repo: finish RepoStorage move

bug/bug_test.go

cache/repo_cache.go

cache/repo_cache_bug.go

cache/repo_cache_common.go

cache/repo_cache_identity.go

cache/repo_cache_test.go

commands/env.go

commands/select/select.go

doc/gen_docs.go

input/input.go

misc/gen_completion.go

misc/random_bugs/cmd/main.go

repository/git.go

repository/gogit.go

repository/gogit_config.go

repository/gogit_test.go

repository/keyring.go

repository/repo.go

util/lamport/persisted_clock.go

util/lamport/persisted_clock_test.go