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 it, the file named or the one found in a directory
argument, instead of the current directory. So `mfer check /media/drive`
checks a drive against its own index.mf from anywhere. check of a manifest
given by URL still uses the current directory, and --base still overrides,
even when it names the current directory. The --base help text of both
commands and the README's Tool Examples state the default; the README gains
a freshen entry for this, which also names the hidden files and symlinks
freshen leaves out by default and the flags that include them.

Model: opus-5-5

internal/cli/check.go

@@ -299,6 +299,10 @@ func (mfa *CLIApp) checkManifestOperation(
 		return fmt.Errorf("check: %w", err)
 	}
 
+	// Done before a URL is swapped for the temp file it is downloaded to,
+	// whose directory is not the base.
+	basePath := resolveBasePath(cmd, manifestPath)
+
 	// URL manifests need to be downloaded to a temp file for the checker
 	if isHTTPURL(manifestPath) {
 		tmpPath, tmpErr := mfa.fetchManifestToTemp(ctx, manifestPath)
@@ -311,7 +315,6 @@ func (mfa *CLIApp) checkManifestOperation(
 		manifestPath = tmpPath
 	}
 
-	basePath := cmd.String("base")
 	showProgress := cmd.Bool("progress")
 
 	log.Infof("checking manifest %s with base %s", manifestPath, basePath)