Resolve check and freshen paths against the manifest's directory (closes #177)

Without --base, check and freshen now look for a manifest's files in the
directory that holds the manifest, the file named or the one found in a
directory argument, instead of the current directory. check of a manifest
given by URL still uses the current directory, and a --base given on the
command line, the current directory included, still overrides. The --base
help text of both commands and the README's Tool Examples state the
default; the README gains a freshen entry to do so.

Model: opus-5-5

internal/cli/freshen.go

@@ -497,7 +497,6 @@ func (mfa *CLIApp) freshenManifestOperation(
 ) error {
 	log.Debug("freshenManifestOperation()")
 
-	basePath := cmd.String("base")
 	showProgress := cmd.Bool("progress")
 
 	// Find manifest file
@@ -506,6 +505,13 @@ func (mfa *CLIApp) freshenManifestOperation(
 		return fmt.Errorf("freshen: %w", err)
 	}
 
+	// Without --base, the manifest's paths are resolved against the
+	// directory holding it.
+	basePath := filepath.Dir(manifestPath)
+	if cmd.IsSet(flagBase) {
+		basePath = cmd.String(flagBase)
+	}
+
 	//nolint:contextcheck // mfer loads a manifest without a context
 	existingByPath, err := mfa.loadExistingEntries(manifestPath)
 	if err != nil {