indexing all parents of visited directories (#2109)

**What type of PR is this?**
Feature

**What package or component does this PR mostly affect?**

walk

**What does this PR do? Why is it needed?**
This is an alternative implementation of #2101. As suggested in the
comments in #2101:

> Alternatively, what do you think we should index all parent
directories here unconditionally? It wouldn't be that much extra work
since we're already parsing them and applying configuration.

This also simplify the logic, so we no longer need to distinguish
between "visited" and "called", because once a directory is "visited",
it's also indexed. This also means all directories are "visited" at most
once.

**Which issues(s) does this PR fix?**

This fixes the issue of `foo/BUILD.bazel` file contains targets that
provides imports like `foo.bar` which is common in Python, or generated
Go packages like `foo/bar/baz`, which is common in Go code generated by
Thrift.

**Other notes for review**