luke@phage(0) $ cat ~/bin/test.pp
#!/usr/bin/env puppet --verbose

mymod::subdir::test { yay: }
luke@phage(0) $ cat ~/tmp/modules/main/mymod/
files/     manifests/ plugins/   
luke@phage(0) $ cat ~/tmp/modules/main/mymod/manifests/
init.pp  subdir/  
luke@phage(0) $ cat ~/tmp/modules/main/mymod/manifests/subdir/test.pp 
define mymod::subdir::test {
    notify { "testing in $name": }
}
luke@phage(0) $ test.pp --modulepath ~/tmp/modules/main/
info: Loading fact test
info: Autoloaded module mymod
info: Autoloaded file mymod/subdir/test from module mymod
notice: testing in yay
luke@phage(0) $