test(cmd/mdsmith): add dedicated unit tests for runCheck/runFix

The 2026-08-02 architecture audit flagged runCheck and runFix — the
check and fix CLI subcommand entry points — as missing dedicated
in-process unit tests, only reachable via binary-spawn e2e tests.
audit-checklist.md promotes a missing test on a CLI subcommand entry
to blocker severity.

Adds TestRunCheck_*/TestRunFix_* covering the flag-error, stdin,
explicit-files, and config-discovered branches, matching the
TestRunInit_* precedent already used for the init subcommand.

Also records the full audit sweep in architecture-audit.md and files
plans for the two structural tax findings (query-subcommand
placement, internal/githooks package split).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016AbFuwvqqq2fBiYWa3ubap

Author: claude

PLAN.md

@@ -259,4 +259,6 @@ footer: |
 | 2607191918 | ✅     | haiku  | [Deduplicate isClaimed between internal/schema and requiredstructure](plan/2607191918_arch-fix-isclaimed-dedup.md)                                      |
 | 2607242010 | 🔲     | sonnet | [MDS072 external-link-check: SSRF and egress hardening](plan/2607242010_mds072-ssrf-network-hardening.md)                                               |
 | 2607242011 | 🔲     | haiku  | [Security hardening batch — 2026-07-24](plan/2607242011_security-hardening-batch-2026-07-24.md)                                                         |
+| 2608021915 | 🔲     | haiku  | [Move list-query subcommand logic out of cmd/mdsmith/main.go into query.go](plan/2608021915_arch-fix-query-subcommand-placement.md)                     |
+| 2608021916 | 🔲     | sonnet | [Split internal/githooks by responsibility](plan/2608021916_arch-fix-githooks-package-split.md)                                                         |
 <?/catalog?>

cmd/mdsmith/main_unit_test.go

@@ -811,6 +811,136 @@ func TestFixDiscovered_BadMaxInputSize_ExitsTwo(t *testing.T) {
 	assert.Contains(t, stderr, "max-input-size")
 }
 
+// --- runCheck ---
+//
+// runCheck is the "check" subcommand entry dispatched from dispatch() in
+// main.go; go.md/audit-checklist.md name a CLI subcommand entry as a
+// public surface, so a missing dedicated test here is a blocker, not tax.
+// These exercise the three branches it routes to (flag error, stdin,
+// explicit files, config-discovered files) in-process, mirroring the
+// TestRunInit_* pattern in init_unit_test.go rather than relying solely
+// on the binary-spawn e2e tests in e2e_coverage_test.go.
+
+func TestRunCheck_UnknownFlag_ExitsTwo(t *testing.T) {
+	var code int
+	stderr := captureStderr(func() {
+		code = runCheck([]string{"--definitely-not-a-flag"})
+	})
+	assert.Equal(t, 2, code)
+	assert.Contains(t, stderr, "unknown flag")
+}
+
+func TestRunCheck_Stdin_ChecksSource(t *testing.T) {
+	t.Chdir(t.TempDir())
+
+	oldStdin := os.Stdin
+	r, w, err := os.Pipe()
+	require.NoError(t, err)
+	os.Stdin = r
+	defer func() { os.Stdin = oldStdin }()
+	go func() {
+		_, _ = w.WriteString("# Title\n\nContent here.\n")
+		_ = w.Close()
+	}()
+
+	var code int
+	captureStderr(func() {
+		code = runCheck([]string{"-"})
+	})
+	assert.Equal(t, 0, code)
+}
+
+func TestRunCheck_Files_ExitsOneOnDiagnostics(t *testing.T) {
+	dir := t.TempDir()
+	t.Chdir(dir)
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "dirty.md"),
+		[]byte("# Title\n\nHello   \n"), 0o644))
+
+	var code int
+	stderr := captureStderr(func() {
+		code = runCheck([]string{"dirty.md"})
+	})
+	assert.Equal(t, 1, code)
+	assert.Contains(t, stderr, "dirty.md")
+}
+
+func TestRunCheck_Discovered_ChecksConfiguredFiles(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, ".mdsmith.yml"),
+		[]byte("files: [\"**/*.md\"]\n"), 0o644))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "test.md"),
+		[]byte("# Title\n\nContent here.\n"), 0o644))
+	t.Chdir(dir)
+
+	var code int
+	captureStderr(func() {
+		code = runCheck(nil)
+	})
+	assert.Equal(t, 0, code)
+}
+
+// --- runFix ---
+//
+// runFix is the "fix" subcommand entry, the same public-surface tier as
+// runCheck above. These cover the stdin-rejection branch and the two
+// file-resolution branches (explicit files, config-discovered files) that
+// runCheck's tests exercise, plus the disk write that runCheck has no
+// equivalent of.
+
+func TestRunFix_UnknownFlag_ExitsTwo(t *testing.T) {
+	var code int
+	stderr := captureStderr(func() {
+		code = runFix([]string{"--definitely-not-a-flag"})
+	})
+	assert.Equal(t, 2, code)
+	assert.Contains(t, stderr, "unknown flag")
+}
+
+func TestRunFix_StdinArg_ExitsTwo(t *testing.T) {
+	var code int
+	stderr := captureStderr(func() {
+		code = runFix([]string{"-"})
+	})
+	assert.Equal(t, 2, code)
+	assert.Contains(t, stderr, "cannot fix stdin in place")
+}
+
+func TestRunFix_Files_FixesGivenFile(t *testing.T) {
+	dir := t.TempDir()
+	t.Chdir(dir)
+	path := filepath.Join(dir, "fixme.md")
+	require.NoError(t, os.WriteFile(path, []byte("# Title\n\nHello   \n"), 0o644))
+
+	var code int
+	captureStderr(func() {
+		code = runFix([]string{"fixme.md"})
+	})
+	assert.Equal(t, 0, code)
+
+	fixed, err := os.ReadFile(path)
+	require.NoError(t, err)
+	assert.Equal(t, "# Title\n\nHello\n", string(fixed))
+}
+
+func TestRunFix_Discovered_FixesConfiguredFiles(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, ".mdsmith.yml"),
+		[]byte("files: [\"**/*.md\"]\n"), 0o644))
+	path := filepath.Join(dir, "fixme.md")
+	require.NoError(t, os.WriteFile(path, []byte("# Title\n\nHello   \n"), 0o644))
+	t.Chdir(dir)
+
+	var code int
+	captureStderr(func() {
+		code = runFix(nil)
+	})
+	assert.Equal(t, 0, code)
+
+	fixed, err := os.ReadFile(path)
+	require.NoError(t, err)
+	assert.Equal(t, "# Title\n\nHello\n", string(fixed))
+}
+
 // --- printErrors ---
 
 func TestPrintErrors_Empty_NoOutput(t *testing.T) {

docs/development/architecture-audit.md

@@ -6,7 +6,7 @@ summary: >-
   solid-architecture skill (audit mode)
   appends here; blockers are also filed as
   plans.
-audit-from: 6680ff53d440337d780e62d19d6eb65a4e1b6e2c
+audit-from: 2ab4b2949e9420b2eb73f4239091fd647c4b5e80
 ---
 # Architecture audit log
 
@@ -17,6 +17,108 @@ to [the archive](architecture-audit-archive.md)
 this cycle to stay under the file-length budget;
 every finding there is resolved.
 
+## Audit 2026-08-02 (range: 6680ff5..2ab4b29)
+
+134 touched files. Notable new surfaces: MDS073
+slide-structure and MDS060 occurrence. MDS073 was
+renamed from MDS072; no leftover duplication was
+found. Also new: foreign-managed regions and
+user-extensible wordlists.
+
+No rule-to-rule imports. No reverse-layer imports. No
+Liskov breaks. The prior cycle's `isClaimed` dedup
+(plan 2607191918) is confirmed resolved — `schema.IsClaimed`
+is now exported and `requiredstructure` calls it directly.
+
+### blockers (2026-08-02)
+
+- `cmd/mdsmith/check.go`'s `runCheck` and
+  `cmd/mdsmith/fix.go`'s `runFix` — the `check` and `fix`
+  CLI subcommand entry points — had no dedicated in-process
+  unit test; only binary-spawn e2e tests
+  (`internal/integration`, `cmd/mdsmith/e2e_*_test.go`)
+  exercised them.
+  [audit-checklist.md][audit-checklist]: "blocker if the
+  function is on a public surface ... a CLI subcommand
+  entry." Fixed: added `TestRunCheck_UnknownFlag_ExitsTwo`,
+  `TestRunCheck_Stdin_ChecksSource`,
+  `TestRunCheck_Files_ExitsOneOnDiagnostics`,
+  `TestRunCheck_Discovered_ChecksConfiguredFiles`,
+  `TestRunFix_UnknownFlag_ExitsTwo`,
+  `TestRunFix_StdinArg_ExitsTwo`,
+  `TestRunFix_Files_FixesGivenFile`, and
+  `TestRunFix_Discovered_FixesConfiguredFiles` to
+  `cmd/mdsmith/main_unit_test.go`, matching the
+  `TestRunInit_*` precedent from the 2026-07-19 cycle.
+  `go test ./cmd/mdsmith/...` and
+  `go tool golangci-lint run` are green.
+
+### tax (2026-08-02)
+
+- `cmd/mdsmith/main.go` still carries the `list query`
+  subcommand's full domain logic (`parseQueryFlags`,
+  `runQuery`, `queryFiles`, `readFrontMatterRaw`) instead
+  of a dedicated file, even though `list.go` dispatches to
+  it the same way it dispatches to `backlinks.go`.
+  [go.md][go] "Clean wiring in `cmd/mdsmith`" —
+  [plan/2608021915][2608021915].
+- `internal/githooks`'s package doc comment joins three
+  responsibilities with "and" (hook-script generation,
+  `.gitattributes` I/O, directive-file discovery) —
+  [go.md][go] refactor-moves: "Split a package by
+  question" — [plan/2608021916][2608021916].
+- `internal/lint/files.go`'s CLI-path/glob resolution
+  overlaps the question `internal/discovery` already
+  answers for config-glob-driven discovery. No plan filed
+  this cycle; flagged for the next package-boundary pass.
+- A broad set of unexported, branching helper functions
+  across the touched rule packages
+  (`requiredstructure`, `crossfilereferenceintegrity`,
+  `noreferencestyle`, `include`, `linkstyle`,
+  `slidevstructure`, `occurrence`, `tablefmt`,
+  `tocdirective`, `githooksync`, `build`) and
+  `cmd/mdsmith` (`checkFiles`, `checkBatchOptions`,
+  `batchMaxBytes`, `parseFixFlags`, `setFixUsage`,
+  `fixFiles`, `readStdinLimited`, `regenDirectiveNames`)
+  lack a dedicated `TestFuncName` symbol per
+  [tests.md][tests], though each is exercised
+  transitively through its caller's scenario tests. None
+  sit on a public surface by themselves, so tax rather
+  than blocker.
+- Trivial one-line accessors (`FixTitle` across several
+  rule packages, plus a few `rule.Rule` capability
+  predicates) carry only an "implements rule.X" comment,
+  not the exemption statement [tests.md][tests] requires
+  to distinguish "no test by design" from "no test,
+  forgotten."
+- Similar untested-but-covered helper clusters exist in
+  `internal/lsp/server_codeaction.go`,
+  `internal/config/merge.go`, and `internal/fix/fix.go`.
+
+[tests]: architecture/tests.md
+[go]: architecture/go.md
+[audit-checklist]: architecture/audit-checklist.md
+[2608021915]: ../../plan/2608021915_arch-fix-query-subcommand-placement.md
+[2608021916]: ../../plan/2608021916_arch-fix-githooks-package-split.md
+
+### nice-to-have (2026-08-02)
+
+- Several tests covering the flagged helper clusters use
+  scenario names (e.g. `TestDriftParts_ResolvesHooksDirOnce`)
+  rather than the literal `TestReceiver_Foo` binding —
+  coverage exists, only the naming convention drifts.
+- `stagingHelperShellFunc` (`internal/githooks/githooks.go`)
+  contains "Helper" in its name — go.md flags this as a
+  smell, though the function is well-scoped. Rename on next
+  touch.
+- `Override.Patterns()` / `KindAssignmentEntry.Patterns()`
+  (`internal/config/config.go`) are two-line branching
+  methods exercised only inside larger config tests, not by
+  a dedicated `Test*`. Low regression risk.
+- `parseCheckFlags` / `parseFixFlags` cross go.md's ~50-line
+  guidance for `cmd/mdsmith` handlers, but the body is pure
+  flag-registration boilerplate, not domain logic.
+
 ## Audit 2026-07-19 (range: 834b560..6680ff5)
 
 89 touched files. Notable new surfaces: SARIF output,
@@ -86,8 +188,6 @@ None.
   to an interface... once two rules needed the same shape"
   — [plan/2607191918][2607191918].
 
-[tests]: architecture/tests.md
-[go]: architecture/go.md
 [2607191917]: ../../plan/2607191917_arch-fix-printinitcatalog-unit-test.md
 [2607191918]: ../../plan/2607191918_arch-fix-isclaimed-dedup.md
 

plan/2608021915_arch-fix-query-subcommand-placement.md

@@ -0,0 +1,74 @@
+---
+id: 2608021915
+title: >-
+  Move list-query subcommand logic out of
+  cmd/mdsmith/main.go into query.go
+status: "🔲"
+model: haiku
+summary: >-
+  parseQueryFlags, runQuery, queryFiles, and
+  readFrontMatterRaw implement the `mdsmith list
+  query` subcommand but live in main.go instead of a
+  dedicated per-subcommand file. Flagged by the
+  2026-08-02 audit.
+---
+# Move list-query subcommand logic out of cmd/mdsmith/main.go into query.go
+
+## Goal
+
+Relocate the `list query` subcommand's implementation
+into its own file. That keeps `main.go` as
+dispatch-and-glue, matching the pattern already used
+for every sibling subcommand.
+
+## Background
+
+The 2026-08-02 audit (see
+[the audit log](../docs/development/architecture-audit.md))
+found this placement gap:
+
+- [main.go](../cmd/mdsmith/main.go) defines
+  `parseQueryFlags`, `runQuery`, `queryFiles`, and
+  `readFrontMatterRaw` — the full domain logic for the
+  `list query` subcommand (CUE-expression matching
+  against front matter, its own file walk).
+- [list.go](../cmd/mdsmith/list.go)'s `runList`
+  dispatches `case "query": return runQuery(...)`, the
+  same way it dispatches `case "backlinks":` to
+  `runBacklinks`, which lives in its own
+  [backlinks.go](../cmd/mdsmith/backlinks.go).
+- [go.md](../docs/development/architecture/go.md)'s
+  "Clean wiring in `cmd/mdsmith`" section: domain logic
+  belongs in `pkg/mdsmith`, `internal/engine`, or a
+  subcommand's own file — not in `main.go`.
+- The 2026-07-19 audit already applied this exact move
+  once, relocating the `init` subcommand's logic out of
+  `main.go` into
+  [init.go](../cmd/mdsmith/init.go); this plan repeats
+  that move for `query`.
+
+## Tasks
+
+1. Create `cmd/mdsmith/query.go` and move
+   `parseQueryFlags`, `runQuery`, `queryFiles`, and
+   `readFrontMatterRaw` into it, unchanged.
+2. Move the query-only tests covering those functions
+   out of `main_unit_test.go` into a new
+   `cmd/mdsmith/query_unit_test.go`, following the
+   `init_unit_test.go` precedent.
+3. Confirm `list.go`'s `runList` still compiles against
+   the relocated `runQuery` with no signature change.
+4. `go build ./...` passes.
+5. `go test ./cmd/mdsmith/...` passes.
+6. `go tool -modfile=tools/go.mod golangci-lint run`
+   reports no issues.
+
+## Acceptance Criteria
+
+- [ ] `parseQueryFlags`, `runQuery`, `queryFiles`, and
+      `readFrontMatterRaw` no longer appear in
+      `cmd/mdsmith/main.go`.
+- [ ] `cmd/mdsmith/query.go` holds the relocated code
+      with no behavior change.
+- [ ] `go test ./...` is green.
+- [ ] `mdsmith check .` is green.