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developing against cloudVMs and cloud black box services (for example Azure Document DB) - makes it hard for me to safely store the passwords. Currently, I keep all my passwords for the VMs + DBs as environment variables (nothing in source control).

However, let's say someone breaks to my desktop. He can "understand" where is the code, +to see the envirnoment varialbes, +to open robomongo\mobaXterm and auto-connect - what would be the best way to secure my cloud agains hacker in MY development machine? is there like "2-phase authentication" to developer desktop various tools? hashing methods with password only I would know by heart?

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You have quite a few options here.

  1. Creating a web page for a LAMP stack with PHP encoding of passwords into MySQL
  2. Use password salting with SHA256 locally on a machine. Google password salting sha256 The example at: crackstation.net is a good one.
  3. There are open source password managers like this list http://www.techradar.com/news/software/applications/8-of-the-best-linux-password-managers-916152/8
  4. Or use a cloud based password managers like Lastpass which make things uber easy. Here is a link to many: http://www.pcmag.com/article2/0,2817,2407168,00.asp
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