Default the manifest to index.mf and keep it out of its own listing (closes #100)

mfer gen now writes index.mf instead of .index.mf, the name fetch
requests and the README calls the standard filename. Given a
directory, check, freshen, list and export look only for index.mf;
.index.mf is no longer recognized. Because index.mf is not hidden, gen
and freshen leave out of their own listing the manifest they write and
a temp file an interrupted run left beside it, matched by file
identity (os.SameFile) however the path is spelled. The scanner takes
these as a plain ExcludePaths list; manifestTempPath alone names the
temp file, for both writes, both skips and the tests.

Model: opus-5-5

internal/cli/gen.go

@@ -89,11 +89,15 @@ func (mfa *CLIApp) collectInputPaths(args cli.Args) ([]string, error) {
 
 // buildScannerOptions constructs scanner options from the CLI flags.
 func (mfa *CLIApp) buildScannerOptions(ctx *cli.Context) *mfer.ScannerOptions {
+	output := ctx.String("output")
 	opts := &mfer.ScannerOptions{
 		IncludeDotfiles:   ctx.Bool("include-dotfiles"),
 		FollowSymLinks:    ctx.Bool("follow-symlinks"),
 		IncludeTimestamps: ctx.Bool("include-timestamps"),
 		Fs:                mfa.Fs,
+		// Neither a manifest being replaced nor a temp file left by an
+		// interrupted run belongs in the new manifest.
+		ExcludePaths: []string{output, manifestTempPath(output)},
 	}
 
 	// Set seed for deterministic UUID if provided
@@ -217,7 +221,7 @@ func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
 	}
 
 	// Create temp file for atomic write
-	tmpPath := outputPath + ".tmp"
+	tmpPath := manifestTempPath(outputPath)
 
 	outFile, err := mfa.Fs.Create(tmpPath)
 	if err != nil {