remove: conf.config_file_age and repo.repo_config_age.

Don't play the config-file-age charade, the values are not used.
doc: api: Base.read_all_repos()
fixed JSON decode error in persistor.py (RhBug:1032455)
rename: Base.update*() -> Base.upgrade*()

To have the API sync with the preferred nomenclature.
doc: api: document marking packages for transactions in Base.
doc:  clarify 'Specifying Transaction' a bit.
Package.localPkg(): don't strip path prefix (RhBug:1034607)