Respect remote aliases

Previously, change I7150e449341ed8655d398956a095261978d95870
had broken alias support in order to fix the manifest command to keep
it from spitting projects that point to an alias that wasn't recorded.
This commit reverts that commit and instead solves the issue more
correctly, outputting the alias in the remote node of the manifest and
respecting that alias when outputting the list of projects.

Change-Id: I941fc4adb7121d2e61cedc5838e80d3918c977c3