rsereno I'm still not sure why those extra files are there - if you've extracted the .phar files, the contents of each will overwrite the others. In theory it shouldn't matter as long as the original .phars are present, but ideally it shouldn't have any superfluous files present. As an example, here's mine:
-rw-r--r--. 1 root root 273635 Jul 31 11:29 auth-ldap.phar
-rw-r--r--. 1 root root 37821 Jul 31 11:29 auth-passthru.phar
-rw-r--r--. 1 root root 32664 Jul 31 11:29 storage-fs.phar
-rw-r--r--. 1 root root 1194 Jul 31 11:28 updates.pem