List a directory named through a symlink in gen and freshen (closes #185)

The walk in gen and freshen does not follow a symlink at its top. A
directory given as a symlink, or a working directory whose path names
one, was listed as empty and gen exited 0, while freshen removed every
entry from the manifest. Each walk now resolves its starting directory
with filepath.EvalSymlinks first, as check's search for extra files
does, and starts at the path as named if that fails. Symlinks inside the
tree are still skipped unless --follow-symlinks is given.

Model: opus-5-5

internal/cli/entry_test.go

@@ -1369,6 +1369,51 @@ func TestGenerateSeveralPathsDefaultOutput(t *testing.T) {
 	}
 }
 
+// testLink is the name of the symlink to a tree that the
+// DirectoryNamedThroughSymlink tests make in a temp dir.
+const testLink = "link"
+
+// TestGenerateDirectoryNamedThroughSymlink runs gen on a directory named
+// through a symlink, given as the argument or as the working directory: the
+// manifest lists the files in the directory the symlink points to, and
+// leaves out a symlink inside it, as gen does without --follow-symlinks.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestGenerateDirectoryNamedThroughSymlink(t *testing.T) {
+	// Paths are relative to a temp dir holding data and link, a symlink to
+	// data.
+	for name, tc := range map[string]struct {
+		workDir string
+		args    []string
+	}{
+		"argument":          {".", []string{testLink}},
+		"working directory": {testLink, nil},
+	} {
+		t.Run(name, func(t *testing.T) {
+			root := t.TempDir()
+			data := filepath.Join(root, "data")
+
+			fs := afero.NewOsFs()
+			writeTestTree(t, fs, data)
+			require.NoError(t,
+				os.Symlink(testFileTxt, filepath.Join(data, "alias.txt")))
+			require.NoError(t, os.Symlink(data, filepath.Join(root, testLink)))
+
+			// t.Chdir sets PWD to the path it is given, as a shell does, and
+			// os.Getwd returns PWD when it names the working directory.
+			t.Chdir(filepath.Join(root, tc.workDir))
+
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdGenerate, "-q"}, tc.args,
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assert.ElementsMatch(t, []string{testFileTxt, "sub/nested.txt"},
+				manifestPaths(t, fs, filepath.Join(data, defaultManifestName)))
+		})
+	}
+}
+
 // TestGenerateBytesDoNotDependOnOutput runs gen --seed on one tree, each
 // time writing to another file, over a file already there and beside an
 // earlier run's temp file: neither is listed, and what is listed depends

internal/cli/freshen.go

@@ -379,6 +379,14 @@ func (mfa *CLIApp) freshenScan(
 		}
 	}
 
+	// The walk does not follow a symlink at its top, so a base directory
+	// named through one is resolved first. If that fails, the base is
+	// walked as named and the walk reports the problem.
+	resolved, err := filepath.EvalSymlinks(absBase)
+	if err == nil {
+		absBase = resolved
+	}
+
 	scanner := &freshenScanner{
 		fs:                 mfa.Fs,
 		absBase:            absBase,
@@ -390,7 +398,7 @@ func (mfa *CLIApp) freshenScan(
 		existingByPath:     existingByPath,
 	}
 
-	err := afero.Walk(mfa.Fs, absBase, scanner.walk)
+	err = afero.Walk(mfa.Fs, absBase, scanner.walk)
 
 	if showProgress {
 		log.ProgressDone()

internal/cli/freshen_test.go

@@ -336,6 +336,49 @@ func TestFreshenResolvesEntriesAgainstManifestDirectory(t *testing.T) {
 	}
 }
 
+// TestFreshenDirectoryNamedThroughSymlink adds a file to a tree after gen
+// made its manifest, then freshens it with the tree named through a symlink,
+// given as the argument or as the working directory: the manifest lists the
+// files in the tree, and leaves out a symlink inside it, as freshen does
+// without --follow-symlinks.
+//
+//nolint:paralleltest // changes the process-global working directory
+func TestFreshenDirectoryNamedThroughSymlink(t *testing.T) {
+	// Paths are relative to a temp dir holding link, a symlink to the tree.
+	for name, tc := range map[string]struct {
+		workDir string
+		args    []string
+	}{
+		"argument":          {".", []string{testLink}},
+		"working directory": {testLink, nil},
+	} {
+		t.Run(name, func(t *testing.T) {
+			fs := afero.NewOsFs()
+			tree, manifestPath := setupFreshenDir(t, fs,
+				map[string]string{testFileTxt: "in the tree"})
+			writeTestFile(t, fs, filepath.Join(tree, "later.txt"), "added later")
+			require.NoError(t,
+				os.Symlink(testFileTxt, filepath.Join(tree, "alias.txt")))
+
+			root := t.TempDir()
+			require.NoError(t, os.Symlink(tree, filepath.Join(root, testLink)))
+
+			// t.Chdir sets PWD to the path it is given, as a shell does, and
+			// os.Getwd returns PWD when it names the working directory.
+			t.Chdir(filepath.Join(root, tc.workDir))
+
+			opts := testOpts(slices.Concat(
+				[]string{testApp, cmdFreshen, "-q"}, tc.args,
+			), fs)
+			require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
+
+			assertManifestLists(t, fs, tree, manifestPath, map[string]string{
+				testFileTxt: "in the tree", "later.txt": "added later",
+			})
+		})
+	}
+}
+
 // TestFreshenRecordEntryMtimePresence pins the behavior of recordEntry
 // with respect to MFFilePath.Mtime, which is a message pointer with
 // proto3 field presence and may legitimately be absent.