Do not shadow submodules

using object that have the same name as submodules as the weird effect
of makeing `import pip.commands.<something> as <anothername>` fail with
a key error. This fixes it by renamin commands as command_dict and fixin
a few imports to accomodate.

Related to #2149
RELEASE notes
Merge pull request #2172 from Carreau/shadow-submodule

Shadow submodule