Fix knife cookbook upload messages

Fixes two errors when using `knife upload cookbook`:

#### Upload message on successful uploads with `--include-dependencies`

Some correct uploads are detected as failed:

```
$ knife cookbook upload --include-dependencies owncloud
Uploading owncloud       [0.5.0]
Uploading apache2        [2.0.0]
Uploading apt            [2.6.0]
Uploading database       [2.3.0]
Uploading mysql          [5.5.4]
Uploading nginx          [2.7.4]
Uploading openssl        [2.0.0]
Uploading php            [1.4.6]
Uploading php-fpm        [0.6.10]
Uploading postfix        [3.6.0]
Uploading postgresql     [3.4.2]
Uploading iptables       [0.14.0]
Uploading logrotate      [1.7.0]
Uploading pacman         [1.1.1]
Uploading aws            [2.4.0]
Uploading xfs            [1.1.0]
Uploading mysql-chef_gem [0.0.2]
Uploading yum-mysql-community [0.1.10]
Uploading bluepill       [2.3.1]
Uploading build-essential [2.0.6]
Uploading ohai           [2.0.1]
Uploading runit          [1.5.11]
Uploading yum-epel       [0.5.1]
Uploading chef-sugar     [2.2.0]
Uploading xml            [1.2.6]
Uploading windows        [1.34.2]
Uploading iis            [2.1.5]
Uploading yum            [3.3.2]
Uploading rsyslog        [1.12.2]
Uploading chef_handler   [1.1.6]
WARNING: Uploaded 30 cookbooks ok but 20 cookbooks upload failed.
```

#### Failed count message on failures

Failures in uploads are counted wrong:

```
$ knife cookbook upload --include-dependencies test_cookbook3
ERROR: Could not find cookbook test_cookbook2 in your cookbook path, skipping it
ERROR: Could not find cookbook test_cookbook3 in your cookbook path, skipping it
ERROR: Could not find cookbook test_cookbook1 in your cookbook path, skipping it
ERROR: Failed to upload 6 cookbooks.
```
I agree with @btm here, it's odd that this is wrapped in a timeout. Also, I dislike running the system under test in an after block like this.