Hold runMu in internal/cli tests that log outside a CLI run (closes #210)

A CLI run under runMu points the process-global logger at its own
buffers, so a line another test logged outside runMu could land in that
run's output. TestCheckQuietShowsFailedFiles caught one: a "loaded
manifest" line in the stderr of a passing check -q run.

The test helpers that scan or load a manifest now hold runMu
themselves, and so do the remaining direct loads and scans, the
recordEntry call and the retrying download. Two dotfile tests use
manifestPaths instead of loading the manifest themselves.

Judgement call: a downloadFile call that gets its answer on the first
request does not log, so those calls are left as they are.

Model: opus-5-5

internal/cli/entry_test.go

@@ -771,13 +771,9 @@ func TestGenerateExcludesDotfilesByDefault(t *testing.T) {
 	assert.True(t, exists)
 
 	// Verify manifest only has 1 file (the non-dotfile)
-	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
-		Path: testMF,
-		Fs:   fs,
-	})
-	require.NoError(t, err)
-	assert.Len(t, manifest.Files(), 1)
-	assert.Equal(t, "file1.txt", manifest.Files()[0].GetPath())
+	paths := manifestPaths(t, fs, testMF)
+	require.Len(t, paths, 1)
+	assert.Equal(t, "file1.txt", paths[0])
 }
 
 func TestGenerateWithIncludeDotfiles(t *testing.T) {
@@ -798,12 +794,7 @@ func TestGenerateWithIncludeDotfiles(t *testing.T) {
 	require.Equal(t, 0, exitCode)
 
 	// Verify manifest has 2 files (including dotfile)
-	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
-		Path: testMF,
-		Fs:   fs,
-	})
-	require.NoError(t, err)
-	assert.Len(t, manifest.Files(), 2)
+	assert.Len(t, manifestPaths(t, fs, testMF), 2)
 }
 
 func TestMultipleInputPaths(t *testing.T) {
@@ -1224,6 +1215,11 @@ func TestGenerateFailsWithoutForceWhenOutputExists(t *testing.T) {
 func manifestPaths(t *testing.T, fs afero.Fs, path string) []string {
 	t.Helper()
 
+	// Loading a manifest logs to the process-global logger, so serialize
+	// with the CLI runs.
+	runMu.Lock()
+	defer runMu.Unlock()
+
 	manifest, err := mfer.NewManifestFromFile(&mfer.ManifestFromFileOptions{
 		Path: path,
 		Fs:   fs,