Rename a variable.

serverPackageData -> allPackageData
Fix a PackageLoader argument
Fix mysterious inconsistency in PackageLoader.versions format.

Also fix some indentation.
Separate bootstrapping from localPackageDirs in catalog initialization.

Previously, if localPackageDirs contained an app package that used a
troposphere package, the constraint solver would bomb out on that app
package. This commit separates out the checkout packages that we need for
bootstrapping catalog initialization from other local packages, which
are allowed to use troposphere packages.