ruby: Rename destroy to destroy!

According to the common Ruby function naming convention, potentially
dangerous functions or functions which operate on the object itself are
suffixed with an exclamation mark. Both of these are true for object
destroying functions.

The following modules are affected:
- Notmuch::Directory
- Notmuch::FileNames
- Notmuch::Query
- Notmuch::Threads
- Notmuch::Thread
- Notmuch::Messages
- Notmuch::Message
- Notmuch::Tags