Several improvements and fixes

Fix #622 #708 #609 and #710 

Also:

- Fix an issue where parent -> child would not be set, causing some dependencies to not appear on the tree printed at the end of the `install` and `update` commands (edge case)
- Ignore linked packages in `bower init`

I could not make a separate PR for everything since they all depend on the same logical change in the `Project/Manager` files