Replace java cookbook with git submodule

Setting java cookbook to commit to a5c2585b74739df9deaee4 where it was
originally imported to this repo.  No differences.
Upgrade java cookbook
Add tomcat cookbook (via submodule)
Add a note about initializing submodules
Add definitions for creating postgres users
Add option for installing ruby via apt

This is not enabled by default so functionality should not change.
Replace mysql cookbook with submodule

Setting the submodule to 237a1a8d49658767537a305568cb2983bd606bc6 where
it was when it was imported into Rapid7's repo.  No significant changes.
Upgrade mysql cookbook

This requires setting the mysql passwords for chef-solo, but you need to
do that anyway or else scripts are not idempotent.
Replace apache2 cookbook with submodule

Setting the submodule to 618dcac0f8e791d842 where it was
when it was imported into the Rapid7 repo.  No changes.
Add web-target cookbook

Configures a server with insecure server components and several
vulnerable web apps.
Merge pull request #1 from bturner-r7/feature/web-app-target

[Delivers #43488585]