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/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()