State: Migrate instanceId

Add an upgrade step to migrate the depricated "instanceid" machine
field into "instanceid" in the instanceData doc.
fix conflicts
State, upgrade step: Add EnvUUID to Sequence doc IDs

Adds an upgrade step to add the EnvUUID to sequence doc IDs.
Move code out of package_test.go.
Do not use MgoTestPackage in backups.
Expose backups.StoreArchive.
Set meta.Stored properly.
State upgrade step: Add EnvUUID to cleanup docs.

Add an upgrade step which stringifies the cleanup doc (bson.ObjectId)
and prepends State's environment UUID. Update state.docID() to take an
interface and return a string.
Move .UTC() into setBackupStored.
testing -> backupstesting.
Changed warning display for unknown config, remove tools-url on upgrade, added/modified tests. Bug 1383070.
generate-tools now merges metadata from different streams
SHASumFile -> SHA1SumFile.
Merge pull request #992 from ericsnowcurrently/backups-create-set-metadata-stored

Set Stored on stored metadata.

The "stored" timestamp in the DB was set incorrectly.  The value was not set on the metadata at all during create.  Both of these changes should have happened in a previous changeset.

This patch also factors extra code out of state/backups/package_test.go, as well as dropping use of MgoTestPackage within state/backups.
Add a --download option to "juju backups create".
Add a --filename option.
Drop superfluous if statement.
Use a more meaningful (in help) "default" for --filename.
version: Reset version to alpha3

An earlier branch accidentially reverted the version to alpha2,
change it back to alpha3 here.
Upgrade gomaasapi to v 58

Fixes https://bugs.launchpad.net/juju-core/+bug/1384001