shell files"* ]]
 }
 
-# ============================================================================
 # Discovery correctness
-# ============================================================================
 
 @test "or-true: discovery skips non-bash/sh shebangs (fish, zsh, …)" {
   # Regression: the shebang regex '^#!.*(bash|sh)\b' matched 'sh' as
@@ -255,9 +245,7 @@ EOF
   rm -rf "$tmp"
 }
 
-# ============================================================================
 # Comment handling
-# ============================================================================
 
 @test "or-true: does not flag '|| true' inside a single-quoted string" {
   # Accidental protection: the closing quote ''' is not in the
@@ -293,9 +281,7 @@ EOF
   rm -rf "$tmp"
 }
 
-# ============================================================================
 # Multi-target
-# ============================================================================
 
 @test "or-true: checks multiple targets and reports each" {
   run codebase lint:or-true "$FIXTURES/clean" "$FIXTURES/dirty"
@@ -309,9 +295,7 @@ EOF
   [ "$status" -eq 2 ]
 }
 
-# ============================================================================
 # Error paths
-# ============================================================================
 
 @test "or-true: fails when target does not exist" {
   run codebase lint:or-true "$FIXTURES/does-not-exist"
@@ -328,9 +312,7 @@ EOF
   [[ "$output" == *"<targets>"* ]]
 }
 
-# ============================================================================
 # Relative path resolution (regression: codebase#24)
-# ============================================================================
 
 @test "or-true: relative path resolves against CODEBASE_CALLER_PWD, not codebase install dir" {
   # Regression: when invoked via the shiv shim, relative paths resolved
diff --git a/test/lint/shellcheck/shellcheck.bats b/test/lint/shellcheck/shellcheck.bats
index 370c7d6..f0ac032 100644
--- a/test/lint/shellcheck/shellcheck.bats
+++ b/test/lint/shellcheck/shellcheck.bats
@@ -7,9 +7,7 @@ setup() {
   FIXTURES="$BATS_TEST_DIRNAME/fixtures"
 }
 
-# ============================================================================
 # Detection
-# ============================================================================
 
 @test "lint: passes on a clean codebase" {
   run codebase lint:shellcheck "$FIXTURES/clean"
@@ -37,9 +35,7 @@ setup() {
   [[ "$output" == *"SC"* ]]
 }
 
-# ============================================================================
 # Ignore directive
-# ============================================================================
 
 @test "lint: skips when codebase:ignore shellcheck is set in mise.toml" {
   run codebase lint:shellcheck "$FIXTURES/ignored"
@@ -76,9 +72,7 @@ setup() {
   [[ "$output" == *"SC2154"* ]]
 }
 
-# ============================================================================
 # Scope
-# ============================================================================
 
 @test "lint: works on a codebase with no mise.toml" {
   run codebase lint:shellcheck "$FIXTURES/no-toml"
@@ -100,9 +94,7 @@ setup() {
   [[ "$output" == *"bad.sh"* ]]
 }
 
-# ============================================================================
 # Multi-target
-# ============================================================================
 
 @test "lint: checks multiple targets and reports each" {
   run codebase lint:shellcheck "$FIXTURES/clean" "$FIXTURES/dirty"
@@ -116,9 +108,7 @@ setup() {
   [ "$status" -eq 2 ]
 }
 
-# ============================================================================
 # Error paths
-# ============================================================================
 
 @test "lint: fails when target does not exist" {
   run codebase lint:shellcheck "$FIXTURES/does-not-exist"
diff --git a/test/migrations/task-pattern/task-pattern.bats b/test/migrations/task-pattern/task-pattern.bats
index d86c33e..5f8a90d 100644
--- a/test/migrations/task-pattern/task-pattern.bats
+++ b/test/migrations/task-pattern/task-pattern.bats
@@ -23,9 +23,7 @@ assert_matches_before() {
   diff -u "$FIXTURES/before/$file" "$WORK_DIR/$file"
 }
 
-# ============================================================================
 # Individual variant tests
-# ============================================================================
 
 @test "migrate: simple mise run → _task" {
   codebase migrate:task-pattern "$WORK_DIR"
@@ -57,9 +55,7 @@ assert_matches_before() {
   assert_matches_after ".mise/tasks/error-strings"
 }
 
-# ============================================================================
 # Full migration test
-# ============================================================================
 
 @test "migrate: all files match expected after state" {
   codebase migrate:task-pattern "$WORK_DIR"
@@ -68,9 +64,7 @@ assert_matches_before() {
   [ "$status" -eq 0 ]
 }
 
-# ============================================================================
 # Reverse migration tests
-# ============================================================================
 
 @test "reverse: _task → mise run" {
   # Start from the after state
@@ -101,9 +95,7 @@ assert_matches_before() {
   ! grep -q '_task' "$WORK_DIR/.mise/tasks/in-subshell"
 }
 
-# ============================================================================
 # Round-trip tests
-# ============================================================================
 
 @test "round-trip: forward then reverse restores lossless fixtures" {
   # Only test fixtures where forward is lossless (no -q flag)
@@ -114,9 +106,7 @@ assert_matches_before() {
   assert_matches_before ".mise/tasks/error-strings"
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "migrate: fails when target does not exist" {
   run codebase migrate:task-pattern /nonexistent
diff --git a/test/pre-commit/pre-commit.bats b/test/pre-commit/pre-commit.bats
index 96bd4f2..c0fbddc 100644
--- a/test/pre-commit/pre-commit.bats
+++ b/test/pre-commit/pre-commit.bats
@@ -24,9 +24,7 @@ EOF
   export CODEBASE_CALLER_PWD="$REPO"
 }
 
-# ============================================================================
 # Install — fresh repo
-# ============================================================================
 
 @test "install: creates dispatcher" {
   codebase pre-commit
@@ -97,9 +95,7 @@ EOF
   [ -x "$REPO/.git/hooks/pre-commit" ]
 }
 
-# ============================================================================
 # Install — existing dispatcher
-# ============================================================================
 
 @test "install: preserves existing dispatcher and other hooks" {
   mkdir -p "$REPO/.git/hooks/pre-commit.d"
@@ -121,9 +117,7 @@ EOF
   [ -f "$REPO/.git/hooks/pre-commit.d/codebase" ]
 }
 
-# ============================================================================
 # Install — existing plain hook (not a dispatcher)
-# ============================================================================
 
 @test "install: errors when existing plain hook is not a dispatcher" {
   cat > "$REPO/.git/hooks/pre-commit" <<'EOF'
@@ -137,9 +131,7 @@ EOF
   [[ "$output" == *"not a dispatcher"* ]]
 }
 
-# ============================================================================
 # Idempotent
-# ============================================================================
 
 @test "install: running twice is safe" {
   codebase pre-commit
@@ -149,9 +141,7 @@ EOF
   [ -f "$REPO/.git/hooks/pre-commit.d/codebase" ]
 }
 
-# ============================================================================
 # --check
-# ============================================================================
 
 @test "check: exits 0 when hook is current" {
   codebase pre-commit
@@ -189,9 +179,7 @@ EOF
   [ "$status" -ne 0 ]
 }
 
-# ============================================================================
 # --revert
-# ============================================================================
 
 @test "revert: removes codebase hook" {
   codebase pre-commit
@@ -225,9 +213,7 @@ EOF
   [[ "$output" == *"No codebase hook"* ]]
 }
 
-# ============================================================================
 # Scope
-# ============================================================================
 
 @test "scope: default scopes are delegated to aggregate lint" {
   cat > "$REPO/mise.toml" <<'EOF'
@@ -258,9 +244,7 @@ EOF
   ! grep -q 'src/scripts' "$REPO/.git/hooks/pre-commit.d/codebase"
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "error: fails outside git repo" {
   export CODEBASE_CALLER_PWD="$BATS_TEST_TMPDIR"
diff --git a/test/scan/scan.bats b/test/scan/scan.bats
index 9552433..e52a500 100644
--- a/test/scan/scan.bats
+++ b/test/scan/scan.bats
@@ -8,9 +8,7 @@ setup() {
   FIXTURES_B="$BATS_TEST_DIRNAME/fixtures-b"
 }
 
-# ============================================================================
 # Single target (basic matching)
-# ============================================================================
 
 @test "scan: finds mise run calls in extension-less task files" {
   run codebase scan -p 'mise run $$$ARGS' "$FIXTURES_A"
@@ -39,9 +37,7 @@ setup() {
   [[ -z "$output" ]]
 }
 
-# ============================================================================
 # Different patterns
-# ============================================================================
 
 @test "scan: finds _task calls with custom pattern" {
   run codebase scan -p '_task $$$ARGS' "$FIXTURES_A"
@@ -56,9 +52,7 @@ setup() {
   [ "$count" -eq 4 ]
 }
 
-# ============================================================================
 # Multiple targets
-# ============================================================================
 
 @test "multi: finds matches across multiple codebases" {
   run codebase scan -p 'mise run $$$ARGS' "$FIXTURES_A" "$FIXTURES_B"
@@ -84,9 +78,7 @@ setup() {
   [[ "$output" != *"fixtures-b:"* ]]
 }
 
-# ============================================================================
 # Exclude filter
-# ============================================================================
 
 @test "exclude: filters out files matching glob" {
   run codebase scan -p 'mise run $$$ARGS' -e '.mise/tasks/ci/*' "$FIXTURES_A"
@@ -110,9 +102,7 @@ setup() {
   [[ "$output" != *"ci/deploy"* ]]
 }
 
-# ============================================================================
 # Error handling
-# ============================================================================
 
 @test "error: fails when no pattern provided" {
   run codebase scan "$FIXTURES_A"