Multi file add does not work as I would expect

It seams that even if `-w` is not specified, files added via `ipfs add ...` are added to a mfs directory. As I see it this leads to two unexpected behaviors:

1) The command will fail if a file with the same name is added twice, even if they are separate files:

```
$ mkdir a b
$ echo "Hello World!" > a/hello
$ echo 'HELLO WORLD!' > b/hello
$ ipfs add a/hello b/hello
added QmfM2r8seH2GiRaC4esTjeraXEachRt8ZsSeGaWTPLyMoG hello
Error: directory already has entry by that name
```

2) The files are pinned indirectly via the created directory

```
$ mv b/hello b/hello2
$ ipfs add a/hello b/hello2
added QmfM2r8seH2GiRaC4esTjeraXEachRt8ZsSeGaWTPLyMoG hello
added QmemWc3tw1HEM5oTTE1bxwvjKkn1yGFKJF1zVCZXD5wXgi hello2
$ ipfs pin rm QmfM2r8seH2GiRaC4esTjeraXEachRt8ZsSeGaWTPLyMoG
Error: QmfM2r8seH2GiRaC4esTjeraXEachRt8ZsSeGaWTPLyMoG is pinned indirectly under QmXpzvr3QHQ2Yxwb264HsNQsASJkD7jLhFBArCy6DX5iKV
```

Without `-w` the behavior I would expect is that each file is added and pinned individually.