Ignore directories and files on auto-generation (watch)

Related Issues: #1184, #1870, #2450, #2302

Summary:
- When you specify inconsistent values for `source` and `destination`, that is switching between absolute and relative, the watch option doesn't properly ignore the destination directory. 
- Editing the config file outputs `Regenerating: 1 files at...` though this is confusing since these changes do not take effect.

Fixes:
- Use `realpath` to get absolute paths
- Add the config files to the list of files/directories to ignore
- Remove `Command#globs` since it's not used anymore (it was used when Jekyll used `directory_watcher` gem.)