This seems to work:
gulp.src([
baseDir + '/**', // Include all
'!' + baseDir + '/excl1{,/**}', // Exclude excl1 dir
'!' + baseDir + '/excl2/**/!(.gitignore)', // Exclude excl2 dir, except .gitignore
], { dot: true });
Excluding single file from glob match was tricky because there’s no similar examples in minimatch docs.
https://github.com/isaacs/minimatch
“If the pattern starts with a !
character, then it is negated”.