forbid using subrepo as a target

[pared]

Please provide information about your setup
DVC version(i.e. dvc --version), Platform and method of installation (pip, homebrew, pkg Mac, exe (Windows), DEB(Linux), RPM(Linux))

After introducing support for multiple DVC roots in #3257, in case of following setup:

.
├── .dvc
├── .git
└── subrepo
    ├── data
    ├── data.dvc
    ├── .dvc
    └── .gitignore

Running command dvc push/pull/fetch subrepo/data.dvc will have some unexpected results.
Eg. push will push to remote stored in parent repo.
The reason for that is that we are not resolving Repo basing on target, but cwd.
To solve this, we should either forbid initializing Repo under other Repo, or implement dynamic resolving of target paths.
Other commands that need to be checked for this issue:
destroy, remove, move, repro, status, import, get, root, update, pipeline.

As simply forbidding seems like easier way, we will probably need to solve this problem anyway, to support import and get.

Related to iterative/dvc.org#1022

[efiop]

Ok, so discussed with @pmrowla and @pared that it makes sense to forbid it. If someone asks for this in the future, we could introduce --subrepos or smth like that for push/pull/etc.

[efiop]

The reason it does't throw an error right now is https://github.com/iterative/dvc/blob/1.0.0a1/dvc/repo/__init__.py#L210 . It opens dvcfile directly without consulting with the clean tree.

As discovered by @skshetry , repo.tree doesn't use dvcignore when checking if something exists (only uses it when walk()ing). So we need to revisit CleanTree to fix that.