Typically proto files depend on and make use of proto definitions in
other files. When invoking protoc user can supply paths to inspect for
dependencies.
This patch makes it possible to configure flags passed to protoc. This
makes it e.g., possible to change include paths of the linter's protoc
invocation.
The test already handled arbitrary paths reasonably well, but setting
the directory interfered via leakage with others tests for some reason.
This patch removes the call to `SetDirectory` in the fixture setup and
the subsequent cleanup in the teardown as they are not required.
