Don't SFTP PUT directory contents twice

[amake]

This fixes #218 (put method generates "Failed SFTP MKDIR"), int128/gradle-ssh-plugin#285, and potentially #228.

When recursively gathering files to PUT, directory contents are apparently intended to be inspected separately depending on whether the child is a file or a dir:

1. first, child files with File.eachFile
2. then child dirs with File.eachDir

but the File.eachFile invocation used includes both files and directories, thus resulting in directories being gathered twice.

Steps to verify the fix

1. Use the FilePut.put method with a from argument indicating a directory tree multiple levels deep
2. Note that prior to the fix, subdirectories were traversed twice, while after the fix they are not (adding a logging statement to the Instructions class constructor makes this more apparent)

ssh.run {
  session(remotes.myremote) {
     put from: someFileTree, into: '/remote/dir'
  }
}

Backward compatibility

Other than eliminating redundant traversals, this fix changes the order of traversal: previously all items were traversed in lexicographical order, with directory-children interleaved with regular file-children (and then the directories were traversed a second time). Now, all file-children are traversed first, and then directory-children are traversed. This is what I gleaned to be the original intent of the code, based on the separate calls to File.eachFile and File.eachDir.

[matthiasbalke]

@amake Please update your PR, as another one was merged and your PR is not up to date anymore. Currently it cannot be merged.