Add note to the Proto file structure guide

[alexander-yevsyukov]

We used to have this note in the “Naming Conventions” document in the “Introduction” section:

<p class="note">We recommend using the `java_outer_classname` option in proto files to make
    the name of the corresponding Java outer class obvious.
    Otherwise Protobuf Compiler tries to use the name of the file for
    the Java class. For example, for `identifiers.proto` it will be `Identifiers.java`.
    Though sometimes it can be `SomethingOuterClass` when there is a type which conflicts with
    the CamelCase version of the file name. You may also want to use names like `Identifiers` for
    utility classes related to your domain.</p>

It is too early to speak about these matters in the Introduction section. These are too fine details.